update bioconductor packages to bioconductor 3.14 (#28900)

221 files changed, 1682 insertions, 1124 deletions

diff --git a/var/spack/repos/builtin/packages/r-a4/package.py b/var/spack/repos/builtin/packages/r-a4/package.py
index ad008b9a6b..eb71a3f894 100644
--- a/var/spack/repos/builtin/packages/r-a4/package.py
+++ b/var/spack/repos/builtin/packages/r-a4/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RA4(RPackage):
-    """Automated Affymetrix Array Analysis Umbrella Package
+    """Automated Affymetrix Array Analysis Umbrella Package.
 
     Umbrella package is available for the entire Automated Affymetrix Array
     Analysis suite of package."""
 
-    homepage = "https://bioconductor.org/packages/a4"
-    git      = "https://git.bioconductor.org/packages/a4.git"
+    bioc = "a4"
 
+    version('1.42.0', commit='fc26809e2bce7cd50d99d6f6dd5f85c38342fdea')
     version('1.38.0', commit='5b7a9087bab10c55e24707e96e48046995236c94')
     version('1.32.0', commit='03770d4e53be4eed1bd0ab8f8cddba66854b4712')
     version('1.30.0', commit='771e01ae3aaac1c4db12f781c41d90fa7191b64d')
diff --git a/var/spack/repos/builtin/packages/r-a4base/package.py b/var/spack/repos/builtin/packages/r-a4base/package.py
index 9d008bc589..ae17ec8bc4 100644
--- a/var/spack/repos/builtin/packages/r-a4base/package.py
+++ b/var/spack/repos/builtin/packages/r-a4base/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RA4base(RPackage):
-    """Automated Affymetrix Array Analysis Base Package
+    """Automated Affymetrix Array Analysis Base Package.
 
     Base utility functions are available for the Automated Affymetrix Array
     Analysis set of packages."""
 
-    homepage = "https://bioconductor.org/packages/a4Base"
-    git      = "https://git.bioconductor.org/packages/a4Base.git"
+    bioc = "a4Base"
 
+    version('1.42.0', commit='d7296e2792020e9c5b1c19101104326ee8bebfe6')
     version('1.38.0', commit='4add242fa9c62795aca5b0dfca34a43484c5aa82')
     version('1.32.0', commit='8a1e15d25494c54db8c1de5dbbd69e628569e3d7')
     version('1.30.0', commit='fc370b2bd8286acc1e42a10344d91974f5b94229')
@@ -32,4 +32,5 @@ class RA4base(RPackage):
     depends_on('r-multtest', type=('build', 'run'))
     depends_on('r-glmnet', type=('build', 'run'))
     depends_on('r-gplots', type=('build', 'run'))
-    depends_on('r-annotationdbi', when='@:1.32.0', type=('build', 'run'))
+
+    depends_on('r-annotationdbi', type=('build', 'run'), when='@:1.32.0')
diff --git a/var/spack/repos/builtin/packages/r-a4classif/package.py b/var/spack/repos/builtin/packages/r-a4classif/package.py
index 5a646d34cc..4a3a0207fa 100644
--- a/var/spack/repos/builtin/packages/r-a4classif/package.py
+++ b/var/spack/repos/builtin/packages/r-a4classif/package.py
@@ -7,15 +7,15 @@ from spack import *
 
 
 class RA4classif(RPackage):
-    """Automated Affymetrix Array Analysis Classification Package
+    """Automated Affymetrix Array Analysis Classification Package.
 
     Functionalities for classification of Affymetrix microarray data,
     integrating within the Automated Affymetrix Array Analysis set of
     packages."""
 
-    homepage = "https://bioconductor.org/packages/a4Classif"
-    git      = "https://git.bioconductor.org/packages/a4Classif.git"
+    bioc = "a4Classif"
 
+    version('1.42.0', commit='820854a7ca9ed0c295479a25b7e3375c6d01d0b5')
     version('1.38.0', commit='c4d058813efb835774813b2d69c52912162f8e75')
     version('1.32.0', commit='aa4f22df2da54b71e1a238d2b9cbcb3afa6f7f88')
     version('1.30.0', commit='b62841bff2f8894a3011a4e74afc37076d1322a3')
@@ -25,9 +25,10 @@ class RA4classif(RPackage):
 
     depends_on('r-a4core', type=('build', 'run'))
     depends_on('r-a4preproc', type=('build', 'run'))
-    depends_on('r-biobase', when='@1.38.0:', type=('build', 'run'))
+    depends_on('r-biobase', type=('build', 'run'), when='@1.38.0:')
     depends_on('r-rocr', type=('build', 'run'))
     depends_on('r-pamr', type=('build', 'run'))
     depends_on('r-glmnet', type=('build', 'run'))
     depends_on('r-varselrf', type=('build', 'run'))
-    depends_on('r-mlinterfaces', when='@:1.32.0', type=('build', 'run'))
+
+    depends_on('r-mlinterfaces', type=('build', 'run'), when='@:1.32.0')
diff --git a/var/spack/repos/builtin/packages/r-a4core/package.py b/var/spack/repos/builtin/packages/r-a4core/package.py
index bef3fb71fd..8e36d4d69a 100644
--- a/var/spack/repos/builtin/packages/r-a4core/package.py
+++ b/var/spack/repos/builtin/packages/r-a4core/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RA4core(RPackage):
-    """Automated Affymetrix Array Analysis Core Package
+    """Automated Affymetrix Array Analysis Core Package.
 
     Utility functions for the Automated Affymetrix Array Analysis set of
     packages."""
 
-    homepage = "https://bioconductor.org/packages/a4Core"
-    git      = "https://git.bioconductor.org/packages/a4Core.git"
+    bioc = "a4Core"
 
+    version('1.42.0', commit='6985950b72c2a0f20ec44fe2067d8864e004bfaa')
     version('1.38.0', commit='a027dcd3486c64950815ec7c7271f1f65ba3d8a1')
     version('1.32.0', commit='2916a29723bdd514d5d987f89725d141d1d2dfce')
     version('1.30.0', commit='e392b1b4339a34f93d5d9bc520a1a9385ea63141')
diff --git a/var/spack/repos/builtin/packages/r-a4preproc/package.py b/var/spack/repos/builtin/packages/r-a4preproc/package.py
index 8d7fad15c2..76ebcb3469 100644
--- a/var/spack/repos/builtin/packages/r-a4preproc/package.py
+++ b/var/spack/repos/builtin/packages/r-a4preproc/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RA4preproc(RPackage):
-    """Automated Affymetrix Array Analysis Preprocessing Package
+    """Automated Affymetrix Array Analysis Preprocessing Package.
 
     Utility functions to pre-process data for the Automated Affymetrix Array
     Analysis set of packages."""
 
-    homepage = "https://bioconductor.org/packages/a4Preproc"
-    git      = "https://git.bioconductor.org/packages/a4Preproc.git"
+    bioc = "a4Preproc"
 
+    version('1.42.0', commit='773a91e884d2ada16fe9cf57d5ed53c0155e3fa2')
     version('1.38.0', commit='c93c223bd531bff090531a109b51f8dcd710d0cb')
     version('1.32.0', commit='0da742e500892b682feeb39256906282ad20c558')
     version('1.30.0', commit='e6fb9fa2e7c703974e6ca10c0e9681b097b05978')
@@ -22,6 +22,7 @@ class RA4preproc(RPackage):
     version('1.26.0', commit='be7403acc06670c05ead1adaf60533b0fe3a65ea')
     version('1.24.0', commit='651014b8102807aea4f1274e34e083e70b5e7ee7')
 
-    depends_on('r-biocgenerics', when='@1.38.0:', type=('build', 'run'))
-    depends_on('r-biobase', when='@1.38.0:', type=('build', 'run'))
-    depends_on('r-annotationdbi', when='@:1.32.0', type=('build', 'run'))
+    depends_on('r-biocgenerics', type=('build', 'run'), when='@1.38.0:')
+    depends_on('r-biobase', type=('build', 'run'), when='@1.38.0:')
+
+    depends_on('r-annotationdbi', type=('build', 'run'), when='@:1.32.0')
diff --git a/var/spack/repos/builtin/packages/r-a4reporting/package.py b/var/spack/repos/builtin/packages/r-a4reporting/package.py
index 5edf49c30d..2216c3364e 100644
--- a/var/spack/repos/builtin/packages/r-a4reporting/package.py
+++ b/var/spack/repos/builtin/packages/r-a4reporting/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RA4reporting(RPackage):
-    """Automated Affymetrix Array Analysis Reporting Package
+    """Automated Affymetrix Array Analysis Reporting Package.
 
     Utility functions to facilitate the reporting of the Automated Affymetrix
     Array Analysis Reporting set of packages."""
 
-    homepage = "https://bioconductor.org/packages/a4Reporting"
-    git      = "https://git.bioconductor.org/packages/a4Reporting.git"
+    bioc = "a4Reporting"
 
+    version('1.42.0', commit='b0d715b9cdac80bc412f0a9a6b33941c4a7582bb')
     version('1.38.0', commit='cd3cf244e7a299b2485684ed15519cbbda1c590f')
     version('1.32.0', commit='8d781899c625892080eb50f322694dd640d5f792')
     version('1.30.0', commit='ae9b9ade45cfac2636d0445a7e0a029dfe3b9390')
@@ -23,4 +23,5 @@ class RA4reporting(RPackage):
     version('1.24.0', commit='bf22c4d50daf40fc9eaf8c476385bf4a24a5b5ce')
 
     depends_on('r-xtable', type=('build', 'run'))
-    depends_on('r-annaffy', when='@:1.32.0', type=('build', 'run'))
+
+    depends_on('r-annaffy', type=('build', 'run'), when='@:1.32.0')
diff --git a/var/spack/repos/builtin/packages/r-abadata/package.py b/var/spack/repos/builtin/packages/r-abadata/package.py
index 04ec686b86..9695cc41ea 100644
--- a/var/spack/repos/builtin/packages/r-abadata/package.py
+++ b/var/spack/repos/builtin/packages/r-abadata/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RAbadata(RPackage):
-    """Averaged gene expression in human brain regions from Allen Brain Atlas
+    """Averaged gene expression in human brain regions from Allen Brain Atlas.
 
        Provides the data for the gene expression enrichment analysis conducted
        in the package 'ABAEnrichment'. The package includes three datasets
@@ -18,9 +18,9 @@ class RAbadata(RPackage):
        Developing Human Brain expression data. All datasets are restricted to
        protein coding genes."""
 
-    homepage = "https://bioconductor.org/packages/ABAData"
-    git      = "https://git.bioconductor.org/packages/ABAData.git"
+    bioc = "ABAData"
 
+    version('1.24.0', commit='c4c42701f995ab8d5ede7f36ff06650493c82e36')
     version('1.20.0', commit='c08a841ffb54d6555eb80b90a7a8afe7e48201b3')
     version('1.14.0', commit='ed7460e7d2948684db69dd4b4f8e135af50198bd')
     version('1.12.0', commit='9c2f0fbda75b06a0807bd714528915920899282d')
diff --git a/var/spack/repos/builtin/packages/r-abaenrichment/package.py b/var/spack/repos/builtin/packages/r-abaenrichment/package.py
index e972828390..b9501c29bb 100644
--- a/var/spack/repos/builtin/packages/r-abaenrichment/package.py
+++ b/var/spack/repos/builtin/packages/r-abaenrichment/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RAbaenrichment(RPackage):
-    """Gene expression enrichment in human brain regions
+    """Gene expression enrichment in human brain regions.
 
        The package ABAEnrichment is designed to test for enrichment of user
        defined candidate genes in the set of expressed genes in different human
@@ -22,9 +22,9 @@ class RAbaenrichment(RPackage):
        tests are implemented, e.g. for cases when genes are ranked instead of
        divided into candidate and background."""
 
-    homepage = "https://bioconductor.org/packages/ABAEnrichment"
-    git      = "https://git.bioconductor.org/packages/ABAEnrichment.git"
+    bioc = "ABAEnrichment"
 
+    version('1.24.0', commit='5d20752263ae8f18ea5f5a6cfbdd5921a0f236d7')
     version('1.20.0', commit='608433a0b07e6dd99915dc536a038d960f1be1d5')
     version('1.14.1', commit='e1ebfb5de816b924af16675a5ba9ed1a6b527b23')
     version('1.12.0', commit='1320e932deafd71d67c7a6f758d15b00d6d7f7d7')
@@ -34,10 +34,10 @@ class RAbaenrichment(RPackage):
 
     depends_on('r+X', type=('build', 'run'))
     depends_on('r@3.2:', type=('build', 'run'))
-    depends_on('r@3.4:', when='@1.8.0:', type=('build', 'run'))
+    depends_on('r@3.4:', type=('build', 'run'), when='@1.8.0:')
     depends_on('r-rcpp@0.11.5:', type=('build', 'run'))
     depends_on('r-gplots@2.14.2:', type=('build', 'run'))
     depends_on('r-gtools@3.5.0:', type=('build', 'run'))
     depends_on('r-abadata@0.99.2:', type=('build', 'run'))
-    depends_on('r-data-table@1.10.4:', when='@1.8.0:', type=('build', 'run'))
-    depends_on('r-gofuncr@1.1.2:', when='@1.12.0:', type=('build', 'run'))
+    depends_on('r-data-table@1.10.4:', type=('build', 'run'), when='@1.8.0:')
+    depends_on('r-gofuncr@1.1.2:', type=('build', 'run'), when='@1.12.0:')
diff --git a/var/spack/repos/builtin/packages/r-absseq/package.py b/var/spack/repos/builtin/packages/r-absseq/package.py
index b0db7f2ee8..a78748aca5 100644
--- a/var/spack/repos/builtin/packages/r-absseq/package.py
+++ b/var/spack/repos/builtin/packages/r-absseq/package.py
@@ -8,16 +8,16 @@ from spack import *
 
 class RAbsseq(RPackage):
     """ABSSeq: a new RNA-Seq analysis method based on modelling absolute
-       expression differences
+       expression differences.
 
        Inferring differential expression genes by absolute counts difference
        between two groups, utilizing Negative binomial distribution and
        moderating fold-change according to heterogeneity of dispersion across
        expression level."""
 
-    homepage = "https://bioconductor.org/packages/ABSSeq"
-    git      = "https://git.bioconductor.org/packages/ABSSeq.git"
+    bioc = "ABSSeq"
 
+    version('1.48.0', commit='b237c967d44d075ca306c35e92df8b66a60ce72d')
     version('1.44.0', commit='c202b4a059021ed1228ccee7303c69b0aa4ca1ee')
     version('1.38.0', commit='b686d92f0f0efdb835982efe761d059bc24b34ce')
     version('1.36.0', commit='bd419072432cba4ef58b4b37b3c69c85d78b1c4a')
diff --git a/var/spack/repos/builtin/packages/r-acde/package.py b/var/spack/repos/builtin/packages/r-acde/package.py
index a4ee88d51e..7143029d67 100644
--- a/var/spack/repos/builtin/packages/r-acde/package.py
+++ b/var/spack/repos/builtin/packages/r-acde/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RAcde(RPackage):
-    """Artificial Components Detection of Differentially Expressed Genes
+    """Artificial Components Detection of Differentially Expressed Genes.
 
        This package provides a multivariate inferential analysis method for
        detecting differentially expressed genes in gene expression data. It
@@ -20,9 +20,9 @@ class RAcde(RPackage):
        Expression Experiments' by J. P. Acosta, L. Lopez-Kleine and S. Restrepo
        (2015, pending publication)."""
 
-    homepage = "https://bioconductor.org/packages/acde"
-    git      = "https://git.bioconductor.org/packages/acde.git"
+    bioc = "acde"
 
+    version('1.24.0', commit='0c3c4d47af7eaff37420032ea5245743a65124cf')
     version('1.20.0', commit='cefb4f2e2b0ef3c5f51944c0ece7a71294020350')
     version('1.14.0', commit='6017c7436a46f186b2a3cea9d2b93274f6dd3417')
     version('1.12.0', commit='f6ce5926ac915c2d73436f47daf7f9791645dad4')
diff --git a/var/spack/repos/builtin/packages/r-acgh/package.py b/var/spack/repos/builtin/packages/r-acgh/package.py
index ec12f17263..5ab1245868 100644
--- a/var/spack/repos/builtin/packages/r-acgh/package.py
+++ b/var/spack/repos/builtin/packages/r-acgh/package.py
@@ -7,16 +7,16 @@ from spack import *
 
 
 class RAcgh(RPackage):
-    """Classes and functions for Array Comparative Genomic Hybridization data
+    """Classes and functions for Array Comparative Genomic Hybridization data.
 
        Functions for reading aCGH data from image analysis output files and
        clone information files, creation of aCGH S3 objects for storing these
        data. Basic methods for accessing/replacing, subsetting, printing and
        plotting aCGH objects."""
 
-    homepage = "https://bioconductor.org/packages/aCGH"
-    git      = "https://git.bioconductor.org/packages/aCGH.git"
+    bioc = "aCGH"
 
+    version('1.72.0', commit='b5d4022ac487125194d3913f1b8c2948db6e2792')
     version('1.68.0', commit='91f41a3917ddce43eb05e11c90eb99c467ba2247')
     version('1.62.0', commit='3b68b69c3380fa3b66dfb060457628a4a9c22d4f')
     version('1.60.0', commit='ae581758aaa1755448f0cfef5adfb30d1e820b21')
diff --git a/var/spack/repos/builtin/packages/r-acme/package.py b/var/spack/repos/builtin/packages/r-acme/package.py
index 78f7736350..a3e79454da 100644
--- a/var/spack/repos/builtin/packages/r-acme/package.py
+++ b/var/spack/repos/builtin/packages/r-acme/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RAcme(RPackage):
-    """Algorithms for Calculating Microarray Enrichment (ACME)
+    """Algorithms for Calculating Microarray Enrichment (ACME).
 
        ACME (Algorithms for Calculating Microarray Enrichment) is a set of
        tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or
@@ -19,9 +19,9 @@ class RAcme(RPackage):
        fast and can be applied on whole-genome tiling array experiments quite
        easily with enough memory."""
 
-    homepage = "https://bioconductor.org/packages/ACME"
-    git      = "https://git.bioconductor.org/packages/ACME.git"
+    bioc = "ACME"
 
+    version('2.50.0', commit='d55a19a8c091e8ea5fd35041520107a7f7603e14')
     version('2.46.0', commit='68f45c9f7d34c28adf6a0fc4245fdf63881109de')
     version('2.40.0', commit='38499e512998d54d874a0bfdc173f4ba5de5f01a')
     version('2.38.0', commit='cd03196428e8adf62e84f25c4d4545429e2c908b')
diff --git a/var/spack/repos/builtin/packages/r-adsplit/package.py b/var/spack/repos/builtin/packages/r-adsplit/package.py
index a160ccbad2..5f21fe1e21 100644
--- a/var/spack/repos/builtin/packages/r-adsplit/package.py
+++ b/var/spack/repos/builtin/packages/r-adsplit/package.py
@@ -7,16 +7,16 @@ from spack import *
 
 
 class RAdsplit(RPackage):
-    """Annotation-Driven Clustering
+    """Annotation-Driven Clustering.
 
        This package implements clustering of microarray gene expression
        profiles according to functional annotations. For each term genes are
        annotated to, splits into two subclasses are computed and a significance
        of the supporting gene set is determined."""
 
-    homepage = "https://bioconductor.org/packages/adSplit"
-    git      = "https://git.bioconductor.org/packages/adSplit.git"
+    bioc = "adSplit"
 
+    version('1.64.0', commit='32f150eb51c66b867301dceeb527de5b97f9f490')
     version('1.60.0', commit='de5abccfe652cbc5b5f49fb6ed77cdd15cc760cd')
     version('1.54.0', commit='ce8fb61f4a3d0942294da2baa28be1472acb0652')
     version('1.52.0', commit='3bd105dbd76c52798b7d52f60c17de62ef13da19')
@@ -29,5 +29,7 @@ class RAdsplit(RPackage):
     depends_on('r-biobase@1.5.12:', type=('build', 'run'))
     depends_on('r-cluster@1.9.1:', type=('build', 'run'))
     depends_on('r-go-db@1.8.1:', type=('build', 'run'))
-    depends_on('r-kegg-db@1.8.1:', type=('build', 'run'))
+    depends_on('r-keggrest@1.30.1:', type=('build', 'run'), when='@1.62.0:')
     depends_on('r-multtest@1.6.0:', type=('build', 'run'))
+
+    depends_on('r-kegg-db@1.8.1:', type=('build', 'run'), when='@:1.60.0')
diff --git a/var/spack/repos/builtin/packages/r-affxparser/package.py b/var/spack/repos/builtin/packages/r-affxparser/package.py
index c1c931d7d8..6b691d5a4e 100644
--- a/var/spack/repos/builtin/packages/r-affxparser/package.py
+++ b/var/spack/repos/builtin/packages/r-affxparser/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RAffxparser(RPackage):
-    """Affymetrix File Parsing SDK
+    """Affymetrix File Parsing SDK.
 
        Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It
        provides methods for fast and memory efficient parsing of Affymetrix
@@ -18,9 +18,9 @@ class RAffxparser(RPackage):
        probesets can be extracted very quickly from a set of CEL files into a
        convenient list structure."""
 
-    homepage = "https://bioconductor.org/packages/affxparser"
-    git      = "https://git.bioconductor.org/packages/affxparser.git"
+    bioc = "affxparser"
 
+    version('1.66.0', commit='2ea72d4c924ac14bdd807b23563c8501c226ce3a')
     version('1.62.0', commit='b3e988e5c136c3f1a064e1da13730b403c8704c0')
     version('1.56.0', commit='20d27701ad2bdfacf34d857bb8ecb4f505b4d056')
     version('1.54.0', commit='dce83d23599a964086a84ced4afd13fc43e7cd4f')
diff --git a/var/spack/repos/builtin/packages/r-affy/package.py b/var/spack/repos/builtin/packages/r-affy/package.py
index c73cef1c9b..5b2b11fbab 100644
--- a/var/spack/repos/builtin/packages/r-affy/package.py
+++ b/var/spack/repos/builtin/packages/r-affy/package.py
@@ -7,15 +7,15 @@ from spack import *
 
 
 class RAffy(RPackage):
-    """Methods for Affymetrix Oligonucleotide Arrays
+    """Methods for Affymetrix Oligonucleotide Arrays.
 
        The package contains functions for exploratory oligonucleotide array
        analysis. The dependence on tkWidgets only concerns few convenience
        functions. 'affy' is fully functional without it."""
 
-    homepage = "https://bioconductor.org/packages/affy"
-    git      = "https://git.bioconductor.org/packages/affy.git"
+    bioc = "affy"
 
+    version('1.72.0', commit='3750b4eb8e5224b19100f6c881b67e568d8968a2')
     version('1.68.0', commit='1664399610c9aa519399445a2ef8bb9ea2233eac')
     version('1.62.0', commit='097ab4aa98a1700c5fae65d07bed44a477714605')
     version('1.60.0', commit='fcae363e58b322ad53584d9e15e80fa2f9d17206')
@@ -24,10 +24,12 @@ class RAffy(RPackage):
     version('1.54.0', commit='a815f02906fcf491b28ed0a356d6fce95a6bd20e')
 
     depends_on('r@2.8.0:4.0', type=('build', 'run'), when='@:1.68.0')
+    depends_on('r@:4.0', type=('build', 'run'), when='@:1.68.0')
     depends_on('r-biocgenerics@0.1.12:', type=('build', 'run'))
     depends_on('r-biobase@2.5.5:', type=('build', 'run'))
     depends_on('r-affyio@1.13.3:', type=('build', 'run'))
-    depends_on('r-biocmanager', when='@1.60.0:', type=('build', 'run'))
+    depends_on('r-biocmanager', type=('build', 'run'), when='@1.60.0:')
     depends_on('r-preprocesscore', type=('build', 'run'))
     depends_on('r-zlibbioc', type=('build', 'run'))
-    depends_on('r-biocinstaller', when='@1.54.0:1.58.0', type=('build', 'run'))
+
+    depends_on('r-biocinstaller', type=('build', 'run'), when='@1.54.0:1.58.0')
diff --git a/var/spack/repos/builtin/packages/r-affycomp/package.py b/var/spack/repos/builtin/packages/r-affycomp/package.py
index a3e47c2bd8..6d2b546be1 100644
--- a/var/spack/repos/builtin/packages/r-affycomp/package.py
+++ b/var/spack/repos/builtin/packages/r-affycomp/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RAffycomp(RPackage):
-    """Graphics Toolbox for Assessment of Affymetrix Expression Measures
+    """Graphics Toolbox for Assessment of Affymetrix Expression Measures.
 
        The package contains functions that can be used to compare expression
        measures for Affymetrix Oligonucleotide Arrays."""
 
-    homepage = "https://bioconductor.org/packages/affycomp"
-    git      = "https://git.bioconductor.org/packages/affycomp.git"
+    bioc = "affycomp"
 
+    version('1.70.0', commit='487f6775975092475581a6c02ddb27590559cf07')
     version('1.66.0', commit='388d01af8b1e6ab11051407f77d0206512df8424')
     version('1.60.0', commit='5dbe61fa04941529a0fc70b728021c8e00c4ba0c')
     version('1.58.0', commit='99607b2c4aad37e3e63eccbd12d0d533762f28ef')
diff --git a/var/spack/repos/builtin/packages/r-affycompatible/package.py b/var/spack/repos/builtin/packages/r-affycompatible/package.py
index 373f94c71d..cd20e9f0ba 100644
--- a/var/spack/repos/builtin/packages/r-affycompatible/package.py
+++ b/var/spack/repos/builtin/packages/r-affycompatible/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RAffycompatible(RPackage):
-    """Affymetrix GeneChip software compatibility
+    """Affymetrix GeneChip software compatibility.
 
        This package provides an interface to Affymetrix chip annotation and
        sample attribute files. The package allows an easy way for users to
@@ -16,9 +16,9 @@ class RAffycompatible(RPackage):
        (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation
        files."""
 
-    homepage = "https://bioconductor.org/packages/AffyCompatible"
-    git      = "https://git.bioconductor.org/packages/AffyCompatible.git"
+    bioc = "AffyCompatible"
 
+    version('1.54.0', commit='fde7d86ccdb03c13c4838c18ac25477ffe6e0fe5')
     version('1.50.0', commit='3b12d12bd6d1a9f0d45e012817231d137d47089e')
     version('1.44.0', commit='98a27fbe880551fd32a5febb6c7bde0807eac476')
     version('1.42.0', commit='699303cc20f292591e2faa12e211c588efb9eaa8')
diff --git a/var/spack/repos/builtin/packages/r-affycontam/package.py b/var/spack/repos/builtin/packages/r-affycontam/package.py
index eb7bf1d0cf..810abec572 100644
--- a/var/spack/repos/builtin/packages/r-affycontam/package.py
+++ b/var/spack/repos/builtin/packages/r-affycontam/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RAffycontam(RPackage):
-    """structured corruption of affymetrix cel file data
+    """structured corruption of affymetrix cel file data.
 
        structured corruption of cel file data to demonstrate QA
        effectiveness"""
 
-    homepage = "https://bioconductor.org/packages/affyContam"
-    git      = "https://git.bioconductor.org/packages/affyContam.git"
+    bioc  = "affyContam"
 
+    version('1.52.0', commit='47c1d86da330f157d3ece0e26b0657d66a5ca0c9')
     version('1.48.0', commit='88387a2ad4be4234d36710c65f2ca3a5b06b67da')
     version('1.42.0', commit='8a5e94a5ae8c2ecfafa6177b84a6e8ab07e14fbe')
     version('1.40.0', commit='dfd5fd6ae04941dddbda03f656540b71b2fbc614')
diff --git a/var/spack/repos/builtin/packages/r-affycoretools/package.py b/var/spack/repos/builtin/packages/r-affycoretools/package.py
index cea3da9d92..f4eca87f30 100644
--- a/var/spack/repos/builtin/packages/r-affycoretools/package.py
+++ b/var/spack/repos/builtin/packages/r-affycoretools/package.py
@@ -8,14 +8,14 @@ from spack import *
 
 class RAffycoretools(RPackage):
     """Functions useful for those doing repetitive analyses with Affymetrix
-       GeneChips
+       GeneChips.
 
        Various wrapper functions that have been written to streamline the more
        common analyses that a core Biostatistician might see."""
 
-    homepage = "https://bioconductor.org/packages/affycoretools"
-    git      = "https://git.bioconductor.org/packages/affycoretools.git"
+    bioc = "affycoretools"
 
+    version('1.66.0', commit='6bf769d70e196634097f465ed2fa85cce5312a6d')
     version('1.62.0', commit='c9779e4da648fd174c9bd575c6020be1c03047c4')
     version('1.56.0', commit='71eab04056a8d696470420a600b14900186be898')
     version('1.54.0', commit='1e1f9680bc3e1fa443f4a81ce5ab81349959b845')
@@ -41,5 +41,5 @@ class RAffycoretools(RPackage):
     depends_on('r-edger', type=('build', 'run'))
     depends_on('r-rsqlite', type=('build', 'run'))
     depends_on('r-biocgenerics', type=('build', 'run'))
-    depends_on('r-dbi', when='@1.50.6:', type=('build', 'run'))
-    depends_on('r-glimma', when='@1.62.0:', type=('build', 'run'))
+    depends_on('r-dbi', type=('build', 'run'), when='@1.50.6:')
+    depends_on('r-glimma', type=('build', 'run'), when='@1.62.0:')
diff --git a/var/spack/repos/builtin/packages/r-affydata/package.py b/var/spack/repos/builtin/packages/r-affydata/package.py
index f8e494a8a7..93dfcfbb2b 100644
--- a/var/spack/repos/builtin/packages/r-affydata/package.py
+++ b/var/spack/repos/builtin/packages/r-affydata/package.py
@@ -7,15 +7,15 @@ from spack import *
 
 
 class RAffydata(RPackage):
-    """Affymetrix Data for Demonstration Purpose
+    """Affymetrix Data for Demonstration Purpose.
 
        Example datasets of a slightly large size. They represent 'real world
        examples', unlike the artificial examples included in the package
        affy."""
 
-    homepage = "https://bioconductor.org/packages/affydata"
-    git      = "https://git.bioconductor.org/packages/affydata.git"
+    bioc = "affydata"
 
+    version('1.42.0', commit='4b54c1206bedd27ff9be32affc999a279f4e96f0')
     version('1.38.0', commit='b5e843b2514789d0d87bea44d762c89a95314ee7')
     version('1.32.0', commit='c7cef93f6edd23024f4b1985b90e89058874c2bd')
     version('1.30.0', commit='d5408d84b37ebae73b40a448dd52baf7b4a13bea')
diff --git a/var/spack/repos/builtin/packages/r-affyexpress/package.py b/var/spack/repos/builtin/packages/r-affyexpress/package.py
index 2d559e3e27..b5c0e0c3e6 100644
--- a/var/spack/repos/builtin/packages/r-affyexpress/package.py
+++ b/var/spack/repos/builtin/packages/r-affyexpress/package.py
@@ -7,14 +7,13 @@ from spack import *
 
 
 class RAffyexpress(RPackage):
-    """Affymetrix Quality Assessment and Analysis Tool
+    """Affymetrix Quality Assessment and Analysis Tool.
 
        The purpose of this package is to provide a comprehensive and easy-to-
        use tool for quality assessment and to identify differentially expressed
        genes in the Affymetrix gene expression data."""
 
-    homepage = "https://bioconductor.org/packages/AffyExpress"
-    git      = "https://git.bioconductor.org/packages/AffyExpress.git"
+    bioc = "AffyExpress"
 
     version('1.56.0', commit='e07085833de2bbf81537410cad526d39f8a82478')
     version('1.50.0', commit='8b98703b63396df9692afb0e15b594658125cc96')
diff --git a/var/spack/repos/builtin/packages/r-affyilm/package.py b/var/spack/repos/builtin/packages/r-affyilm/package.py
index 5f861b72d7..a996e860be 100644
--- a/var/spack/repos/builtin/packages/r-affyilm/package.py
+++ b/var/spack/repos/builtin/packages/r-affyilm/package.py
@@ -7,16 +7,16 @@ from spack import *
 
 
 class RAffyilm(RPackage):
-    """Linear Model of background subtraction and the Langmuir isotherm
+    """Linear Model of background subtraction and the Langmuir isotherm.
 
        affyILM is a preprocessing tool which estimates gene expression levels
        for Affymetrix Gene Chips. Input from physical chemistry is employed to
        first background subtract intensities before calculating concentrations
        on behalf of the Langmuir model."""
 
-    homepage = "https://bioconductor.org/packages/affyILM"
-    git      = "https://git.bioconductor.org/packages/affyILM.git"
+    bioc = "affyILM"
 
+    version('1.46.0', commit='67ffbfa6c881ed83d15604bf4463fe5dba81036b')
     version('1.42.0', commit='b97b29786b866de38802ebbb995169be91e90942')
     version('1.36.0', commit='619ced931ba72860ce4cb41c841bbca1636a1132')
     version('1.34.0', commit='2c02ed2d8fa9a9585d41cf4db0b75d0a07ad8564')
diff --git a/var/spack/repos/builtin/packages/r-affyio/package.py b/var/spack/repos/builtin/packages/r-affyio/package.py
index 4e546839e0..6b9cd31341 100644
--- a/var/spack/repos/builtin/packages/r-affyio/package.py
+++ b/var/spack/repos/builtin/packages/r-affyio/package.py
@@ -7,15 +7,15 @@ from spack import *
 
 
 class RAffyio(RPackage):
-    """Tools for parsing Affymetrix data files
+    """Tools for parsing Affymetrix data files.
 
        Routines for parsing Affymetrix data files based upon file format
        information. Primary focus is on accessing the CEL and CDF file
        formats."""
 
-    homepage = "https://bioconductor.org/packages/affyio"
-    git      = "https://git.bioconductor.org/packages/affyio.git"
+    bioc = "affyio"
 
+    version('1.64.0', commit='aa7ce48f3f4110431f6f488d45961fde4019ffb0')
     version('1.60.0', commit='ee20528b32700e99768da48143d6d45c9a7bbe91')
     version('1.54.0', commit='c0e306e1805a556a1074d1af1acdd18e0a04477f')
     version('1.52.0', commit='9da725ac1098a22a370fa96eb03e51e4f6d5d963')
diff --git a/var/spack/repos/builtin/packages/r-affypdnn/package.py b/var/spack/repos/builtin/packages/r-affypdnn/package.py
index e7cdce2c56..5be82ef00e 100644
--- a/var/spack/repos/builtin/packages/r-affypdnn/package.py
+++ b/var/spack/repos/builtin/packages/r-affypdnn/package.py
@@ -12,8 +12,7 @@ class RAffypdnn(RPackage):
        The package contains functions to perform the PDNN method described by
        Li Zhang et al."""
 
-    homepage = "https://bioconductor.org/packages/affypdnn"
-    git      = "https://git.bioconductor.org/packages/affypdnn.git"
+    bioc = "affypdnn"
 
     version('1.58.0', commit='83d8b6b0d9606845bd77dbf7164dd5b160f32ccf')
     version('1.56.0', commit='5fd9c5265fb895a1f646cf72e8d5169669d979f2')
diff --git a/var/spack/repos/builtin/packages/r-affyplm/package.py b/var/spack/repos/builtin/packages/r-affyplm/package.py
index cf32a939d0..2fc2d79231 100644
--- a/var/spack/repos/builtin/packages/r-affyplm/package.py
+++ b/var/spack/repos/builtin/packages/r-affyplm/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RAffyplm(RPackage):
-    """Methods for fitting probe-level models
+    """Methods for fitting probe-level models.
 
        A package that extends and improves the functionality of the base affy
        package. Routines that make heavy use of compiled code for speed.
@@ -15,9 +15,9 @@ class RAffyplm(RPackage):
        models and tools using these models. PLM based quality assessment
        tools."""
 
-    homepage = "https://bioconductor.org/packages/affyPLM"
-    git      = "https://git.bioconductor.org/packages/affyPLM.git"
+    bioc = "affyPLM"
 
+    version('1.70.0', commit='64abfec92b347aa340b54a8c7b2fbd524fe9c312')
     version('1.66.0', commit='f0780c3d0e9dccaff83861b98beb5c1d324c4399')
     version('1.60.0', commit='b11e377d6af3fd0f28aba8195ebf171003da1a9d')
     version('1.58.0', commit='32764c7691d9a72a301d50042a8844112887a1c8')
diff --git a/var/spack/repos/builtin/packages/r-affyqcreport/package.py b/var/spack/repos/builtin/packages/r-affyqcreport/package.py
index 62a00d7047..05bc17899b 100644
--- a/var/spack/repos/builtin/packages/r-affyqcreport/package.py
+++ b/var/spack/repos/builtin/packages/r-affyqcreport/package.py
@@ -7,14 +7,13 @@ from spack import *
 
 
 class RAffyqcreport(RPackage):
-    """QC Report Generation for affyBatch objects
+    """QC Report Generation for affyBatch objects.
 
        This package creates a QC report for an AffyBatch object. The report is
        intended to allow the user to quickly assess the quality of a set of
        arrays in an AffyBatch object."""
 
-    homepage = "https://bioconductor.org/packages/affyQCReport"
-    git      = "https://git.bioconductor.org/packages/affyQCReport.git"
+    bioc = "affyQCReport"
 
     version('1.68.0', commit='34b42a16f87a90a595146f4a1802ed04f6bfccca')
     version('1.62.0', commit='92d4124b688b90a6a9b8a21ab9d13d92b368cee4')
@@ -27,7 +26,7 @@ class RAffyqcreport(RPackage):
     depends_on('r-affy', type=('build', 'run'))
     depends_on('r-lattice', type=('build', 'run'))
     depends_on('r-affyplm', type=('build', 'run'))
-    depends_on('r-biobase', when='@1.68.0:', type=('build', 'run'))
+    depends_on('r-biobase', type=('build', 'run'), when='@1.68.0:')
     depends_on('r-genefilter', type=('build', 'run'))
     depends_on('r-rcolorbrewer', type=('build', 'run'))
     depends_on('r-simpleaffy', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py b/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py
index 2357111437..8669331a78 100644
--- a/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py
+++ b/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py
@@ -8,7 +8,7 @@ from spack import *
 
 class RAffyrnadegradation(RPackage):
     """Analyze and correct probe positional bias in microarray data due to RNA
-       degradation
+       degradation.
 
        The package helps with the assessment and correction of RNA degradation
        effects in Affymetrix 3' expression arrays. The parameter d gives a
@@ -16,9 +16,9 @@ class RAffyrnadegradation(RPackage):
        probe positional bias, and thus improves comparability of samples that
        are affected by RNA degradation."""
 
-    homepage = "https://bioconductor.org/packages/AffyRNADegradation"
-    git      = "https://git.bioconductor.org/packages/AffyRNADegradation.git"
+    bioc  = "AffyRNADegradation"
 
+    version('1.40.0', commit='8539a91ee464d692a267bb17c91dc1ef9a231f41')
     version('1.36.0', commit='89662b93076659db2967a526899184c12c156bc5')
     version('1.30.0', commit='620c464fb09248e1c7a122828eab59a4fb778cc1')
     version('1.28.0', commit='aff91d78fa9e76edaa3ef6a9a43b98b86cc44c24')
diff --git a/var/spack/repos/builtin/packages/r-agdex/package.py b/var/spack/repos/builtin/packages/r-agdex/package.py
index afbba0d26b..53a0442fc2 100644
--- a/var/spack/repos/builtin/packages/r-agdex/package.py
+++ b/var/spack/repos/builtin/packages/r-agdex/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RAgdex(RPackage):
-    """Agreement of Differential Expression Analysis
+    """Agreement of Differential Expression Analysis.
 
        A tool to evaluate agreement of differential expression for cross-
        species genomics"""
 
-    homepage = "https://bioconductor.org/packages/AGDEX"
-    git      = "https://git.bioconductor.org/packages/AGDEX.git"
+    bioc = "AGDEX"
 
+    version('1.42.0', commit='175cf1b384b0942103d841b1feb9e4f7d141ba06')
     version('1.38.0', commit='7e2c1f5f27ccbea6a7157f5122212e40408b74da')
     version('1.32.0', commit='254ad2c876ab9ac48c3c3b395160dccabc084acf')
     version('1.30.0', commit='d6cc21ed7e11e6644399495fa5f8b36368625d4b')
diff --git a/var/spack/repos/builtin/packages/r-agilp/package.py b/var/spack/repos/builtin/packages/r-agilp/package.py
index 348b60d787..2f800e6dd0 100644
--- a/var/spack/repos/builtin/packages/r-agilp/package.py
+++ b/var/spack/repos/builtin/packages/r-agilp/package.py
@@ -7,13 +7,13 @@ from spack import *
 
 
 class RAgilp(RPackage):
-    """Agilent expression array processing package
+    """Agilent expression array processing package.
 
        More about what it does (maybe more than one line)."""
 
-    homepage = "https://bioconductor.org/packages/agilp"
-    git      = "https://git.bioconductor.org/packages/agilp.git"
+    bioc = "agilp"
 
+    version('3.26.0', commit='3170fe2b1cc459d5e2ca7f61a127aac17cd66a96')
     version('3.22.0', commit='7d089d576752e0526f15a1007e94436089954313')
     version('3.16.0', commit='2900d6066317f21d076b3a043b16f32eca168c47')
     version('3.14.0', commit='8feb047d70216013462ea7806e9227d192b60c61')
diff --git a/var/spack/repos/builtin/packages/r-agimicrorna/package.py b/var/spack/repos/builtin/packages/r-agimicrorna/package.py
index 09f0709c1f..b3ede02ce7 100644
--- a/var/spack/repos/builtin/packages/r-agimicrorna/package.py
+++ b/var/spack/repos/builtin/packages/r-agimicrorna/package.py
@@ -8,13 +8,13 @@ from spack import *
 
 class RAgimicrorna(RPackage):
     """Processing and Differential Expression Analysis of Agilent microRNA
-       chips
+       chips.
 
     Processing and Analysis of Agilent microRNA data."""
 
-    homepage = "https://bioconductor.org/packages/AgiMicroRna"
-    git      = "https://git.bioconductor.org/packages/AgiMicroRna.git"
+    bioc = "AgiMicroRna"
 
+    version('2.44.0', commit='8b308baa3b1b0afc0855ea263630a288689e3864')
     version('2.40.0', commit='cfa4acb2215da44767ab3a45845bcd587c309e74')
     version('2.34.0', commit='aaa8cdd70ed2696c313f6240ffbfa044f0d97a7a')
     version('2.32.0', commit='681ae17d07e8e533f798a607b761b71a31f407d8')
diff --git a/var/spack/repos/builtin/packages/r-aims/package.py b/var/spack/repos/builtin/packages/r-aims/package.py
index 45d63f8197..c6558ee15b 100644
--- a/var/spack/repos/builtin/packages/r-aims/package.py
+++ b/var/spack/repos/builtin/packages/r-aims/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RAims(RPackage):
-    """AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype
+    """Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype.
 
        This package contains the AIMS implementation. It contains necessary
        functions to assign the five intrinsic molecular subtypes (Luminal A,
@@ -15,9 +15,9 @@ class RAims(RPackage):
        done on individual samples as well as on dataset of gene expression
        data."""
 
-    homepage = "https://bioconductor.org/packages/AIMS"
-    git      = "https://git.bioconductor.org/packages/AIMS.git"
+    bioc = "AIMS"
 
+    version('1.26.0', commit='5dcf60eb4cdcf563ea848482c9c488f465c27bbd')
     version('1.22.0', commit='34a38978b24377abb864eff7683bb36344ff171d')
     version('1.16.0', commit='86cb8c998ade3003cd34a5405b218ae07d97bf84')
     version('1.14.1', commit='4125c4217a7e4f00169b5ba65dcc3778fdd33c6f')
diff --git a/var/spack/repos/builtin/packages/r-aldex2/package.py b/var/spack/repos/builtin/packages/r-aldex2/package.py
index 55bf2bb8e7..621a4bec5f 100644
--- a/var/spack/repos/builtin/packages/r-aldex2/package.py
+++ b/var/spack/repos/builtin/packages/r-aldex2/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RAldex2(RPackage):
-    """Analysis Of Differential Abundance Taking Sample Variation Into Account
+    """Analysis Of Differential Abundance Taking Sample Variation Into Account.
 
        A differential abundance analysis for the comparison of two or more
        conditions. Useful for analyzing data from standard RNA-seq or meta-RNA-
@@ -21,9 +21,9 @@ class RAldex2(RPackage):
        aldex.glm), or a correlation test (via aldex.corr). All tests report
        p-values and Benjamini-Hochberg corrected p-values."""
 
-    homepage = "https://bioconductor.org/packages/ALDEx2"
-    git      = "https://git.bioconductor.org/packages/ALDEx2.git"
+    bioc = "ALDEx2"
 
+    version('1.26.0', commit='0876a2eac08d3f1c01df7414d97d391c80182ada')
     version('1.22.0', commit='ac7f0ab3f094ec52713da7620a27058b14c7181d')
     version('1.16.0', commit='bd698a896a5bea91187e3060e56a147bad1d586f')
     version('1.14.1', commit='a8b970c594a00a37c064227bf312d5f89dccabe8')
@@ -31,10 +31,11 @@ class RAldex2(RPackage):
     version('1.10.0', commit='e43f99e4009ad4d5ed200cc8a19faf7091c0c98a')
     version('1.8.0', commit='24104824ca2402ad4f54fbf1ed9cee7fac2aaaf1')
 
-    depends_on('r-zcompositions', when='@1.22.0:', type=('build', 'run'))
+    depends_on('r-zcompositions', type=('build', 'run'), when='@1.22.0:')
+    depends_on('r-rfast', type=('build', 'run'), when='@1.26.0:')
     depends_on('r-biocparallel', type=('build', 'run'))
     depends_on('r-genomicranges', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
     depends_on('r-summarizedexperiment', type=('build', 'run'))
-    depends_on('r-multtest', when='@1.10.0:', type=('build', 'run'))
+    depends_on('r-multtest', type=('build', 'run'), when='@1.10.0:')
diff --git a/var/spack/repos/builtin/packages/r-allelicimbalance/package.py b/var/spack/repos/builtin/packages/r-allelicimbalance/package.py
index f11ff1bcc1..fa0de7f212 100644
--- a/var/spack/repos/builtin/packages/r-allelicimbalance/package.py
+++ b/var/spack/repos/builtin/packages/r-allelicimbalance/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RAllelicimbalance(RPackage):
-    """Investigates Allele Specific Expression
+    """Investigates Allele Specific Expression.
 
        Provides a framework for allelic specific expression investigation using
        RNA-seq data."""
 
-    homepage = "https://bioconductor.org/packages/AllelicImbalance"
-    git      = "https://git.bioconductor.org/packages/AllelicImbalance.git"
+    bioc = "AllelicImbalance"
 
+    version('1.32.0', commit='428ab8c96bb15fab45e4084da25f98b01b9d60b6')
     version('1.28.0', commit='ac5d13c9ee0935bf9500ee542792644e752a1fde')
     version('1.22.0', commit='04692e367e8c6aac475d06adfd7cfa629baab05a')
     version('1.20.0', commit='4cd3a789d872151b0d906ec419677271fecdf7c3')
@@ -23,29 +23,29 @@ class RAllelicimbalance(RPackage):
     version('1.14.0', commit='35958534945819baafde0e13d1eb4d05a514142c')
 
     depends_on('r@3.2.0:', type=('build', 'run'))
-    depends_on('r@4.0.0:', when='@1.28.0:', type=('build', 'run'))
+    depends_on('r@4.0.0:', type=('build', 'run'), when='@1.28.0:')
     depends_on('r-genomicranges', type=('build', 'run'))
-    depends_on('r-genomicranges@1.31.8:', when='@1.18.0:', type=('build', 'run'))
+    depends_on('r-genomicranges@1.31.8:', type=('build', 'run'), when='@1.18.0:')
     depends_on('r-summarizedexperiment@0.2.0:', type=('build', 'run'))
     depends_on('r-genomicalignments', type=('build', 'run'))
-    depends_on('r-genomicalignments@1.15.6:', when='@1.18.0:', type=('build', 'run'))
+    depends_on('r-genomicalignments@1.15.6:', type=('build', 'run'), when='@1.18.0:')
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-annotationdbi', type=('build', 'run'))
     depends_on('r-bsgenome', type=('build', 'run'))
-    depends_on('r-bsgenome@1.47.3:', when='@1.18.0:', type=('build', 'run'))
+    depends_on('r-bsgenome@1.47.3:', type=('build', 'run'), when='@1.18.0:')
     depends_on('r-variantannotation', type=('build', 'run'))
-    depends_on('r-variantannotation@1.25.11:', when='@1.18.0:', type=('build', 'run'))
+    depends_on('r-variantannotation@1.25.11:', type=('build', 'run'), when='@1.18.0:')
     depends_on('r-biostrings', type=('build', 'run'))
-    depends_on('r-biostrings@2.47.6:', when='@1.18.0:', type=('build', 'run'))
+    depends_on('r-biostrings@2.47.6:', type=('build', 'run'), when='@1.18.0:')
     depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.17.25:', when='@1.18.0:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.25:', type=('build', 'run'), when='@1.18.0:')
     depends_on('r-iranges', type=('build', 'run'))
-    depends_on('r-iranges@2.13.12:', when='@1.18.0:', type=('build', 'run'))
+    depends_on('r-iranges@2.13.12:', type=('build', 'run'), when='@1.18.0:')
     depends_on('r-rsamtools', type=('build', 'run'))
-    depends_on('r-rsamtools@1.31.2:', when='@1.18.0:', type=('build', 'run'))
-    depends_on('r-rsamtools@1.99.3:', when='@1.22.0:', type=('build', 'run'))
+    depends_on('r-rsamtools@1.31.2:', type=('build', 'run'), when='@1.18.0:')
+    depends_on('r-rsamtools@1.99.3:', type=('build', 'run'), when='@1.22.0:')
     depends_on('r-genomicfeatures', type=('build', 'run'))
-    depends_on('r-genomicfeatures@1.31.3:', when='@1.18.0:', type=('build', 'run'))
+    depends_on('r-genomicfeatures@1.31.3:', type=('build', 'run'), when='@1.18.0:')
     depends_on('r-gviz', type=('build', 'run'))
     depends_on('r-lattice', type=('build', 'run'))
     depends_on('r-latticeextra', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-alpine/package.py b/var/spack/repos/builtin/packages/r-alpine/package.py
index d063efbb90..5031416049 100644
--- a/var/spack/repos/builtin/packages/r-alpine/package.py
+++ b/var/spack/repos/builtin/packages/r-alpine/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RAlpine(RPackage):
-    """alpine
+    """alpine.
 
        Fragment sequence bias modeling and correction for RNA-seq transcript
        abundance estimation."""
 
-    homepage = "https://bioconductor.org/packages/alpine"
-    git      = "https://git.bioconductor.org/packages/alpine.git"
+    bioc = "alpine"
 
+    version('1.20.0', commit='9348ef14128aa6be10cca1987736ddbc385df7e9')
     version('1.16.0', commit='aee397774ac6cd17ad45dc05be14c526647f3c13')
     version('1.10.0', commit='bf22597eb2c6c6aaa26900ed4ece96ce7256e77c')
     version('1.8.0', commit='ddaa0b4517f0909460aa1bd33c8e43dc6c8d23d4')
diff --git a/var/spack/repos/builtin/packages/r-alsace/package.py b/var/spack/repos/builtin/packages/r-alsace/package.py
index f191b4a3db..e8c1f7fa3d 100644
--- a/var/spack/repos/builtin/packages/r-alsace/package.py
+++ b/var/spack/repos/builtin/packages/r-alsace/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RAlsace(RPackage):
-    """ALS for the Automatic Chemical Exploration of mixtures
+    """ALS for the Automatic Chemical Exploration of mixtures.
 
        Alternating Least Squares (or Multivariate Curve Resolution) for
        analytical chemical data, in particular hyphenated data where the first
@@ -16,9 +16,9 @@ class RAlsace(RPackage):
        functionality for high-throughput analysis, including definition of time
        windows, clustering of profiles, retention time correction, etcetera."""
 
-    homepage = "https://bioconductor.org/packages/alsace"
-    git      = "https://git.bioconductor.org/packages/alsace.git"
+    bioc = "alsace"
 
+    version('1.30.0', commit='d0e09b283da2b4869d5d6e6801399676246bc5bc')
     version('1.26.0', commit='40a76404acb1466723a78a55d87c67eec3e6f306')
     version('1.20.0', commit='47f1cf8daafc864e5e3418009f349ce85d6b0389')
     version('1.18.0', commit='c9fc43c7b441de43b14ef1be69926c4c4a566191')
diff --git a/var/spack/repos/builtin/packages/r-altcdfenvs/package.py b/var/spack/repos/builtin/packages/r-altcdfenvs/package.py
index 36eb98f19c..fe9b93a8e1 100644
--- a/var/spack/repos/builtin/packages/r-altcdfenvs/package.py
+++ b/var/spack/repos/builtin/packages/r-altcdfenvs/package.py
@@ -7,13 +7,13 @@ from spack import *
 
 
 class RAltcdfenvs(RPackage):
-    """alternative CDF environments (aka probeset mappings)
+    """alternative CDF environments (aka probeset mappings).
 
        Convenience data structures and functions to handle cdfenvs."""
 
-    homepage = "https://bioconductor.org/packages/altcdfenvs"
-    git      = "https://git.bioconductor.org/packages/altcdfenvs.git"
+    bioc = "altcdfenvs"
 
+    version('2.56.0', commit='941e00b97a33662a8230991e387070324b2e76bf')
     version('2.52.0', commit='21329abf82eae26f84b7c0270e81c8e089c548ce')
     version('2.46.0', commit='90a11e748a5af98cabfd6670a5b7b256420d172b')
     version('2.44.0', commit='d804f6432422bd532abab415710f890b36cc8133')
diff --git a/var/spack/repos/builtin/packages/r-ampliqueso/package.py b/var/spack/repos/builtin/packages/r-ampliqueso/package.py
index 747d27b42c..4da54c94e8 100644
--- a/var/spack/repos/builtin/packages/r-ampliqueso/package.py
+++ b/var/spack/repos/builtin/packages/r-ampliqueso/package.py
@@ -12,8 +12,7 @@ class RAmpliqueso(RPackage):
        The package provides tools and reports for the analysis of amplicon
        sequencing panels, such as AmpliSeq"""
 
-    homepage = "https://bioconductor.org/packages/3.8/bioc/html/ampliQueso.html"
-    git      = "https://git.bioconductor.org/packages/ampliQueso.git"
+    bioc = "ampliQueso"
 
     version('1.21.0', commit='ed99c5194a452ee299a93e981da2224e4dab5bdd')
     version('1.20.0', commit='ed064ffe9c5f2b47136e5f0f2e2c4214af4deae8')
diff --git a/var/spack/repos/builtin/packages/r-analysispageserver/package.py b/var/spack/repos/builtin/packages/r-analysispageserver/package.py
index d21d18285d..e626957693 100644
--- a/var/spack/repos/builtin/packages/r-analysispageserver/package.py
+++ b/var/spack/repos/builtin/packages/r-analysispageserver/package.py
@@ -13,8 +13,7 @@ class RAnalysispageserver(RPackage):
        AnalysisPageServer is a modular system that enables sharing of
        customizable R analyses via the web."""
 
-    homepage = "https://bioconductor.org/packages/AnalysisPageServer"
-    git      = "https://git.bioconductor.org/packages/AnalysisPageServer.git"
+    bioc = "AnalysisPageServer"
 
     version('1.18.1', commit='08bd85e872d3f2b0c1fa148cf30bcd2d1a29b630')
     version('1.16.0', commit='67b063523f80e2af1d26262367ff50f34e195174')
diff --git a/var/spack/repos/builtin/packages/r-anaquin/package.py b/var/spack/repos/builtin/packages/r-anaquin/package.py
index 14e969d4f9..944494d997 100644
--- a/var/spack/repos/builtin/packages/r-anaquin/package.py
+++ b/var/spack/repos/builtin/packages/r-anaquin/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RAnaquin(RPackage):
-    """Statistical analysis of sequins
+    """Statistical analysis of sequins.
 
        The project is intended to support the use of sequins (synthetic
        sequencing spike-in controls) owned and made available by the Garvan
@@ -15,9 +15,9 @@ class RAnaquin(RPackage):
        source library for quantitative analysis, modelling and visualization of
        spike-in controls."""
 
-    homepage = "https://bioconductor.org/packages/Anaquin"
-    git      = "https://git.bioconductor.org/packages/Anaquin.git"
+    bioc = "Anaquin"
 
+    version('2.18.0', commit='c8e3df3e299c32daac0dda23cea59a18673d886b')
     version('2.14.0', commit='d0a34c931a0e72080bff91dacb37dbbe26b45386')
     version('2.8.0', commit='f591d420740b77881ae0a4c16b208c63d460c601')
     version('2.6.1', commit='22b6c71697fe1e2db8f6d18f77728d0fd96fa6d6')
diff --git a/var/spack/repos/builtin/packages/r-aneufinder/package.py b/var/spack/repos/builtin/packages/r-aneufinder/package.py
index a50a9ae884..f24f6bd55c 100644
--- a/var/spack/repos/builtin/packages/r-aneufinder/package.py
+++ b/var/spack/repos/builtin/packages/r-aneufinder/package.py
@@ -7,15 +7,15 @@ from spack import *
 
 
 class RAneufinder(RPackage):
-    """Analysis of Copy Number Variation in Single-Cell-Sequencing Data
+    """Analysis of Copy Number Variation in Single-Cell-Sequencing Data.
 
        AneuFinder implements functions for copy-number detection, breakpoint
        detection, and karyotype and heterogeneity analysis in single-cell whole
        genome sequencing and strand-seq data."""
 
-    homepage = "https://bioconductor.org/packages/AneuFinder"
-    git      = "https://git.bioconductor.org/packages/AneuFinder.git"
+    bioc = "AneuFinder"
 
+    version('1.22.0', commit='ea0beb3d827c2dd4bc56708a839a93c55304918b')
     version('1.18.0', commit='76ec9af947f97212084ca478e8e82f9e0eb79de9')
     version('1.12.1', commit='e788fd0c864f0bf0abd93df44c6d42f82eb37e0e')
     version('1.10.2', commit='56578ae69abac93dfea6bcac1fc205b14b6ba9dd')
@@ -24,22 +24,22 @@ class RAneufinder(RPackage):
     version('1.4.0', commit='e5bdf4d5e4f84ee5680986826ffed636ed853b8e')
 
     depends_on('r@3.3:', type=('build', 'run'))
-    depends_on('r@3.5:', when='@1.10.2:', type=('build', 'run'))
+    depends_on('r@3.5:', type=('build', 'run'), when='@1.10.2:')
     depends_on('r-genomicranges', type=('build', 'run'))
     depends_on('r-ggplot2', type=('build', 'run'))
     depends_on('r-cowplot', type=('build', 'run'))
     depends_on('r-aneufinderdata', type=('build', 'run'))
     depends_on('r-foreach', type=('build', 'run'))
     depends_on('r-doparallel', type=('build', 'run'))
-    depends_on('r-biocgenerics', when='@1.4.0:1.6.0', type=('build', 'run'))
-    depends_on('r-biocgenerics@0.31.6:', when='@1.18.0:', type=('build', 'run'))
+    depends_on('r-biocgenerics', type=('build', 'run'), when='@1.4.0:1.6.0')
+    depends_on('r-biocgenerics@0.31.6:', type=('build', 'run'), when='@1.18.0:')
     depends_on('r-s4vectors', type=('build', 'run'))
     depends_on('r-genomeinfodb', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
     depends_on('r-rsamtools', type=('build', 'run'))
     depends_on('r-bamsignals', type=('build', 'run'))
     depends_on('r-dnacopy', type=('build', 'run'))
-    depends_on('r-ecp', when='@1.8.0:', type=('build', 'run'))
+    depends_on('r-ecp', type=('build', 'run'), when='@1.8.0:')
     depends_on('r-biostrings', type=('build', 'run'))
     depends_on('r-genomicalignments', type=('build', 'run'))
     depends_on('r-reshape2', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-aneufinderdata/package.py b/var/spack/repos/builtin/packages/r-aneufinderdata/package.py
index ece58876a9..47ffd1ee86 100644
--- a/var/spack/repos/builtin/packages/r-aneufinderdata/package.py
+++ b/var/spack/repos/builtin/packages/r-aneufinderdata/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RAneufinderdata(RPackage):
-    """WGSCS Data for Demonstration Purposes
+    """WGSCS Data for Demonstration Purposes.
 
        Whole-genome single cell sequencing data for demonstration purposes in
        the AneuFinder package."""
 
-    homepage = "https://bioconductor.org/packages/AneuFinderData"
-    git      = "https://git.bioconductor.org/packages/AneuFinderData.git"
+    bioc = "AneuFinderData"
 
+    version('1.22.0', commit='ae8eec3b0afdc351dc447aad2024df5b2c75e56b')
     version('1.18.0', commit='1bf1657b28fc8c1425e611980a692da952ce3d1e')
     version('1.12.0', commit='7350f38856b6278e07eca141f7f3cb24bc60c3a1')
     version('1.10.0', commit='ef7fc27f9af4f178fa45a21aba30709e1ebde035')
diff --git a/var/spack/repos/builtin/packages/r-annaffy/package.py b/var/spack/repos/builtin/packages/r-annaffy/package.py
index 927bc8f253..87430f1cd6 100644
--- a/var/spack/repos/builtin/packages/r-annaffy/package.py
+++ b/var/spack/repos/builtin/packages/r-annaffy/package.py
@@ -7,16 +7,16 @@ from spack import *
 
 
 class RAnnaffy(RPackage):
-    """Annotation tools for Affymetrix biological metadata
+    """Annotation tools for Affymetrix biological metadata.
 
        Functions for handling data from Bioconductor Affymetrix annotation data
        packages. Produces compact HTML and text reports including experimental
        data and URL links to many online databases. Allows searching biological
        metadata using various criteria."""
 
-    homepage = "https://bioconductor.org/packages/annaffy"
-    git      = "https://git.bioconductor.org/packages/annaffy.git"
+    bioc = "annaffy"
 
+    version('1.66.0', commit='aa1afa1509754128d27508228c1f39f51a8da043')
     version('1.62.0', commit='ad9c37e0e7e45e0f35c208ce528ba48000b37432')
     version('1.56.0', commit='8c8e16aa0f3073880c39684fd8e554a052ec6233')
     version('1.54.0', commit='e1b3bf10515255eb994cd8bdf85697ea728c3484')
@@ -26,7 +26,9 @@ class RAnnaffy(RPackage):
 
     depends_on('r@2.5.0:', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
+    depends_on('r-biocmanager', type=('build', 'run'), when='@1.64.2:')
     depends_on('r-go-db', type=('build', 'run'))
-    depends_on('r-kegg-db', type=('build', 'run'))
     depends_on('r-annotationdbi@0.1.15:', type=('build', 'run'))
     depends_on('r-dbi', type=('build', 'run'))
+
+    depends_on('r-kegg-db', type=('build', 'run'), when='@:1.62.0')
diff --git a/var/spack/repos/builtin/packages/r-annotate/package.py b/var/spack/repos/builtin/packages/r-annotate/package.py
index bfa3e86e17..9fa7d17adc 100644
--- a/var/spack/repos/builtin/packages/r-annotate/package.py
+++ b/var/spack/repos/builtin/packages/r-annotate/package.py
@@ -7,13 +7,13 @@ from spack import *
 
 
 class RAnnotate(RPackage):
-    """Annotation for microarrays
+    """Annotation for microarrays.
 
        Using R enviroments for annotation."""
 
-    homepage = "https://bioconductor.org/packages/annotate"
-    git      = "https://git.bioconductor.org/packages/annotate.git"
+    bioc = "annotate"
 
+    version('1.72.0', commit='67ac76a9ff6d60dc1620763d3aa98aef39443110')
     version('1.68.0', commit='98cdb12c612b3f3fc06329a89a1ffb0a92b555c0')
     version('1.62.0', commit='19af0b39747ea83fe8fe9b8bbb6036363bc815cd')
     version('1.60.1', commit='9d8f87db02bf0c1593e79da754335a24d3a8ed16')
@@ -28,5 +28,6 @@ class RAnnotate(RPackage):
     depends_on('r-dbi', type=('build', 'run'))
     depends_on('r-xtable', type=('build', 'run'))
     depends_on('r-biocgenerics@0.13.8:', type=('build', 'run'))
-    depends_on('r-httr', when='@1.68.0:', type=('build', 'run'))
-    depends_on('r-rcurl', when='@:1.62.0', type=('build', 'run'))
+    depends_on('r-httr', type=('build', 'run'), when='@1.68.0:')
+
+    depends_on('r-rcurl', type=('build', 'run'), when='@:1.62.0')
diff --git a/var/spack/repos/builtin/packages/r-annotationdbi/package.py b/var/spack/repos/builtin/packages/r-annotationdbi/package.py
index 9f8c6d285a..3a19789fa6 100644
--- a/var/spack/repos/builtin/packages/r-annotationdbi/package.py
+++ b/var/spack/repos/builtin/packages/r-annotationdbi/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RAnnotationdbi(RPackage):
-    """Manipulation of SQLite-based annotations in Bioconductor
+    """Manipulation of SQLite-based annotations in Bioconductor.
 
        Implements a user-friendly interface for querying SQLite-based
        annotation data packages."""
 
-    homepage = "https://bioconductor.org/packages/AnnotationDbi"
-    git      = "https://git.bioconductor.org/packages/AnnotationDbi.git"
+    bioc = "AnnotationDbi"
 
+    version('1.56.2', commit='13fdc4a93852199ca6ec120a2fe1078f9f445f67')
     version('1.52.0', commit='c4e0ca9bd65362ae9cad6a98d90f54267b0ae838')
     version('1.46.1', commit='ff260913741d0fcf9487eeb1f44a6c6968ced5b9')
     version('1.44.0', commit='ce191b08cfd612d014431325c26c91b11c5f13ac')
@@ -24,10 +24,11 @@ class RAnnotationdbi(RPackage):
 
     depends_on('r@2.7.0:', type=('build', 'run'))
     depends_on('r-biocgenerics@0.15.10:', type=('build', 'run'))
-    depends_on('r-biocgenerics@0.23.1:', when='@1.40.0:', type=('build', 'run'))
-    depends_on('r-biocgenerics@0.29.2:', when='@1.46.1:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.23.1:', type=('build', 'run'), when='@1.40.0:')
+    depends_on('r-biocgenerics@0.29.2:', type=('build', 'run'), when='@1.46.1:')
     depends_on('r-biobase@1.17.0:', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
     depends_on('r-dbi', type=('build', 'run'))
     depends_on('r-rsqlite', type=('build', 'run'))
     depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
+    depends_on('r-keggrest', type=('build', 'run'), when='@1.56.2:')
diff --git a/var/spack/repos/builtin/packages/r-annotationfilter/package.py b/var/spack/repos/builtin/packages/r-annotationfilter/package.py
index 71c8265e6b..6bad6a7aa5 100644
--- a/var/spack/repos/builtin/packages/r-annotationfilter/package.py
+++ b/var/spack/repos/builtin/packages/r-annotationfilter/package.py
@@ -7,15 +7,15 @@ from spack import *
 
 
 class RAnnotationfilter(RPackage):
-    """Facilities for Filtering Bioconductor Annotation Resources
+    """Facilities for Filtering Bioconductor Annotation Resources.
 
        This package provides class and other infrastructure to implement
        filters for manipulating Bioconductor annotation resources. The filters
        will be used by ensembldb, Organism.dplyr, and other packages."""
 
-    homepage = "https://bioconductor.org/packages/AnnotationFilter"
-    git      = "https://git.bioconductor.org/packages/AnnotationFilter.git"
+    bioc = "AnnotationFilter"
 
+    version('1.18.0', commit='60a9b666d7362d7ed5c357fd4a5d2744d8598c20')
     version('1.14.0', commit='6ee3a13ed93a535ed452cbc8c118151a2cbb732c')
     version('1.8.0', commit='9bf70ead899e32e84e2908f2b29cd38250d2d1ed')
     version('1.6.0', commit='fa40a7e17e93fac9e85091ff93f256adf145dec3')
diff --git a/var/spack/repos/builtin/packages/r-annotationforge/package.py b/var/spack/repos/builtin/packages/r-annotationforge/package.py
index 5364096858..7682847374 100644
--- a/var/spack/repos/builtin/packages/r-annotationforge/package.py
+++ b/var/spack/repos/builtin/packages/r-annotationforge/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RAnnotationforge(RPackage):
-    """Tools for building SQLite-based annotation data packages
+    """Tools for building SQLite-based annotation data packages.
 
        Provides code for generating Annotation packages and their databases.
        Packages produced are intended to be used with AnnotationDbi."""
 
-    homepage = "https://bioconductor.org/packages/AnnotationForge"
-    git      = "https://git.bioconductor.org/packages/AnnotationForge.git"
+    bioc = "AnnotationForge"
 
+    version('1.36.0', commit='523b5f0c3ffb77e59e1568e5f36a5a470bfeeae5')
     version('1.32.0', commit='3d17c2a945951c02fe152e5a8a8e9c6cb41e30f7')
     version('1.26.0', commit='5d181f32df1fff6446af64a2538a7d25c23fe46e')
     version('1.24.0', commit='3e1fe863573e5b0f69f35a9ad6aebce11ef83d0d')
diff --git a/var/spack/repos/builtin/packages/r-annotationhub/package.py b/var/spack/repos/builtin/packages/r-annotationhub/package.py
index 709f540086..ec6fe1b6a9 100644
--- a/var/spack/repos/builtin/packages/r-annotationhub/package.py
+++ b/var/spack/repos/builtin/packages/r-annotationhub/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RAnnotationhub(RPackage):
-    """Client to access AnnotationHub resources
+    """Client to access AnnotationHub resources.
 
        This package provides a client for the Bioconductor AnnotationHub web
        resource. The AnnotationHub web resource provides a central location
@@ -18,9 +18,9 @@ class RAnnotationhub(RPackage):
        cache of files retrieved by the user, helping with quick and
        reproducible access."""
 
-    homepage = "https://bioconductor.org/packages/AnnotationHub"
-    git      = "https://git.bioconductor.org/packages/AnnotationHub.git"
+    bioc = "AnnotationHub"
 
+    version('3.2.1', commit='ad1dfe86f0b0ea4711cc9cdb89e073e8794ec9aa')
     version('2.22.0', commit='3ab7dceebbc31ac14ca931f66c662cf9538b7d0a')
     version('2.16.1', commit='f8cefaae603b782e1c1ad277a3fb89d44e3aa1ed')
     version('2.14.5', commit='993a98ce3de04a0bbddcbde5b1ab2a9550275a12')
@@ -29,16 +29,17 @@ class RAnnotationhub(RPackage):
     version('2.8.3', commit='8aa9c64262a8d708d2bf1c82f82dfc3d7d4ccc0c')
 
     depends_on('r-biocgenerics@0.15.10:', type=('build', 'run'))
-    depends_on('r-biocfilecache@1.5.1:', when='@2.16.1:', type=('build', 'run'))
+    depends_on('r-biocfilecache@1.5.1:', type=('build', 'run'), when='@2.16.1:')
     depends_on('r-rsqlite', type=('build', 'run'))
-    depends_on('r-biocmanager', when='@2.14.5:', type=('build', 'run'))
-    depends_on('r-biocversion', when='@2.22.0:', type=('build', 'run'))
-    depends_on('r-curl', when='@2.10.1:', type=('build', 'run'))
-    depends_on('r-rappdirs', when='@2.16.1:', type=('build', 'run'))
+    depends_on('r-biocmanager', type=('build', 'run'), when='@2.14.5:')
+    depends_on('r-biocversion', type=('build', 'run'), when='@2.22.0:')
+    depends_on('r-curl', type=('build', 'run'), when='@2.10.1:')
+    depends_on('r-rappdirs', type=('build', 'run'), when='@2.16.1:')
     depends_on('r-annotationdbi@1.31.19:', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
     depends_on('r-interactivedisplaybase', type=('build', 'run'))
     depends_on('r-httr', type=('build', 'run'))
     depends_on('r-yaml', type=('build', 'run'))
-    depends_on('r-dplyr', when='@2.16.1:', type=('build', 'run'))
-    depends_on('r-biocinstaller', when='@:2.16.1', type=('build', 'run'))
+    depends_on('r-dplyr', type=('build', 'run'), when='@2.16.1:')
+
+    depends_on('r-biocinstaller', type=('build', 'run'), when='@:2.16.1')
diff --git a/var/spack/repos/builtin/packages/r-aplot/package.py b/var/spack/repos/builtin/packages/r-aplot/package.py
new file mode 100644
index 0000000000..2b34b8fc79
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-aplot/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RAplot(RPackage):
+    """Decorate a 'ggplot' with Associated Information.
+
+    For many times, we are not just aligning plots as what 'cowplot' and
+    'patchwork' did. Users would like to align associated information that
+    requires axes to be exactly matched in subplots, e.g. hierarchical
+    clustering with a heatmap. This package provides utilities to aligns
+    associated subplots to a main plot at different sides (left, right, top and
+    bottom) with axes exactly matched."""
+
+    cran = "aplot"
+
+    version('0.1.2', sha256='899c4d101ddcedb1eba9803d78cf02288b63de25e2879add8add1165167509f0')
+
+    depends_on('r-ggfun@0.0.4:', type=('build', 'run'))
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-ggplotify', type=('build', 'run'))
+    depends_on('r-patchwork', type=('build', 'run'))
+    depends_on('r-magrittr', type=('build', 'run'))
+    depends_on('r-yulab-utils', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-aroma-light/package.py b/var/spack/repos/builtin/packages/r-aroma-light/package.py
index 5e4935dde2..e56aa3203d 100644
--- a/var/spack/repos/builtin/packages/r-aroma-light/package.py
+++ b/var/spack/repos/builtin/packages/r-aroma-light/package.py
@@ -8,22 +8,22 @@ from spack import *
 
 class RAromaLight(RPackage):
     """Light-Weight Methods for Normalization and Visualization of Microarray
-    Data using Only Basic R Data Types
+    Data using Only Basic R Data Types.
 
     Methods for microarray analysis that take basic data types such as
     matrices and lists of vectors. These methods can be used standalone, be
     utilized in other packages, or be wrapped up in higher-level classes."""
 
-    homepage = "https://www.aroma-project.org/"
-    git      = "https://git.bioconductor.org/packages/aroma.light"
+    bioc = "aroma.light"
 
+    version('3.24.0', commit='3ff48b8f546acc9803b3c652363cac78d3b81ae5')
     version('3.20.0', commit='02cde7fa166259bce73c396a87dca2ecc8249c39')
     version('3.16.0', commit='fc16179fc4bee8954c5415d7cd13e3112b75b4fd')
 
     depends_on('r@2.15.2:', type=('build', 'run'))
     depends_on('r-r-methodss3@1.7.1:', type=('build', 'run'))
     depends_on('r-r-oo@1.22.0:', type=('build', 'run'))
-    depends_on('r-r-oo@1.23.0:', when='@3.20.0:', type=('build', 'run'))
+    depends_on('r-r-oo@1.23.0:', type=('build', 'run'), when='@3.20.0:')
     depends_on('r-r-utils@2.9.0:', type=('build', 'run'))
     depends_on('r-matrixstats@0.54.0:', type=('build', 'run'))
-    depends_on('r-matrixstats@0.55.0:', when='@3.20.0:', type=('build', 'run'))
+    depends_on('r-matrixstats@0.55.0:', type=('build', 'run'), when='@3.20.0:')
diff --git a/var/spack/repos/builtin/packages/r-bamsignals/package.py b/var/spack/repos/builtin/packages/r-bamsignals/package.py
index 808dab8934..79d676cd21 100644
--- a/var/spack/repos/builtin/packages/r-bamsignals/package.py
+++ b/var/spack/repos/builtin/packages/r-bamsignals/package.py
@@ -7,16 +7,16 @@ from spack import *
 
 
 class RBamsignals(RPackage):
-    """Extract read count signals from bam files
+    """Extract read count signals from bam files.
 
        This package allows to efficiently obtain count vectors from indexed bam
        files. It counts the number of reads in given genomic ranges and it
        computes reads profiles and coverage profiles. It also handles paired-
        end data."""
 
-    homepage = "https://bioconductor.org/packages/bamsignals"
-    git      = "https://git.bioconductor.org/packages/bamsignals.git"
+    bioc = "bamsignals"
 
+    version('1.26.0', commit='d57643441d04f77db0907637dc9e7cd5bed5842f')
     version('1.22.0', commit='5f533969c84212406bcb3ebf725ebb6d77e9947a')
     version('1.16.0', commit='dba9a4ae1613d2700f122ade1e9b90ca8fce5657')
     version('1.14.0', commit='3107d3a35830e879eeddf127a81016ea1ca9b53d')
@@ -31,9 +31,9 @@ class RBamsignals(RPackage):
     depends_on('r-genomicranges', type=('build', 'run'))
     depends_on('r-zlibbioc', type=('build', 'run'))
     depends_on('r-rhtslib', type=('build', 'run'))
-    depends_on('r-rhtslib@1.12.1:', when='@1.12.1:', type=('build', 'run'))
-    depends_on('r-rhtslib@1.13.1:', when='@1.14.0:', type=('build', 'run'))
+    depends_on('r-rhtslib@1.12.1:', type=('build', 'run'), when='@1.12.1:')
+    depends_on('r-rhtslib@1.13.1:', type=('build', 'run'), when='@1.14.0:')
     depends_on('gmake', type='build')
 
-    # this is no listed but is needed
+    # this is not listed but is needed
     depends_on('curl')
diff --git a/var/spack/repos/builtin/packages/r-beachmat/package.py b/var/spack/repos/builtin/packages/r-beachmat/package.py
index afb8a745f3..e974fd6227 100644
--- a/var/spack/repos/builtin/packages/r-beachmat/package.py
+++ b/var/spack/repos/builtin/packages/r-beachmat/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RBeachmat(RPackage):
-    """Compiling Bioconductor to Handle Each Matrix Type
+    """Compiling Bioconductor to Handle Each Matrix Type.
 
        Provides a consistent C++ class interface for reading from and writing
        data to a variety of commonly used matrix types. Ordinary matrices and
@@ -15,9 +15,9 @@ class RBeachmat(RPackage):
        S4 classes may be supported by external linkage, while all other
        matrices are handled by DelayedArray block processing."""
 
-    homepage = "https://bioconductor.org/packages/beachmat"
-    git      = "https://git.bioconductor.org/packages/beachmat.git"
+    bioc = "beachmat"
 
+    version('2.10.0', commit='b7cc532d4a5b26d9073135cc9945258ea08e5079')
     version('2.6.4', commit='7d9dc6379017d723dda3e8dc9fd1f6de7fd33cdb')
     version('2.0.0', commit='2bdac6ce7b636fd16f78641a0bcc2181670107ab')
     version('1.4.0', commit='e3b7a21cae0080d077a0d40e35d1d148f088720a')
@@ -25,17 +25,19 @@ class RBeachmat(RPackage):
     version('1.0.2', commit='6bd57b91d6428ac916f46572d685d3cb01a757f7')
 
     depends_on('r@3.4:', type=('build', 'run'))
-    depends_on('r@3.5:', when='@1.2.1:1.4.0', type=('build', 'run'))
+    depends_on('r@3.5:', type=('build', 'run'), when='@1.2.1:1.4.0')
     depends_on('r-delayedarray', type=('build', 'run'))
-    depends_on('r-delayedarray@0.5.30:', when='@1.2.1', type=('build', 'run'))
-    depends_on('r-delayedarray@0.7.38:', when='@1.4.0', type=('build', 'run'))
-    depends_on('r-delayedarray@0.15.14:', when='@2.6.4', type=('build', 'run'))
-    depends_on('r-biocgenerics', when='@1.4.0:', type=('build', 'run'))
-    depends_on('r-matrix', when='@2.6.4:', type=('build', 'run'))
-    depends_on('r-rhdf5lib', when='@1.0.2:1.4.0', type=('build', 'run'))
-    depends_on('r-rhdf5lib@1.1.4:', when='@1.2.1', type=('build', 'run'))
-    depends_on('r-hdf5array', when='@1.0.2:1.4.0', type=('build', 'run'))
-    depends_on('r-hdf5array@1.7.3:', when='@1.2.1', type=('build', 'run'))
-    depends_on('r-hdf5array@1.9.5:', when='@1.4.0', type=('build', 'run'))
-    depends_on('r-rcpp@0.12.14:', when='@1.0.2:1.4.0', type=('build', 'run'))
-    depends_on('r-rhdf5', when='@1.0.2:1.4.0', type=('build', 'run'))
+    depends_on('r-delayedarray@0.5.30:', type=('build', 'run'), when='@1.2.1')
+    depends_on('r-delayedarray@0.7.38:', type=('build', 'run'), when='@1.4.0')
+    depends_on('r-delayedarray@0.15.14:', type=('build', 'run'), when='@2.6.4')
+    depends_on('r-biocgenerics', type=('build', 'run'), when='@1.4.0:')
+    depends_on('r-matrix', type=('build', 'run'), when='@2.6.4:')
+    depends_on('r-rcpp@0.12.14:', type=('build', 'run'), when='@1.0.2:1.4.0')
+    depends_on('r-rcpp', type=('build', 'run'), when='@2.10.0:')
+
+    depends_on('r-rhdf5lib', type=('build', 'run'), when='@1.0.2:1.4.0')
+    depends_on('r-rhdf5lib@1.1.4:', type=('build', 'run'), when='@1.2.1')
+    depends_on('r-hdf5array', type=('build', 'run'), when='@1.0.2:1.4.0')
+    depends_on('r-hdf5array@1.7.3:', type=('build', 'run'), when='@1.2.1')
+    depends_on('r-hdf5array@1.9.5:', type=('build', 'run'), when='@1.4.0')
+    depends_on('r-rhdf5', type=('build', 'run'), when='@1.0.2:1.4.0')
diff --git a/var/spack/repos/builtin/packages/r-biobase/package.py b/var/spack/repos/builtin/packages/r-biobase/package.py
index 14a194524f..acde3d0e00 100644
--- a/var/spack/repos/builtin/packages/r-biobase/package.py
+++ b/var/spack/repos/builtin/packages/r-biobase/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RBiobase(RPackage):
-    """Biobase: Base functions for Bioconductor
+    """Biobase: Base functions for Bioconductor.
 
        Functions that are needed by many other packages or which replace R
        functions."""
 
-    homepage = "https://bioconductor.org/packages/Biobase"
-    git      = "https://git.bioconductor.org/packages/Biobase.git"
+    bioc = "Biobase"
 
+    version('2.54.0', commit='8215d76ce44899e6d10fe8a2f503821a94ef6b40')
     version('2.50.0', commit='9927f90d0676382f2f99e099d8d2c8e2e6f1b4de')
     version('2.44.0', commit='bde2077f66047986297ec35a688751cdce150dd3')
     version('2.42.0', commit='3e5bd466b99e3cc4af1b0c3b32687fa56d6f8e4d')
@@ -24,4 +24,4 @@ class RBiobase(RPackage):
 
     depends_on('r@2.10:', type=('build', 'run'))
     depends_on('r-biocgenerics@0.3.2:', type=('build', 'run'))
-    depends_on('r-biocgenerics@0.27.1:', when='@2.42.0:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.27.1:', type=('build', 'run'), when='@2.42.0:')
diff --git a/var/spack/repos/builtin/packages/r-biocfilecache/package.py b/var/spack/repos/builtin/packages/r-biocfilecache/package.py
index 9cbbaf7b8a..29555c0962 100644
--- a/var/spack/repos/builtin/packages/r-biocfilecache/package.py
+++ b/var/spack/repos/builtin/packages/r-biocfilecache/package.py
@@ -7,16 +7,16 @@ from spack import *
 
 
 class RBiocfilecache(RPackage):
-    """Manage Files Across Sessions
+    """Manage Files Across Sessions.
 
        This package creates a persistent on-disk cache of files that the user
        can add, update, and retrieve. It is useful for managing resources (such
        as custom Txdb objects) that are costly or difficult to create, web
        resources, and data files used across sessions."""
 
-    homepage = "https://bioconductor.org/packages/BiocFileCache"
-    git      = "https://git.bioconductor.org/packages/BiocFileCache.git"
+    bioc = "BiocFileCache"
 
+    version('2.2.1', commit='cc912123408803193bf37395f4d18baa8dcd6f47')
     version('1.14.0', commit='cdcde4b59ae73dda12aa225948dbd0a058d9be6d')
     version('1.8.0', commit='0e3542b6aae849b01240d8055a48da1b267bd5a0')
     version('1.6.0', commit='c2de6c1cdef6294e5d0adea31e4ebf25865742ba')
@@ -26,9 +26,10 @@ class RBiocfilecache(RPackage):
 
     depends_on('r@3.4.0:', type=('build', 'run'))
     depends_on('r-dplyr', type=('build', 'run'))
-    depends_on('r-dbplyr@1.0.0:', when='@1.2.3:', type=('build', 'run'))
+    depends_on('r-dbplyr@1.0.0:', type=('build', 'run'), when='@1.2.3:')
     depends_on('r-rsqlite', type=('build', 'run'))
     depends_on('r-dbi', type=('build', 'run'))
     depends_on('r-rappdirs', type=('build', 'run'))
-    depends_on('r-curl', when='@1.6.0:', type=('build', 'run'))
+    depends_on('r-filelock', type=('build', 'run'), when='@2.2.1:')
+    depends_on('r-curl', type=('build', 'run'), when='@1.6.0:')
     depends_on('r-httr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-biocgenerics/package.py b/var/spack/repos/builtin/packages/r-biocgenerics/package.py
index 3a300e7a2d..0c0e7dc866 100644
--- a/var/spack/repos/builtin/packages/r-biocgenerics/package.py
+++ b/var/spack/repos/builtin/packages/r-biocgenerics/package.py
@@ -7,13 +7,13 @@ from spack import *
 
 
 class RBiocgenerics(RPackage):
-    """S4 generic functions used in Bioconductor
+    """S4 generic functions used in Bioconductor.
 
        The package defines S4 generic functions used in Bioconductor."""
 
-    homepage = "https://bioconductor.org/packages/BiocGenerics"
-    git      = "https://git.bioconductor.org/packages/BiocGenerics.git"
+    bioc = "BiocGenerics"
 
+    version('0.40.0', commit='0bc1e0ed4d20c7101cd782a14f6373e27478acfc')
     version('0.36.0', commit='0d5d169d7d64d648a22f9043837c93bc784e71ed')
     version('0.34.0', commit='f7c2020')
     version('0.30.0', commit='fc7c3af4a5635a30988a062ed09332c13ca1d1a8')
@@ -22,5 +22,5 @@ class RBiocgenerics(RPackage):
     version('0.24.0', commit='3db111e8c1f876267da89f4f0c5406a9d5c31cd1')
     version('0.22.1', commit='9c90bb8926885289d596a81ff318ee3745cbb6ad')
 
-    depends_on('r@3.6.0:', when='@0.30.0:', type=('build', 'run'))
-    depends_on('r@4.0.0:', when='@0.36.0:', type=('build', 'run'))
+    depends_on('r@3.6.0:', type=('build', 'run'), when='@0.30.0:')
+    depends_on('r@4.0.0:', type=('build', 'run'), when='@0.36.0:')
diff --git a/var/spack/repos/builtin/packages/r-biocinstaller/package.py b/var/spack/repos/builtin/packages/r-biocinstaller/package.py
index 51fe13f765..4118acc5f1 100644
--- a/var/spack/repos/builtin/packages/r-biocinstaller/package.py
+++ b/var/spack/repos/builtin/packages/r-biocinstaller/package.py
@@ -12,8 +12,7 @@ class RBiocinstaller(RPackage):
        This package is used to install and update Bioconductor, CRAN, and
        (some) github packages."""
 
-    homepage = "https://bioconductor.org/packages/3.8/bioc/html/BiocInstaller.html"
-    git      = "https://git.bioconductor.org/packages/BiocInstaller.git"
+    bioc = "BiocInstaller"
 
     version('1.33.1', commit='6193f31c18e7e64d91e0e15ed0ba6924eda1416f')
     version('1.32.1', commit='4c2a39e1cae470af3a5cf1491715f272b70f4bb4')
@@ -22,5 +21,4 @@ class RBiocinstaller(RPackage):
     version('1.26.1', commit='9049b82a77aefa98e3f8e4dd7068317505d70e98')
 
     depends_on('r@3.4.0:', type=('build', 'run'))
-
-    depends_on('r@3.5.0:', when='@1.30.0:', type=('build', 'run'))
+    depends_on('r@3.5.0:', type=('build', 'run'), when='@1.30.0:')
diff --git a/var/spack/repos/builtin/packages/r-biocio/package.py b/var/spack/repos/builtin/packages/r-biocio/package.py
new file mode 100644
index 0000000000..f671dfb2f9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-biocio/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RBiocio(RPackage):
+    """Standard Input and Output for Bioconductor Packages.
+
+    Implements `import()` and `export()` standard generics for importing and
+    exporting biological data formats. `import()` supports whole-file as well
+    as chunk-wise iterative import. The `import()` interface optionally
+    provides a standard mechanism for 'lazy' access via `filter()` (on row or
+    element-like components of the file resource), `select()` (on column-like
+    components of the file resource) and `collect()`. The `import()` interface
+    optionally provides transparent access to remote (e.g. via https) as well
+    as local access. Developers can register a file extension, e.g., `.loom`
+    for dispatch from character-based URIs to specific `import()` / `export()`
+    methods based on classes representing file types, e.g., `LoomFile()`."""
+
+    bioc = "BiocIO"
+
+    version('1.4.0', commit='c335932526a38c75dbfa4970c1d90b8a21466d37')
+
+    depends_on('r@4.0.0:', type=('build', 'run'))
+    depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r-s4vectors', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-biocneighbors/package.py b/var/spack/repos/builtin/packages/r-biocneighbors/package.py
index db2e2aafe5..7b9ccaf764 100644
--- a/var/spack/repos/builtin/packages/r-biocneighbors/package.py
+++ b/var/spack/repos/builtin/packages/r-biocneighbors/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RBiocneighbors(RPackage):
-    """Nearest Neighbor Detection for Bioconductor Packages
+    """Nearest Neighbor Detection for Bioconductor Packages.
 
        Implements exact and approximate methods for nearest neighbor detection,
        in a framework that allows them to be easily switched within
@@ -19,18 +19,19 @@ class RBiocneighbors(RPackage):
        BiocParallel. Functions are also provided to search for all neighbors
        within a given distance."""
 
-    homepage = "https://bioconductor.org/packages/BiocNeighbors"
-    git      = "https://git.bioconductor.org/packages/BiocNeighbors.git"
+    bioc = "BiocNeighbors"
 
+    version('1.12.0', commit='3c8a290f75adc944b408e6e77a36f3a0c1509c4c')
     version('1.8.2', commit='889bc91f8cb45d210b47ae5c0b9cfb86fb071ca2')
     version('1.2.0', commit='f754c6300f835142536a4594ddf750481e0fe273')
     version('1.0.0', commit='e252fc04b6d22097f2c5f74406e77d85e7060770')
 
-    depends_on('r@3.5:', when='@1.0.0', type=('build', 'run'))
+    depends_on('r@3.5:', type=('build', 'run'), when='@1.0.0')
     depends_on('r-rcpp', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
     depends_on('r-biocparallel', type=('build', 'run'))
-    depends_on('r-matrix', when='@1.8.2:', type=('build', 'run'))
-    depends_on('r-rcpphnsw', when='@1.2.0:', type=('build', 'run'))
-    depends_on('r-rcppannoy', when='@:1.2.0', type=('build', 'run'))
-    depends_on('r-biocgenerics', when='@1.2.0', type=('build', 'run'))
+    depends_on('r-matrix', type=('build', 'run'), when='@1.8.2:')
+    depends_on('r-rcpphnsw', type=('build', 'run'), when='@1.2.0:')
+
+    depends_on('r-rcppannoy', type=('build', 'run'), when='@:1.2.0')
+    depends_on('r-biocgenerics', type=('build', 'run'), when='@1.2.0')
diff --git a/var/spack/repos/builtin/packages/r-biocparallel/package.py b/var/spack/repos/builtin/packages/r-biocparallel/package.py
index 6720fbc6ea..8a8afe43e9 100644
--- a/var/spack/repos/builtin/packages/r-biocparallel/package.py
+++ b/var/spack/repos/builtin/packages/r-biocparallel/package.py
@@ -7,15 +7,15 @@ from spack import *
 
 
 class RBiocparallel(RPackage):
-    """Bioconductor facilities for parallel evaluation
+    """Bioconductor facilities for parallel evaluation.
 
        This package provides modified versions and novel implementation of
        functions for parallel evaluation, tailored to use with Bioconductor
        objects."""
 
-    homepage = "https://bioconductor.org/packages/BiocParallel"
-    git      = "https://git.bioconductor.org/packages/BiocParallel.git"
+    bioc = "BiocParallel"
 
+    version('1.28.3', commit='2f9d88ad83659939e7911d49c2d24d2cd599c7cc')
     version('1.24.1', commit='f713caa4314ec0ddeba7fe0eb599ad417efb413f')
     version('1.18.1', commit='348264af782d7dcd41a1879400f348f836767f6e')
     version('1.16.6', commit='7f7a54c47f4949b600b9fd568289a519496bc4d4')
@@ -23,6 +23,7 @@ class RBiocparallel(RPackage):
     version('1.12.0', commit='2143a9addceed0151a27b95c70aadd2add5cbace')
     version('1.10.1', commit='a76c58cf99fd585ba5ea33065649e68f1afe0a7d')
 
+    depends_on('r@3.5.0:', type=('build', 'run'), when='@1.28.3:')
     depends_on('r-futile-logger', type=('build', 'run'))
     depends_on('r-snow', type=('build', 'run'))
-    depends_on('r-bh', when='@1.12.0:', type=('build', 'run'))
+    depends_on('r-bh', type=('build', 'run'), when='@1.12.0:')
diff --git a/var/spack/repos/builtin/packages/r-biocsingular/package.py b/var/spack/repos/builtin/packages/r-biocsingular/package.py
index 2727417aba..0f7d37137a 100644
--- a/var/spack/repos/builtin/packages/r-biocsingular/package.py
+++ b/var/spack/repos/builtin/packages/r-biocsingular/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RBiocsingular(RPackage):
-    """Singular Value Decomposition for Bioconductor Packages
+    """Singular Value Decomposition for Bioconductor Packages.
 
        Implements exact and approximate methods for singular value
        decomposition and principal components analysis, in a framework that
@@ -15,9 +15,9 @@ class RBiocsingular(RPackage):
        workflows. Where possible, parallelization is achieved using the
        BiocParallel framework."""
 
-    homepage = "https://bioconductor.org/packages/BiocSingular"
-    git      = "https://git.bioconductor.org/packages/BiocSingular.git"
+    bioc = "BiocSingular"
 
+    version('1.10.0', commit='6615ae8cb124aba6507447c1081bd2eba655e57d')
     version('1.6.0', commit='11baf1080d6f791439cd5d97357589d6451643d9')
     version('1.0.0', commit='d2b091c072d0312698c9bb6611eb1bdf8aebf833')
 
@@ -26,6 +26,7 @@ class RBiocsingular(RPackage):
     depends_on('r-matrix', type=('build', 'run'))
     depends_on('r-delayedarray', type=('build', 'run'))
     depends_on('r-biocparallel', type=('build', 'run'))
+    depends_on('r-scaledmatrix', type=('build', 'run'), when='@1.10.0:')
     depends_on('r-irlba', type=('build', 'run'))
     depends_on('r-rsvd', type=('build', 'run'))
     depends_on('r-rcpp', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-biocstyle/package.py b/var/spack/repos/builtin/packages/r-biocstyle/package.py
index 276fe948f2..c76a386e65 100644
--- a/var/spack/repos/builtin/packages/r-biocstyle/package.py
+++ b/var/spack/repos/builtin/packages/r-biocstyle/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RBiocstyle(RPackage):
-    """Standard styles for vignettes and other Bioconductor documents
+    """Standard styles for vignettes and other Bioconductor documents.
 
        Provides standard formatting styles for Bioconductor PDF and HTML
        documents. Package vignettes illustrate use and functionality."""
 
-    homepage = "https://bioconductor.org/packages/BiocStyle"
-    git      = "https://git.bioconductor.org/packages/BiocStyle.git"
+    bioc = "BiocStyle"
 
+    version('2.22.0', commit='86250b637afa3a3463fac939b99c0402b47876ea')
     version('2.18.1', commit='956f0654e8e18882ba09305742401128c9c7d47d')
     version('2.12.0', commit='0fba3fe6e6a38504f9aadcd3dc95bb83d7e92498')
     version('2.10.0', commit='8fc946044c6b6a8a3104ddbc546baed49ee3aa70')
@@ -25,7 +25,7 @@ class RBiocstyle(RPackage):
     depends_on('r+X', type=('build', 'run'))
     depends_on('r-bookdown', type=('build', 'run'))
     depends_on('r-knitr@1.12:', type=('build', 'run'))
-    depends_on('r-knitr@1.30:', when='@2.18.1:', type=('build', 'run'))
+    depends_on('r-knitr@1.30:', type=('build', 'run'), when='@2.18.1:')
     depends_on('r-rmarkdown@1.2:', type=('build', 'run'))
     depends_on('r-yaml', type=('build', 'run'))
-    depends_on('r-biocmanager', when='@2.10.0:', type=('build', 'run'))
+    depends_on('r-biocmanager', type=('build', 'run'), when='@2.10.0:')
diff --git a/var/spack/repos/builtin/packages/r-biocversion/package.py b/var/spack/repos/builtin/packages/r-biocversion/package.py
index f15560325e..f72c386148 100644
--- a/var/spack/repos/builtin/packages/r-biocversion/package.py
+++ b/var/spack/repos/builtin/packages/r-biocversion/package.py
@@ -7,14 +7,15 @@ from spack import *
 
 
 class RBiocversion(RPackage):
-    """Set the appropriate version of Bioconductor packages
+    """Set the appropriate version of Bioconductor packages.
 
     This package provides repository information for the appropriate
     version of Bioconductor."""
 
-    homepage = "https://bioconductor.org/packages/BiocVersion/"
-    git      = "https://git.bioconductor.org/packages/BiocVersion"
+    bioc = "BiocVersion"
 
+    version('3.14.0', commit='aa56d93d0ea5dcdbf301f120502981740fd91e1e')
     version('3.12.0', commit='23b971963c6b73550a7e330dab5a046d58ce0223')
 
     depends_on('r@4.0.0:', type=('build', 'run'))
+    depends_on('r@4.1.0:', type=('build', 'run'), when='@3.14.0:')
diff --git a/var/spack/repos/builtin/packages/r-biomart/package.py b/var/spack/repos/builtin/packages/r-biomart/package.py
index b2230bf631..2a8f2e22e7 100644
--- a/var/spack/repos/builtin/packages/r-biomart/package.py
+++ b/var/spack/repos/builtin/packages/r-biomart/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RBiomart(RPackage):
-    """Interface to BioMart databases (i.e. Ensembl)
+    """Interface to BioMart databases (i.e. Ensembl).
 
        In recent years a wealth of biological data has become available in
        public data repositories. Easy access to these valuable data resources
@@ -22,9 +22,9 @@ class RBiomart(RPackage):
        range of powerful online queries from gene annotation to database
        mining."""
 
-    homepage = "https://bioconductor.org/packages/biomaRt"
-    git      = "https://git.bioconductor.org/packages/biomaRt.git"
+    bioc = "biomaRt"
 
+    version('2.50.3', commit='83a519ac13d73dc545cb6aafde5f4b5001e9e08f')
     version('2.46.2', commit='90d6abfdfa04259006f7b47efb10271ada76aec1')
     version('2.40.5', commit='ed9ddafb0d620168ea8e3ab4884f3457b8525c68')
     version('2.38.0', commit='16b997aba19a90a1c5fa64c442b1e7fcff99a658')
@@ -34,11 +34,13 @@ class RBiomart(RPackage):
 
     depends_on('r-xml', type=('build', 'run'))
     depends_on('r-annotationdbi', type=('build', 'run'))
-    depends_on('r-progress', when='@2.34.2:', type=('build', 'run'))
-    depends_on('r-stringr', when='@2.34.2:', type=('build', 'run'))
-    depends_on('r-httr', when='@2.34.2:', type=('build', 'run'))
-    depends_on('r-openssl', when='@2.46.2:', type=('build', 'run'))
-    depends_on('r-biocfilecache', when='@2.46.2:', type=('build', 'run'))
-    depends_on('r-rappdirs', when='@2.46.2:', type=('build', 'run'))
-    depends_on('r-xml2', when='@2.46.2:', type=('build', 'run'))
-    depends_on('r-rcurl', when='@:2.40.5', type=('build', 'run'))
+    depends_on('r-progress', type=('build', 'run'), when='@2.34.2:')
+    depends_on('r-stringr', type=('build', 'run'), when='@2.34.2:')
+    depends_on('r-httr', type=('build', 'run'), when='@2.34.2:')
+    depends_on('r-digest', type=('build', 'run'), when='@2.50.3:')
+    depends_on('r-biocfilecache', type=('build', 'run'), when='@2.46.2:')
+    depends_on('r-rappdirs', type=('build', 'run'), when='@2.46.2:')
+    depends_on('r-xml2', type=('build', 'run'), when='@2.46.2:')
+
+    depends_on('r-rcurl', type=('build', 'run'), when='@:2.40.5')
+    depends_on('r-openssl', type=('build', 'run'), when='@2.46.2')
diff --git a/var/spack/repos/builtin/packages/r-biomformat/package.py b/var/spack/repos/builtin/packages/r-biomformat/package.py
index 86548dcdd6..d71f420e14 100644
--- a/var/spack/repos/builtin/packages/r-biomformat/package.py
+++ b/var/spack/repos/builtin/packages/r-biomformat/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RBiomformat(RPackage):
-    """An interface package for the BIOM file format
+    """An interface package for the BIOM file format.
 
        This is an R package for interfacing with the BIOM format. This package
        includes basic tools for reading biom-format files, accessing and
@@ -19,9 +19,9 @@ class RBiomformat(RPackage):
        includes S4 classes and methods, as well as extensions of common core
        functions/methods."""
 
-    homepage = "https://bioconductor.org/packages/biomformat"
-    git      = "https://git.bioconductor.org/packages/biomformat.git"
+    bioc = "biomformat"
 
+    version('1.22.0', commit='ab7c6411a038fec010baa72e663f362fd972cb34')
     version('1.18.0', commit='dc18859c139f4d76805adb6f01e199573cdd5a8b')
     version('1.12.0', commit='6e946123bb59da262cbb0c17dc5ab49328a89d4a')
     version('1.10.1', commit='e67c6f4b70201f748fa49a4938e1af0cd0613f09')
diff --git a/var/spack/repos/builtin/packages/r-biostrings/package.py b/var/spack/repos/builtin/packages/r-biostrings/package.py
index 849b532eda..e445ba5c61 100644
--- a/var/spack/repos/builtin/packages/r-biostrings/package.py
+++ b/var/spack/repos/builtin/packages/r-biostrings/package.py
@@ -7,15 +7,15 @@ from spack import *
 
 
 class RBiostrings(RPackage):
-    """Efficient manipulation of biological strings
+    """Efficient manipulation of biological strings.
 
        Memory efficient string containers, string matching algorithms, and
        other utilities, for fast manipulation of large biological sequences or
        sets of sequences."""
 
-    homepage = "https://bioconductor.org/packages/Biostrings"
-    git      = "https://git.bioconductor.org/packages/Biostrings.git"
+    bioc = "Biostrings"
 
+    version('2.62.0', commit='53ed287e03d16fa523789af3131c60375ccf587f')
     version('2.58.0', commit='0ec1a5455d5e9eebd14b26228906bb04e2abb197')
     version('2.52.0', commit='b78fe7c1f3cdbbb7affb1ca7164fe5a1f8b868f5')
     version('2.50.2', commit='025e734641a93f6c5d44243297cb4264ea0e34a2')
@@ -24,19 +24,22 @@ class RBiostrings(RPackage):
     version('2.44.2', commit='e4a2b320fb21c5cab3ece7b3c6fecaedfb1e5200')
 
     depends_on('r@2.8.0:', type=('build', 'run'))
-    depends_on('r@3.5.0:', when='@2.50.2:', type=('build', 'run'))
+    depends_on('r@3.5.0:', type=('build', 'run'), when='@2.50.2:')
+    depends_on('r@4.0.0:', type=('build', 'run'), when='@2.62.0:')
     depends_on('r-biocgenerics@0.15.6:', type=('build', 'run'))
-    depends_on('r-biocgenerics@0.31.5:', when='@2.58.0:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.31.5:', type=('build', 'run'), when='@2.58.0:')
+    depends_on('r-biocgenerics@0.37.0:', type=('build', 'run'), when='@2.62.0:')
     depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.17.25:', when='@2.48.0:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.21.13:', when='@2.52.0:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.27.12:', when='@2.58.0:', type=('build', 'run'))
-    depends_on('r-iranges@2.9.18:', when='@2.44.2:', type=('build', 'run'))
-    depends_on('r-iranges@2.13.24:', when='@2.48.0:', type=('build', 'run'))
-    depends_on('r-iranges@2.23.9:', when='@2.58.0:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.25:', type=('build', 'run'), when='@2.48.0:')
+    depends_on('r-s4vectors@0.21.13:', type=('build', 'run'), when='@2.52.0:')
+    depends_on('r-s4vectors@0.27.12:', type=('build', 'run'), when='@2.58.0:')
+    depends_on('r-iranges@2.9.18:', type=('build', 'run'), when='@2.44.2:')
+    depends_on('r-iranges@2.13.24:', type=('build', 'run'), when='@2.48.0:')
+    depends_on('r-iranges@2.23.9:', type=('build', 'run'), when='@2.58.0:')
     depends_on('r-xvector@0.11.6:', type=('build', 'run'))
-    depends_on('r-xvector@0.19.8:', when='@2.48.0:', type=('build', 'run'))
-    depends_on('r-xvector@0.21.4:', when='@2.50.2:', type=('build', 'run'))
-    depends_on('r-xvector@0.23.2:', when='@2.52.0:', type=('build', 'run'))
-    depends_on('r-xvector@0.29.2:', when='@2.58.0:', type=('build', 'run'))
-    depends_on('r-crayon', when='@2.58.0:', type=('build', 'run'))
+    depends_on('r-xvector@0.19.8:', type=('build', 'run'), when='@2.48.0:')
+    depends_on('r-xvector@0.21.4:', type=('build', 'run'), when='@2.50.2:')
+    depends_on('r-xvector@0.23.2:', type=('build', 'run'), when='@2.52.0:')
+    depends_on('r-xvector@0.29.2:', type=('build', 'run'), when='@2.58.0:')
+    depends_on('r-genomeinfodb', type=('build', 'run'), when='@2.62.0:')
+    depends_on('r-crayon', type=('build', 'run'), when='@2.58.0:')
diff --git a/var/spack/repos/builtin/packages/r-biovizbase/package.py b/var/spack/repos/builtin/packages/r-biovizbase/package.py
index 358f6d74ee..d8b6148af5 100644
--- a/var/spack/repos/builtin/packages/r-biovizbase/package.py
+++ b/var/spack/repos/builtin/packages/r-biovizbase/package.py
@@ -14,9 +14,9 @@ class RBiovizbase(RPackage):
        various high-level packages for biological data visualization. This
        saves development effort and encourages consistency."""
 
-    homepage = "https://bioconductor.org/packages/biovizBase"
-    git      = "https://git.bioconductor.org/packages/biovizBase.git"
+    bioc = "biovizBase"
 
+    version('1.42.0', commit='f1627b2b567471837daca6e763acfc3e13937461')
     version('1.38.0', commit='d0f3362e0ad0e90b4b1d3e47b13ed57907d03403')
     version('1.32.0', commit='de044bf236cdcd71214ae7b77689a8f0ab4f5cc8')
     version('1.30.1', commit='b6776d0470e2920f71127652f185f68ca1fd2c82')
@@ -25,14 +25,14 @@ class RBiovizbase(RPackage):
     version('1.24.0', commit='ae9cd2ff665b74a8f45ed9c1d17fc0a778b4af6c')
 
     depends_on('r@2.10:', type=('build', 'run'))
-    depends_on('r@3.5.0:', when='@1.38.0:', type=('build', 'run'))
+    depends_on('r@3.5.0:', type=('build', 'run'), when='@1.38.0:')
     depends_on('r-scales', type=('build', 'run'))
     depends_on('r-hmisc', type=('build', 'run'))
     depends_on('r-rcolorbrewer', type=('build', 'run'))
     depends_on('r-dichromat', type=('build', 'run'))
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.23.19:', when='@1.38.0:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.23.19:', type=('build', 'run'), when='@1.38.0:')
     depends_on('r-iranges@1.99.28:', type=('build', 'run'))
     depends_on('r-genomeinfodb@1.5.14:', type=('build', 'run'))
     depends_on('r-genomicranges@1.23.21:', type=('build', 'run'))
@@ -45,4 +45,4 @@ class RBiovizbase(RPackage):
     depends_on('r-variantannotation@1.11.4:', type=('build', 'run'))
     depends_on('r-ensembldb@1.99.13:', type=('build', 'run'))
     depends_on('r-annotationfilter@0.99.8:', type=('build', 'run'))
-    depends_on('r-rlang', when='@1.28.2:', type=('build', 'run'))
+    depends_on('r-rlang', type=('build', 'run'), when='@1.28.2:')
diff --git a/var/spack/repos/builtin/packages/r-bsgenome-hsapiens-ucsc-hg19/package.py b/var/spack/repos/builtin/packages/r-bsgenome-hsapiens-ucsc-hg19/package.py
index 2a50ddb79d..1f52224518 100644
--- a/var/spack/repos/builtin/packages/r-bsgenome-hsapiens-ucsc-hg19/package.py
+++ b/var/spack/repos/builtin/packages/r-bsgenome-hsapiens-ucsc-hg19/package.py
@@ -8,14 +8,14 @@ from spack import *
 
 class RBsgenomeHsapiensUcscHg19(RPackage):
     """Full genome sequences for Homo sapiens (UCSC version hg19, based on
-    GRCh37.p13)
+    GRCh37.p13).
 
     Full genome sequences for Homo sapiens (Human) as provided by UCSC
     (hg19, Feb. 2009) and stored in Biostrings objects."""
 
     # This is a bioconductor package but there is no available git repo.
-    homepage = "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/"
-    url      = "http://www.bioconductor.org/packages/release/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz"
+    bioc = "BSgenome.Hsapiens.UCSC.hg19"
+    url = "http://www.bioconductor.org/packages/release/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz"
 
     version('1.4.3',
             sha256='5bfa65d7836449d9b30c356968497cdfaa98be48c4e329e71e8f8a120f3e9d1a',
@@ -25,4 +25,4 @@ class RBsgenomeHsapiensUcscHg19(RPackage):
             url='https://bioconductor.org/packages/3.10/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz')
 
     depends_on('r-bsgenome@1.33.5:', type=('build', 'run'))
-    depends_on('r-bsgenome@1.54.0:', when='@1.4.3:', type=('build', 'run'))
+    depends_on('r-bsgenome@1.54.0:', type=('build', 'run'), when='@1.4.3:')
diff --git a/var/spack/repos/builtin/packages/r-bsgenome/package.py b/var/spack/repos/builtin/packages/r-bsgenome/package.py
index c59e29756f..681f0053f4 100644
--- a/var/spack/repos/builtin/packages/r-bsgenome/package.py
+++ b/var/spack/repos/builtin/packages/r-bsgenome/package.py
@@ -8,13 +8,13 @@ from spack import *
 
 class RBsgenome(RPackage):
     """Software infrastructure for efficient representation of full genomes and
-       their SNPs
+       their SNPs.
 
     Infrastructure shared by all the Biostrings-based genome data packages."""
 
-    homepage = "https://bioconductor.org/packages/BSgenome"
-    git      = "https://git.bioconductor.org/packages/BSgenome.git"
+    bioc = "BSgenome"
 
+    version('1.62.0', commit='9b1859e11ffa082833f035a45274af6e4e83e863')
     version('1.58.0', commit='3a4926e03a7a1d7140a10c1b2bf6090808470145')
     version('1.52.0', commit='5398eba1cb56a873b29c04a7ce6858d5d60ff75b')
     version('1.50.0', commit='43910755f7477e4fe9bb968f186fddbb2f7355f9')
@@ -25,22 +25,22 @@ class RBsgenome(RPackage):
     depends_on('r@2.8.0:', type=('build', 'run'))
     depends_on('r-biocgenerics@0.13.8:', type=('build', 'run'))
     depends_on('r-s4vectors@0.9.36:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.17.28:', when='@1.48.0:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.28:', type=('build', 'run'), when='@1.48.0:')
     depends_on('r-iranges@2.1.33:', type=('build', 'run'))
-    depends_on('r-iranges@2.11.16:', when='@1.46.0:', type=('build', 'run'))
-    depends_on('r-iranges@2.13.16:', when='@1.48.0:', type=('build', 'run'))
+    depends_on('r-iranges@2.11.16:', type=('build', 'run'), when='@1.46.0:')
+    depends_on('r-iranges@2.13.16:', type=('build', 'run'), when='@1.48.0:')
     depends_on('r-genomeinfodb@1.11.4:', type=('build', 'run'))
-    depends_on('r-genomeinfodb@1.13.1:', when='@1.46.0:', type=('build', 'run'))
-    depends_on('r-genomeinfodb@1.15.2:', when='@1.48.0:', type=('build', 'run'))
-    depends_on('r-genomeinfodb@1.25.6:', when='@1.58.0:', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.13.1:', type=('build', 'run'), when='@1.46.0:')
+    depends_on('r-genomeinfodb@1.15.2:', type=('build', 'run'), when='@1.48.0:')
+    depends_on('r-genomeinfodb@1.25.6:', type=('build', 'run'), when='@1.58.0:')
     depends_on('r-genomicranges@1.27.6:', type=('build', 'run'))
-    depends_on('r-genomicranges@1.29.14:', when='@1.46.0:', type=('build', 'run'))
-    depends_on('r-genomicranges@1.31.10:', when='@1.48.0:', type=('build', 'run'))
+    depends_on('r-genomicranges@1.29.14:', type=('build', 'run'), when='@1.46.0:')
+    depends_on('r-genomicranges@1.31.10:', type=('build', 'run'), when='@1.48.0:')
     depends_on('r-biostrings@2.35.3:', type=('build', 'run'))
-    depends_on('r-biostrings@2.47.6:', when='@1.48.0:', type=('build', 'run'))
+    depends_on('r-biostrings@2.47.6:', type=('build', 'run'), when='@1.48.0:')
     depends_on('r-rtracklayer@1.25.8:', type=('build', 'run'))
-    depends_on('r-rtracklayer@1.39.7:', when='@1.48.0:', type=('build', 'run'))
-    depends_on('r-matrixstats', when='@1.58.0:', type=('build', 'run'))
+    depends_on('r-rtracklayer@1.39.7:', type=('build', 'run'), when='@1.48.0:')
+    depends_on('r-matrixstats', type=('build', 'run'), when='@1.58.0:')
     depends_on('r-xvector', type=('build', 'run'))
-    depends_on('r-xvector@0.29.3:', when='@1.58.0:', type=('build', 'run'))
+    depends_on('r-xvector@0.29.3:', type=('build', 'run'), when='@1.58.0:')
     depends_on('r-rsamtools', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-bsseq/package.py b/var/spack/repos/builtin/packages/r-bsseq/package.py
index 562621dc18..c5d8828f77 100644
--- a/var/spack/repos/builtin/packages/r-bsseq/package.py
+++ b/var/spack/repos/builtin/packages/r-bsseq/package.py
@@ -7,31 +7,31 @@ from spack import *
 
 
 class RBsseq(RPackage):
-    """Analyze, manage and store bisulfite sequencing data
+    """Analyze, manage and store bisulfite sequencing data.
 
     A collection of tools for analyzing and visualizing bisulfite sequencing
     data."""
 
-    homepage = "https://github.com/kasperdanielhansen/bsseq"
-    git      = "https://git.bioconductor.org/packages/bsseq"
+    bioc = "bsseq"
 
+    version('1.30.0', commit='7eb5223e9ee02fd08a52be56eaa9316a67c0d66b')
     version('1.26.0', commit='fae32292687625012a2938a48c93df55ad4257b5')
     version('1.24.4', commit='8fe7a03')
     version('1.22.0', commit='d4f7301')
     version('1.20.0', commit='07e398b')
 
     depends_on('r@3.5:', type=('build', 'run'))
-    depends_on('r@4.0:', when='@1.26.0:', type=('build', 'run'))
+    depends_on('r@4.0:', type=('build', 'run'), when='@1.26.0:')
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-genomicranges@1.29.14:', type=('build', 'run'))
-    depends_on('r-genomicranges@1.33.6:', when='@1.24.4:', type=('build', 'run'))
-    depends_on('r-genomicranges@1.41.5:', when='@1.26.0:', type=('build', 'run'))
+    depends_on('r-genomicranges@1.33.6:', type=('build', 'run'), when='@1.24.4:')
+    depends_on('r-genomicranges@1.41.5:', type=('build', 'run'), when='@1.26.0:')
     depends_on('r-summarizedexperiment@1.9.18:', type=('build', 'run'))
-    depends_on('r-summarizedexperiment@1.17.4:', when='@1.24.4:', type=('build', 'run'))
-    depends_on('r-summarizedexperiment@1.19.5:', when='@1.26.0:', type=('build', 'run'))
+    depends_on('r-summarizedexperiment@1.17.4:', type=('build', 'run'), when='@1.24.4:')
+    depends_on('r-summarizedexperiment@1.19.5:', type=('build', 'run'), when='@1.26.0:')
     depends_on('r-iranges@2.11.16:', type=('build', 'run'))
-    depends_on('r-iranges@2.22.2:', when='@1.24.4:', type=('build', 'run'))
-    depends_on('r-iranges@2.23.9:', when='@1.26.0:', type=('build', 'run'))
+    depends_on('r-iranges@2.22.2:', type=('build', 'run'), when='@1.24.4:')
+    depends_on('r-iranges@2.23.9:', type=('build', 'run'), when='@1.26.0:')
     depends_on('r-genomeinfodb', type=('build', 'run'))
     depends_on('r-scales', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
@@ -39,20 +39,21 @@ class RBsseq(RPackage):
     depends_on('r-gtools', type=('build', 'run'))
     depends_on('r-data-table@1.11.8:', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
-    depends_on('r-s4vectors@0.23.11:', when='@1.22.0:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.25.14:', when='@1.24.4:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.27.12:', when='@1.26.0:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.23.11:', type=('build', 'run'), when='@1.22.0:')
+    depends_on('r-s4vectors@0.25.14:', type=('build', 'run'), when='@1.24.4:')
+    depends_on('r-s4vectors@0.27.12:', type=('build', 'run'), when='@1.26.0:')
     depends_on('r-r-utils@2.0.0:', type=('build', 'run'))
     depends_on('r-delayedmatrixstats@1.5.2:', type=('build', 'run'))
     depends_on('r-permute', type=('build', 'run'))
     depends_on('r-limma', type=('build', 'run'))
     depends_on('r-delayedarray@0.9.8:', type=('build', 'run'))
-    depends_on('r-delayedarray@0.15.16:', when='@1.26.0:', type=('build', 'run'))
+    depends_on('r-delayedarray@0.15.16:', type=('build', 'run'), when='@1.26.0:')
     depends_on('r-rcpp', type=('build', 'run'))
     depends_on('r-biocparallel', type=('build', 'run'))
     depends_on('r-bsgenome', type=('build', 'run'))
     depends_on('r-biostrings', type=('build', 'run'))
     depends_on('r-hdf5array@1.11.9:', type=('build', 'run'))
-    depends_on('r-hdf5array@1.15.19:', when='@1.26.0:', type=('build', 'run'))
+    depends_on('r-hdf5array@1.15.19:', type=('build', 'run'), when='@1.26.0:')
+    depends_on('r-hdf5array@1.19.11:', type=('build', 'run'), when='@1.30.0:')
     depends_on('r-rhdf5', type=('build', 'run'))
     depends_on('r-beachmat', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-bumphunter/package.py b/var/spack/repos/builtin/packages/r-bumphunter/package.py
index d3927410e0..763d41a556 100644
--- a/var/spack/repos/builtin/packages/r-bumphunter/package.py
+++ b/var/spack/repos/builtin/packages/r-bumphunter/package.py
@@ -7,13 +7,13 @@ from spack import *
 
 
 class RBumphunter(RPackage):
-    """Bump Hunter
+    """Bump Hunter.
 
        Tools for finding bumps in genomic data"""
 
-    homepage = "https://bioconductor.org/packages/bumphunter"
-    git      = "https://git.bioconductor.org/packages/bumphunter.git"
+    bioc = "bumphunter"
 
+    version('1.36.0', commit='db50fcf7798c2eddfe48fd510d081dda82f2ee4e')
     version('1.32.0', commit='b7d39c2a6385ca217dceefc918b3ccd5c31bbaa0')
     version('1.26.0', commit='606bee8708a0911ced3efb197970b4c9fa52f2fa')
     version('1.24.5', commit='29b874033a38e86103b58ef2d4a55f285758147b')
@@ -22,8 +22,8 @@ class RBumphunter(RPackage):
     version('1.16.0', commit='1c3ab4d1fd2d75b1586ccef12665960b3602080a')
 
     depends_on('r@2.10:', type=('build', 'run'))
-    depends_on('r@3.4:', when='@1.20.0:', type=('build', 'run'))
-    depends_on('r@3.5:', when='@1.24.5:', type=('build', 'run'))
+    depends_on('r@3.4:', type=('build', 'run'), when='@1.20.0:')
+    depends_on('r@3.5:', type=('build', 'run'), when='@1.24.5:')
     depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
     depends_on('r-iranges@2.3.23:', type=('build', 'run'))
     depends_on('r-genomeinfodb', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-bwstest/package.py b/var/spack/repos/builtin/packages/r-bwstest/package.py
new file mode 100644
index 0000000000..838646eb3a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-bwstest/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RBwstest(RPackage):
+    """Baumgartner Weiss Schindler Test of Equal Distributions.
+
+    Performs the 'Baumgartner-Weiss-Schindler' two-sample test of equal
+    probability distributions, <doi:10.2307/2533862>. Also performs similar
+    rank-based tests for equal probability distributions due to Neuhauser
+    <doi:10.1080/10485250108832874> and Murakami
+    <doi:10.1080/00949655.2010.551516>."""
+
+    cran = "BWStest"
+
+    version('0.2.2', sha256='faff1dd698f1673a6befacb94d14281077d4c19be035a0a3bf85d77c1dfd5509')
+
+    depends_on('r-memoise', type=('build', 'run'))
+    depends_on('r-rcpp@0.12.3:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-category/package.py b/var/spack/repos/builtin/packages/r-category/package.py
index eb42c26041..a38499b48e 100644
--- a/var/spack/repos/builtin/packages/r-category/package.py
+++ b/var/spack/repos/builtin/packages/r-category/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RCategory(RPackage):
-    """Category Analysis
+    """Category Analysis.
 
        A collection of tools for performing category (gene set enrichment)
        analysis."""
 
-    homepage = "https://bioconductor.org/packages/Category"
-    git      = "https://git.bioconductor.org/packages/Category.git"
+    bioc = "Category"
 
+    version('2.60.0', commit='55210d8c539474954d18cf913a219dce883eac2e')
     version('2.56.0', commit='ad478caa9d693dbc2770608e79dd852375b9a223')
     version('2.50.0', commit='d96f0b29cb778f6697b44d7ba7b0abd7086074a9')
     version('2.48.1', commit='941819a3d9dd129f47b4ea00fa74032e405be3a5')
diff --git a/var/spack/repos/builtin/packages/r-champ/package.py b/var/spack/repos/builtin/packages/r-champ/package.py
index 591ae8a4b2..d94d84c257 100644
--- a/var/spack/repos/builtin/packages/r-champ/package.py
+++ b/var/spack/repos/builtin/packages/r-champ/package.py
@@ -8,14 +8,15 @@ from spack import *
 
 class RChamp(RPackage):
     """Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and
-    EPIC:
+    EPIC.
 
     The package includes quality control metrics, a selection of
     normalization methods and novel methods to identify differentially
     methylated regions and to highlight copy number alterations."""
 
-    bioc     = "ChAMP"
+    bioc = "ChAMP"
 
+    version('2.24.0', commit='7ba19da74b61e1c40ced162ba753f0f9b9c7647a')
     version('2.20.1', commit='99ea0463bce59f5b06bcc91f479dcd4065074896')
 
     depends_on('r@3.3:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-champdata/package.py b/var/spack/repos/builtin/packages/r-champdata/package.py
index 64327236b1..b6cb7ddfa0 100644
--- a/var/spack/repos/builtin/packages/r-champdata/package.py
+++ b/var/spack/repos/builtin/packages/r-champdata/package.py
@@ -7,13 +7,14 @@ from spack import *
 
 
 class RChampdata(RPackage):
-    """Packages for ChAMP package:
+    """Packages for ChAMP package.
 
     Provides datasets needed for ChAMP including a test dataset and blood
     controls for CNA analysis."""
 
-    bioc     = "ChAMPdata"
+    bioc = "ChAMPdata"
 
+    version('2.26.0', commit='ea7882707921af33eefab5133a1ccd4a409f045d')
     version('2.22.0', commit='eeedd4c477fac79f00743da8ff7da064221c5f3d')
 
     depends_on('r@3.3:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-chipseq/package.py b/var/spack/repos/builtin/packages/r-chipseq/package.py
index 4f6127bfd5..217297ef3b 100644
--- a/var/spack/repos/builtin/packages/r-chipseq/package.py
+++ b/var/spack/repos/builtin/packages/r-chipseq/package.py
@@ -7,15 +7,15 @@ from spack import *
 
 
 class RChipseq(RPackage):
-    """A package for analyzing chipseq data
+    """A package for analyzing chipseq data,
 
     Tools for helping process short read data for chipseq experiments"""
 
-    homepage = "https://bioconductor.org/packages/release/bioc/html/chipseq.html"
-    git      = "https://git.bioconductor.org/packages/chipseq"
+    bioc = "chipseq"
 
     maintainers = ['dorton21']
 
+    version('1.44.0', commit='b64d0d28e9fcf0fdab9a7f9c521baf729426a594')
     version('1.40.0', commit='84bcbc0b7ad732730b5989a308f1624a6a358df1')
 
     depends_on('r@2.10:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-clusterprofiler/package.py b/var/spack/repos/builtin/packages/r-clusterprofiler/package.py
index 2b7ffcfa3b..135696279a 100644
--- a/var/spack/repos/builtin/packages/r-clusterprofiler/package.py
+++ b/var/spack/repos/builtin/packages/r-clusterprofiler/package.py
@@ -8,14 +8,14 @@ from spack import *
 
 class RClusterprofiler(RPackage):
     """statistical analysis and visualization of functional profiles for genes
-       and gene clusters
+       and gene clusters.
 
        This package implements methods to analyze and visualize functional
        profiles (GO and KEGG) of gene and gene clusters."""
 
-    homepage = "https://bioconductor.org/packages/clusterProfiler"
-    git      = "https://git.bioconductor.org/packages/clusterProfiler.git"
+    bioc = "clusterProfiler"
 
+    version('4.2.2', commit='4ebb9de8e03eedc971f54a57cf5bf1b250ed43d5')
     version('3.18.0', commit='064a6e612ce27e260e33af78b907bee4065ff821')
     version('3.12.0', commit='6ec88d10832bdfd938e9c065b377015eedb7eee2')
     version('3.10.1', commit='39927ef7ff6f97e27557bcf4147e2133b364fd3c')
@@ -24,23 +24,26 @@ class RClusterprofiler(RPackage):
     version('3.4.4', commit='b86b00e8405fe130e439362651a5567736e2d9d7')
 
     depends_on('r@3.3.1:', type=('build', 'run'))
-    depends_on('r@3.4.0:', when='@3.8.1:', type=('build', 'run'))
+    depends_on('r@3.4.0:', type=('build', 'run'), when='@3.8.1:')
+    depends_on('r@3.5.0:', type=('build', 'run'), when='@4.2.2:')
     depends_on('r-annotationdbi', type=('build', 'run'))
-    depends_on('r-downloader', when='@3.18.0:', type=('build', 'run'))
+    depends_on('r-downloader', type=('build', 'run'), when='@3.18.0:')
     depends_on('r-dose@3.1.3:', type=('build', 'run'))
-    depends_on('r-dose@3.3.2:', when='@3.6.0:', type=('build', 'run'))
-    depends_on('r-dose@3.5.1:', when='@3.8.1:', type=('build', 'run'))
-    depends_on('r-dose@3.13.1:', when='@3.18.0:', type=('build', 'run'))
-    depends_on('r-dplyr', when='@3.18.0:', type=('build', 'run'))
-    depends_on('r-enrichplot@0.99.7:', when='@3.8.1:', type=('build', 'run'))
-    depends_on('r-enrichplot@1.9.3:', when='@3.18.0:', type=('build', 'run'))
+    depends_on('r-dose@3.3.2:', type=('build', 'run'), when='@3.6.0:')
+    depends_on('r-dose@3.5.1:', type=('build', 'run'), when='@3.8.1:')
+    depends_on('r-dose@3.13.1:', type=('build', 'run'), when='@3.18.0:')
+    depends_on('r-dplyr', type=('build', 'run'), when='@3.18.0:')
+    depends_on('r-enrichplot@0.99.7:', type=('build', 'run'), when='@3.8.1:')
+    depends_on('r-enrichplot@1.9.3:', type=('build', 'run'), when='@3.18.0:')
     depends_on('r-go-db', type=('build', 'run'))
     depends_on('r-gosemsim', type=('build', 'run'))
-    depends_on('r-gosemsim@2.0.0:', when='@3.4.4:3.6.0', type=('build', 'run'))
+    depends_on('r-gosemsim@2.0.0:', type=('build', 'run'), when='@3.4.4:3.6.0')
     depends_on('r-magrittr', type=('build', 'run'))
     depends_on('r-plyr', type=('build', 'run'))
     depends_on('r-qvalue', type=('build', 'run'))
-    depends_on('r-rlang', when='@3.18.0:', type=('build', 'run'))
-    depends_on('r-rvcheck', type=('build', 'run'))
+    depends_on('r-rlang', type=('build', 'run'), when='@3.18.0:')
     depends_on('r-tidyr', type=('build', 'run'))
-    depends_on('r-ggplot2', when='@:3.12.0', type=('build', 'run'))
+    depends_on('r-yulab-utils', type=('build', 'run'), when='@4.2.2:')
+
+    depends_on('r-ggplot2', type=('build', 'run'), when='@:3.12.0')
+    depends_on('r-rvcheck', type=('build', 'run'), when='@:3.18.0')
diff --git a/var/spack/repos/builtin/packages/r-cner/package.py b/var/spack/repos/builtin/packages/r-cner/package.py
index f550e91a47..04e65f0576 100644
--- a/var/spack/repos/builtin/packages/r-cner/package.py
+++ b/var/spack/repos/builtin/packages/r-cner/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RCner(RPackage):
-    """CNE Detection and Visualization
+    """CNE Detection and Visualization.
 
        Large-scale identification and advanced visualization of sets of
        conserved noncoding elements."""
 
-    homepage = "https://bioconductor.org/packages/CNEr"
-    git      = "https://git.bioconductor.org/packages/CNEr.git"
+    bioc = "CNEr"
 
+    version('1.30.0', commit='e682f2a7c8ebb561c872cf51a58ba36eed341187')
     version('1.26.0', commit='e5e582da6feeae0618c4460f16ece724215e3b20')
     version('1.20.0', commit='9c25d8e8f6f5fd8a5311f554c86e7ca1140a4ca5')
     version('1.18.1', commit='66aa88af04364c81832f3b09bad898f3c117f606')
@@ -23,10 +23,10 @@ class RCner(RPackage):
     version('1.12.1', commit='90d611f9cd19a73d0fe92ab03ef428519d64c017')
 
     depends_on('r@3.2.2:', type=('build', 'run'))
-    depends_on('r@3.4:', when='@1.14.0:', type=('build', 'run'))
+    depends_on('r@3.4:', type=('build', 'run'), when='@1.14.0:')
     depends_on('r-biostrings@2.33.4:', type=('build', 'run'))
     depends_on('r-dbi@0.6:', type=('build', 'run'))
-    depends_on('r-dbi@0.7:', when='@1.14.0:', type=('build', 'run'))
+    depends_on('r-dbi@0.7:', type=('build', 'run'), when='@1.14.0:')
     depends_on('r-rsqlite@0.11.4:', type=('build', 'run'))
     depends_on('r-genomeinfodb@1.1.3:', type=('build', 'run'))
     depends_on('r-genomicranges@1.23.16:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-codex/package.py b/var/spack/repos/builtin/packages/r-codex/package.py
index ddedceb848..465796e1f9 100644
--- a/var/spack/repos/builtin/packages/r-codex/package.py
+++ b/var/spack/repos/builtin/packages/r-codex/package.py
@@ -8,7 +8,7 @@ from spack import *
 
 class RCodex(RPackage):
     """A Normalization and Copy Number Variation Detection Method for Whole
-    Exome Sequencing
+    Exome Sequencing.
 
     A normalization and copy number variation calling procedure for whole
     exome DNA sequencing data. CODEX relies on the availability of multiple
@@ -20,9 +20,9 @@ class RCodex(RPackage):
     segmentation procedure that explicitly models the count-based exome
     sequencing data."""
 
-    homepage = "https://www.bioconductor.org/packages/release/bioc/html/CODEX.html"
-    git      = "https://git.bioconductor.org/packages/CODEX"
+    bioc = "CODEX"
 
+    version('1.26.0', commit='729fd10bd42d12edcedd65b5a8fb1579e5949718')
     version('1.22.0', commit='aa0ee4278111a46e0c790312b0526ba07aab22eb')
     version('1.18.0', commit='9a95cccc7ff3fe587636317e21e39a07dddf80bc')
 
diff --git a/var/spack/repos/builtin/packages/r-complexheatmap/package.py b/var/spack/repos/builtin/packages/r-complexheatmap/package.py
index 35f0e5ad93..ab51443b52 100644
--- a/var/spack/repos/builtin/packages/r-complexheatmap/package.py
+++ b/var/spack/repos/builtin/packages/r-complexheatmap/package.py
@@ -7,16 +7,16 @@ from spack import *
 
 
 class RComplexheatmap(RPackage):
-    """Make Complex Heatmaps
+    """Make Complex Heatmaps.
 
        Complex heatmaps are efficient to visualize associations between
        different sources of data sets and reveal potential patterns. Here the
        ComplexHeatmap package provides a highly flexible way to arrange
        multiple heatmaps and supports various annotation graphics."""
 
-    homepage = "https://bioconductor.org/packages/ComplexHeatmap"
-    git      = "https://git.bioconductor.org/packages/ComplexHeatmap.git"
+    bioc = "ComplexHeatmap"
 
+    version('2.10.0', commit='170df82a1568e879e4019e0ff6feb0047851684f')
     version('2.6.2', commit='0383bada2c76dc3dde71cf6a625016b619aec4d3')
     version('2.0.0', commit='97863d8ddfe36a52df0149b0b040dc386a03d2e4')
     version('1.20.0', commit='1501ecc92fda07efa3652e41626b21741951ce0f')
@@ -25,19 +25,23 @@ class RComplexheatmap(RPackage):
     version('1.14.0', commit='0acd8974fb5cedde8cd96efea6dfa39324d25b34')
 
     depends_on('r@3.1.2:', type=('build', 'run'))
+    depends_on('r@3.5.0:', type=('build', 'run'), when='@2.10.0:')
     depends_on('r-circlize@0.3.4:', type=('build', 'run'))
-    depends_on('r-circlize@0.4.1:', when='@1.17.1:', type=('build', 'run'))
-    depends_on('r-circlize@0.4.5:', when='@2.0.0:', type=('build', 'run'))
+    depends_on('r-circlize@0.4.1:', type=('build', 'run'), when='@1.17.1:')
+    depends_on('r-circlize@0.4.5:', type=('build', 'run'), when='@2.0.0:')
     depends_on('r-getoptlong', type=('build', 'run'))
     depends_on('r-colorspace', type=('build', 'run'))
-    depends_on('r-clue', when='@2.0.0:', type=('build', 'run'))
+    depends_on('r-clue', type=('build', 'run'), when='@2.0.0:')
     depends_on('r-rcolorbrewer', type=('build', 'run'))
     depends_on('r-globaloptions@0.0.10:', type=('build', 'run'))
-    depends_on('r-globaloptions@0.1.0:', when='@1.20.0:', type=('build', 'run'))
-    depends_on('r-png', when='@2.0.0:', type=('build', 'run'))
-    depends_on('r-cairo', when='@2.6.2:', type=('build', 'run'))
-    depends_on('r-digest', when='@2.6.2:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.26.1:', when='@2.6.2:', type=('build', 'run'))
-    depends_on('r-iranges', when='@2.6.2:', type=('build', 'run'))
-    depends_on('r-matrixstats', when='@2.6.2:', type=('build', 'run'))
-    depends_on('r-dendextend@1.0.1:', when='@1.14.0:1.17.1', type=('build', 'run'))
+    depends_on('r-globaloptions@0.1.0:', type=('build', 'run'), when='@1.20.0:')
+    depends_on('r-png', type=('build', 'run'), when='@2.0.0:')
+    depends_on('r-digest', type=('build', 'run'), when='@2.6.2:')
+    depends_on('r-iranges', type=('build', 'run'), when='@2.6.2:')
+    depends_on('r-matrixstats', type=('build', 'run'), when='@2.6.2:')
+    depends_on('r-foreach', type=('build', 'run'), when='@2.10.0:')
+    depends_on('r-doparallel', type=('build', 'run'), when='@2.10.0:')
+
+    depends_on('r-dendextend@1.0.1:', type=('build', 'run'), when='@1.14.0:1.17.1')
+    depends_on('r-s4vectors@0.26.1:', type=('build', 'run'), when='@2.6.2')
+    depends_on('r-cairo', type=('build', 'run'), when='@2.6.2')
diff --git a/var/spack/repos/builtin/packages/r-ctc/package.py b/var/spack/repos/builtin/packages/r-ctc/package.py
index cb29c5edc1..6e33b7cf0e 100644
--- a/var/spack/repos/builtin/packages/r-ctc/package.py
+++ b/var/spack/repos/builtin/packages/r-ctc/package.py
@@ -12,9 +12,9 @@ class RCtc(RPackage):
        Tools for export and import classification trees and clusters to other
        programs"""
 
-    homepage = "https://bioconductor.org/packages/ctc"
-    git      = "https://git.bioconductor.org/packages/ctc.git"
+    bioc = "ctc"
 
+    version('1.68.0', commit='c2733534ef9d948e07ea654d1998a67ed8f7a98a')
     version('1.64.0', commit='35dbe620a21056b8f69890e6f9a7c320528d8621')
     version('1.58.0', commit='c41df03ac149db20c5e337142142d61cfb9b43fb')
     version('1.56.0', commit='cbd5befdda4630799f8fe0d868d83b094e3d352f')
diff --git a/var/spack/repos/builtin/packages/r-decipher/package.py b/var/spack/repos/builtin/packages/r-decipher/package.py
index 23933d1359..a467980784 100644
--- a/var/spack/repos/builtin/packages/r-decipher/package.py
+++ b/var/spack/repos/builtin/packages/r-decipher/package.py
@@ -7,13 +7,13 @@ from spack import *
 
 
 class RDecipher(RPackage):
-    """Tools for curating, analyzing, and manipulating biological sequences
+    """Tools for curating, analyzing, and manipulating biological sequences.
 
     A toolset for deciphering and managing biological sequences."""
 
-    homepage = "https://bioconductor.org/packages/DECIPHER"
-    git      = "https://git.bioconductor.org/packages/DECIPHER.git"
+    bioc = "DECIPHER"
 
+    version('2.22.0', commit='45da5cab5869d83af797aa82b08ebcd24f5bdab3')
     version('2.18.1', commit='6a708421550e6705d05e2fb50a0f5ab4f9041cb0')
     version('2.12.0', commit='658ae23870383b25b96a03a18d4ecac228a2650f')
     version('2.10.2', commit='db7b017c9050a7ec1d4daa15352994890095e9c3')
@@ -22,8 +22,9 @@ class RDecipher(RPackage):
     version('2.4.0', commit='1a57b8e4c7d7dec1c233f79c9a88d3705e0ad432')
 
     depends_on('r@3.3.0:', type=('build', 'run'))
-    depends_on('r@3.5.0:', when='@2.18.1:', type=('build', 'run'))
+    depends_on('r@3.5.0:', type=('build', 'run'), when='@2.18.1:')
     depends_on('r-biostrings@2.35.12:', type=('build', 'run'))
+    depends_on('r-biostrings@2.59.1:', type=('build', 'run'), when='@2.22.0:')
     depends_on('r-rsqlite@1.1:', type=('build', 'run'))
     depends_on('r-dbi', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-delayedarray/package.py b/var/spack/repos/builtin/packages/r-delayedarray/package.py
index bb3fb94a27..817dde0e7e 100644
--- a/var/spack/repos/builtin/packages/r-delayedarray/package.py
+++ b/var/spack/repos/builtin/packages/r-delayedarray/package.py
@@ -8,7 +8,7 @@ from spack import *
 
 class RDelayedarray(RPackage):
     """A unified framework for working transparently with on-disk and in-memory
-       array-like datasets
+       array-like datasets.
 
        Wrapping an array-like object (typically an on-disk object) in a
        DelayedArray object allows one to perform common array operations on it
@@ -18,9 +18,9 @@ class RDelayedarray(RPackage):
        on in-memory array-like objects like DataFrame objects (typically with
        Rle columns), Matrix objects, and ordinary arrays and data frames."""
 
-    homepage = "https://bioconductor.org/packages/DelayedArray"
-    git      = "https://git.bioconductor.org/packages/DelayedArray.git"
+    bioc = "DelayedArray"
 
+    version('0.20.0', commit='829b52916ec54bb4f1a3c6f06c9955f3e28b3592')
     version('0.16.1', commit='c95eba771ad3fee1b49ec38c51cd8fd1486feadc')
     version('0.10.0', commit='4781d073110a3fd1e20c4083b6b2b0f260d0cb0a')
     version('0.8.0', commit='7c23cf46558de9dbe7a42fba516a9bb660a0f19f')
@@ -29,20 +29,23 @@ class RDelayedarray(RPackage):
     version('0.2.7', commit='909c2ce1665ebae2543172ead50abbe10bd42bc4')
 
     depends_on('r@3.4:', type=('build', 'run'))
-    depends_on('r-matrix', when='@0.10.0:', type=('build', 'run'))
+    depends_on('r@4.0.0:', type=('build', 'run'), when='@0.20.0:')
+    depends_on('r-matrix', type=('build', 'run'), when='@0.10.0:')
     depends_on('r-biocgenerics', type=('build', 'run'))
-    depends_on('r-biocgenerics@0.25.1:', when='@0.6.6:', type=('build', 'run'))
-    depends_on('r-biocgenerics@0.27.1:', when='@0.8.0:', type=('build', 'run'))
-    depends_on('r-biocgenerics@0.31.5:', when='@0.16.1:', type=('build', 'run'))
-    depends_on('r-matrixgenerics@1.1.3:', when='@0.16.1:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.25.1:', type=('build', 'run'), when='@0.6.6:')
+    depends_on('r-biocgenerics@0.27.1:', type=('build', 'run'), when='@0.8.0:')
+    depends_on('r-biocgenerics@0.31.5:', type=('build', 'run'), when='@0.16.1:')
+    depends_on('r-biocgenerics@0.37.0:', type=('build', 'run'), when='@0.20.1:')
+    depends_on('r-matrixgenerics@1.1.3:', type=('build', 'run'), when='@0.16.1:')
     depends_on('r-s4vectors@0.14.3:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.15.3:', when='@0.4.1:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.17.43:', when='@0.6.6:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.19.15:', when='@0.8.0:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.21.7:', when='@0.10.0:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.27.2:', when='@0.16.1:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.15.3:', type=('build', 'run'), when='@0.4.1:')
+    depends_on('r-s4vectors@0.17.43:', type=('build', 'run'), when='@0.6.6:')
+    depends_on('r-s4vectors@0.19.15:', type=('build', 'run'), when='@0.8.0:')
+    depends_on('r-s4vectors@0.21.7:', type=('build', 'run'), when='@0.10.0:')
+    depends_on('r-s4vectors@0.27.2:', type=('build', 'run'), when='@0.16.1:')
     depends_on('r-iranges', type=('build', 'run'))
-    depends_on('r-iranges@2.11.17:', when='@0.4.1:', type=('build', 'run'))
-    depends_on('r-iranges@2.17.3:', when='@0.10.0:', type=('build', 'run'))
-    depends_on('r-matrixstats', when='@:0.10.0', type=('build', 'run'))
-    depends_on('r-biocparallel', when='@0.6.6:0.10.0', type=('build', 'run'))
+    depends_on('r-iranges@2.11.17:', type=('build', 'run'), when='@0.4.1:')
+    depends_on('r-iranges@2.17.3:', type=('build', 'run'), when='@0.10.0:')
+
+    depends_on('r-matrixstats', type=('build', 'run'), when='@:0.10.0')
+    depends_on('r-biocparallel', type=('build', 'run'), when='@0.6.6:0.10.0')
diff --git a/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py b/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py
index 530a51f0bc..a5f108a0e5 100644
--- a/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py
+++ b/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RDelayedmatrixstats(RPackage):
-    """Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects
+    """Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects.
 
        A port of the 'matrixStats' API for use with DelayedMatrix objects from
        the 'DelayedArray' package. High-performing functions operating on rows
@@ -16,29 +16,34 @@ class RDelayedmatrixstats(RPackage):
        for subsetted calculations such that both memory usage and processing
        time is minimized."""
 
-    homepage = "https://github.com/PeteHaitch/DelayedMatrixStats"
-    git      = "https://git.bioconductor.org/packages/DelayedMatrixStats.git"
+    bioc = "DelayedMatrixStats"
 
+    version('1.16.0', commit='d44a3d765769cb022193428a77af25bf19916be7')
     version('1.12.3', commit='2b3091dfa9b3bab914e3a4157182063714ba86ae')
     version('1.6.1', commit='4378d1898a403305a94b122c4f36d1215fa7708d')
     version('1.4.0', commit='eb5b390ef99651fe87a346848f807de95afe8971')
     version('1.2.0', commit='de868e730be6280dfad41a280ab09f4d3083c9ac')
     version('1.0.3', commit='e29a3444980ff727c5b12286884b06dfaebf5b5b')
 
-    depends_on('r-matrixgenerics', when='@1.12.2:', type=('build', 'run'))
+    depends_on('r-matrixgenerics', type=('build', 'run'), when='@1.12.2:')
+    depends_on('r-matrixgenerics@1.5.3:', type=('build', 'run'), when='@1.16.0:')
     depends_on('r-delayedarray', type=('build', 'run'))
-    depends_on('r-delayedarray@0.5.27:', when='@1.2.0:', type=('build', 'run'))
-    depends_on('r-delayedarray@0.7.37:', when='@1.4.0:', type=('build', 'run'))
-    depends_on('r-delayedarray@0.9.8:', when='@1.6.1:', type=('build', 'run'))
-    depends_on('r-delayedarray@0.15.3:', when='@1.12.2:', type=('build', 'run'))
+    depends_on('r-delayedarray@0.5.27:', type=('build', 'run'), when='@1.2.0:')
+    depends_on('r-delayedarray@0.7.37:', type=('build', 'run'), when='@1.4.0:')
+    depends_on('r-delayedarray@0.9.8:', type=('build', 'run'), when='@1.6.1:')
+    depends_on('r-delayedarray@0.15.3:', type=('build', 'run'), when='@1.12.2:')
+    depends_on('r-delayedarray@0.17.6:', type=('build', 'run'), when='@1.16.0:')
     depends_on('r-matrixstats@0.53.1:', type=('build', 'run'))
-    depends_on('r-matrixstats@0.55.0:', when='@1.6.1:', type=('build', 'run'))
-    depends_on('r-matrixstats@0.56.0:', when='@1.12.2:', type=('build', 'run'))
-    depends_on('r-sparsematrixstats', when='@1.12.2:', type=('build', 'run'))
+    depends_on('r-matrixstats@0.55.0:', type=('build', 'run'), when='@1.6.1:')
+    depends_on('r-matrixstats@0.56.0:', type=('build', 'run'), when='@1.12.2:')
+    depends_on('r-matrixstats@0.60.0:', type=('build', 'run'), when='@1.16.0:')
+    depends_on('r-sparsematrixstats', type=('build', 'run'), when='@1.12.2:')
     depends_on('r-matrix', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
-    depends_on('r-s4vectors@0.17.5:', when='@1.2.0:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.5:', type=('build', 'run'), when='@1.2.0:')
     depends_on('r-iranges', type=('build', 'run'))
-    depends_on('r-hdf5array@1.7.10:', when='@1.4.0:', type=('build', 'run'))
-    depends_on('r-hdf5array@1.17.2:', when='@1.12.2:', type=('build', 'run'))
-    depends_on('r-biocparallel', when='@1.4.0:', type=('build', 'run'))
+    depends_on('r-iranges@2.25.10:', type=('build', 'run'), when='@1.16.0:')
+
+    depends_on('r-hdf5array@1.7.10:', type=('build', 'run'), when='@1.4.0:1.12.3')
+    depends_on('r-hdf5array@1.17.2:', type=('build', 'run'), when='@1.12.2:1.12.3')
+    depends_on('r-biocparallel', type=('build', 'run'), when='@1.4.0:1.12.3')
diff --git a/var/spack/repos/builtin/packages/r-deseq/package.py b/var/spack/repos/builtin/packages/r-deseq/package.py
index 2447dffd80..11078e9273 100644
--- a/var/spack/repos/builtin/packages/r-deseq/package.py
+++ b/var/spack/repos/builtin/packages/r-deseq/package.py
@@ -8,14 +8,13 @@ from spack import *
 
 class RDeseq(RPackage):
     """Differential gene expression analysis based on the negative binomial
-       distribution
+       distribution.
 
        Estimate variance-mean dependence in count data from high-throughput
        sequencing assays and test for differential expression based on a model
        using the negative binomial distribution"""
 
-    homepage = "https://bioconductor.org/packages/DESeq"
-    git      = "https://git.bioconductor.org/packages/DESeq.git"
+    bioc = "DESeq"
 
     version('1.42.0', commit='da76bc64e8c4073b58eaf1c93aa4e89bec5c4e50')
     version('1.36.0', commit='db4af67b49d3bd8c321d19efbe9415cd2e4ddb7e')
diff --git a/var/spack/repos/builtin/packages/r-deseq2/package.py b/var/spack/repos/builtin/packages/r-deseq2/package.py
index 29db7e5bea..0bc46c04bb 100644
--- a/var/spack/repos/builtin/packages/r-deseq2/package.py
+++ b/var/spack/repos/builtin/packages/r-deseq2/package.py
@@ -8,7 +8,7 @@ from spack import *
 
 class RDeseq2(RPackage):
     """Differential gene expression analysis based on the negative binomial
-       distribution
+       distribution.
 
        Estimate variance-mean dependence in count data from high-throughput
        sequencing assays and test for differential expression based on a model
@@ -17,6 +17,7 @@ class RDeseq2(RPackage):
     homepage = "https://bioconductor.org/packages/DESeq2"
     git      = "https://git.bioconductor.org/packages/DESeq2.git"
 
+    version('1.34.0', commit='25d4f74be59548122ccfbe8687d30c0bae5cf49a')
     version('1.30.0', commit='f4b47b208ee26ab23fe65c345f907fcfe70b3f77')
     version('1.24.0', commit='3ce7fbbebac526b726a6f85178063d02eb0314bf')
     version('1.22.2', commit='3c6a89b61add635d6d468c7fa00192314f8ca4ce')
@@ -25,7 +26,7 @@ class RDeseq2(RPackage):
     version('1.16.1', commit='f41d9df2de25fb57054480e50bc208447a6d82fb')
 
     depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.23.18:', when='@1.30.0:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.23.18:', type=('build', 'run'), when='@1.30.0:')
     depends_on('r-iranges', type=('build', 'run'))
     depends_on('r-genomicranges', type=('build', 'run'))
     depends_on('r-summarizedexperiment@1.1.6:', type=('build', 'run'))
@@ -36,6 +37,7 @@ class RDeseq2(RPackage):
     depends_on('r-locfit', type=('build', 'run'))
     depends_on('r-geneplotter', type=('build', 'run'))
     depends_on('r-ggplot2', type=('build', 'run'))
-    depends_on('r-hmisc', type=('build', 'run'))
     depends_on('r-rcpp@0.11.0:', type=('build', 'run'))
     depends_on('r-rcpparmadillo', type=('build', 'run'))
+
+    depends_on('r-hmisc', type=('build', 'run'), when='@:1.30.0')
diff --git a/var/spack/repos/builtin/packages/r-dexseq/package.py b/var/spack/repos/builtin/packages/r-dexseq/package.py
index fb521ff70f..b7e0da0ec8 100644
--- a/var/spack/repos/builtin/packages/r-dexseq/package.py
+++ b/var/spack/repos/builtin/packages/r-dexseq/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RDexseq(RPackage):
-    """Inference of differential exon usage in RNA-Seq
+    """Inference of differential exon usage in RNA-Seq.
 
     The package is focused on finding differential exon usage using RNA-seq
     exon counts between samples with different experimental designs. It
@@ -21,16 +21,9 @@ class RDexseq(RPackage):
 
     maintainers = ['dorton21']
 
+    version('1.40.0', commit='7d2d639b3a157e443058fc557132cd2629bb36f3')
     version('1.36.0', commit='f0a361af6954fcc2abb2db801c26e303570669b2')
 
-    depends_on('r-stringr', type=('build', 'run'))
-    depends_on('r-geneplotter', type=('build', 'run'))
-    depends_on('r-genefilter', type=('build', 'run'))
-    depends_on('r-biocgenerics', type=('build', 'run'))
-    depends_on('r-biomart', type=('build', 'run'))
-    depends_on('r-hwriter', type=('build', 'run'))
-    depends_on('r-rsamtools', type=('build', 'run'))
-    depends_on('r-statmod', type=('build', 'run'))
     depends_on('r-biocparallel', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-summarizedexperiment', type=('build', 'run'))
@@ -40,3 +33,11 @@ class RDexseq(RPackage):
     depends_on('r-annotationdbi', type=('build', 'run'))
     depends_on('r-rcolorbrewer', type=('build', 'run'))
     depends_on('r-s4vectors@0.23.18:', type=('build', 'run'))
+    depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r-biomart', type=('build', 'run'))
+    depends_on('r-hwriter', type=('build', 'run'))
+    depends_on('r-stringr', type=('build', 'run'))
+    depends_on('r-rsamtools', type=('build', 'run'))
+    depends_on('r-statmod', type=('build', 'run'))
+    depends_on('r-geneplotter', type=('build', 'run'))
+    depends_on('r-genefilter', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py b/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py
index 66a4b32e0d..7377756b9c 100644
--- a/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py
+++ b/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py
@@ -8,7 +8,7 @@ from spack import *
 
 class RDirichletmultinomial(RPackage):
     """Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome
-       Data
+       Data.
 
        Dirichlet-multinomial mixture models can be used to describe variability
        in microbial metagenomic data. This package is an interface to code
@@ -16,9 +16,9 @@ class RDirichletmultinomial(RPackage):
        7(2): 1-15, as discussed further in the man page for this package,
        ?DirichletMultinomial."""
 
-    homepage = "https://bioconductor.org/packages/DirichletMultinomial"
-    git      = "https://git.bioconductor.org/packages/DirichletMultinomial.git"
+    bioc = "DirichletMultinomial"
 
+    version('1.36.0', commit='926baff6c75cb498945c5895f25cc143c907a357')
     version('1.32.0', commit='6949abab2462b2c09f7a0ca5b5cbf0c95a40ad16')
     version('1.26.0', commit='7daa84948020811bb8a27d2e633fccfdcdd1018f')
     version('1.24.1', commit='50195d9b1986852da29100e77f6f09df5d6e2a35')
diff --git a/var/spack/repos/builtin/packages/r-dmrcate/package.py b/var/spack/repos/builtin/packages/r-dmrcate/package.py
index d9587188da..86a228a807 100644
--- a/var/spack/repos/builtin/packages/r-dmrcate/package.py
+++ b/var/spack/repos/builtin/packages/r-dmrcate/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RDmrcate(RPackage):
-    """Methylation array and sequencing spatial analysis methods:
+    """Methylation array and sequencing spatial analysis methods.
 
     De novo identification and extraction of differentially methylated regions
     (DMRs) from the human genome using Whole Genome Bisulfite Sequencing (WGBS)
@@ -15,22 +15,24 @@ class RDmrcate(RPackage):
     for filtering probes possibly confounded by SNPs and cross-hybridisation.
     Includes GRanges generation and plotting functions."""
 
-    bioc     = "DMRcate"
+    bioc = "DMRcate"
 
+    version('2.8.5', commit='c65dc79a33a047c10932a98b3383709a6bcb8903')
     version('2.4.1', commit='bc6242a0291a9b997872f575a4417d38550c9550')
 
     depends_on('r@3.6.0:', type=('build', 'run'))
-    depends_on('r-minfi', type=('build', 'run'))
-    depends_on('r-summarizedexperiment', type=('build', 'run'))
+    depends_on('r@4.0.0:', type=('build', 'run'), when='@2.8.5:')
     depends_on('r-experimenthub', type=('build', 'run'))
     depends_on('r-bsseq', type=('build', 'run'))
     depends_on('r-genomeinfodb', type=('build', 'run'))
     depends_on('r-limma', type=('build', 'run'))
     depends_on('r-edger', type=('build', 'run'))
     depends_on('r-dss', type=('build', 'run'))
+    depends_on('r-minfi', type=('build', 'run'))
     depends_on('r-missmethyl', type=('build', 'run'))
     depends_on('r-genomicranges', type=('build', 'run'))
     depends_on('r-plyr', type=('build', 'run'))
     depends_on('r-gviz', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-summarizedexperiment', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-dnacopy/package.py b/var/spack/repos/builtin/packages/r-dnacopy/package.py
index 2058f07112..5f860f1088 100644
--- a/var/spack/repos/builtin/packages/r-dnacopy/package.py
+++ b/var/spack/repos/builtin/packages/r-dnacopy/package.py
@@ -7,15 +7,15 @@ from spack import *
 
 
 class RDnacopy(RPackage):
-    """DNA copy number data analysis
+    """DNA copy number data analysis.
 
        Implements the circular binary segmentation (CBS) algorithm to segment
        DNA copy number data and identify genomic regions with abnormal copy
        number."""
 
-    homepage = "https://bioconductor.org/packages/DNAcopy"
-    git      = "https://git.bioconductor.org/packages/DNAcopy.git"
+    bioc = "DNAcopy"
 
+    version('1.68.0', commit='08f039f58bc2f5ed2cc3117ae817dbac333002a6')
     version('1.64.0', commit='01650266ea7a4e5c600de545fe70a1103e79b2d8')
     version('1.58.0', commit='1954745eafca990d6ddeefe84059c54a8c37df23')
     version('1.56.0', commit='e521826f2515b309921272f65db421cbe2ff961a')
diff --git a/var/spack/repos/builtin/packages/r-do-db/package.py b/var/spack/repos/builtin/packages/r-do-db/package.py
index 4d107c4058..bb49023bed 100644
--- a/var/spack/repos/builtin/packages/r-do-db/package.py
+++ b/var/spack/repos/builtin/packages/r-do-db/package.py
@@ -7,15 +7,16 @@ from spack import *
 
 
 class RDoDb(RPackage):
-    """A set of annotation maps describing the entire Disease Ontology
+    """A set of annotation maps describing the entire Disease Ontology.
 
     A set of annotation maps describing the entire Disease
     Ontology assembled using data from DO."""
 
+    # There is no git repository for this package.
     homepage = "https://bioconductor.org/packages/DO.db/"
     url      = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/DO.db_2.9.tar.gz"
 
     version('2.9', sha256='762bcb9b5188274fd81d82f785cf2846a5acc61fad55e2ff8ec1502282c27881')
 
     depends_on('r@2.7.0:', type=('build', 'run'))
-    depends_on('r-annotationdbi', type=('build', 'run'))
+    depends_on('r-annotationdbi@1.9.7:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-dose/package.py b/var/spack/repos/builtin/packages/r-dose/package.py
index b9425c855f..43ef1af519 100644
--- a/var/spack/repos/builtin/packages/r-dose/package.py
+++ b/var/spack/repos/builtin/packages/r-dose/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RDose(RPackage):
-    """Disease Ontology Semantic and Enrichment analysis
+    """Disease Ontology Semantic and Enrichment analysis.
 
        This package implements five methods proposed by Resnik, Schlicker,
        Jiang, Lin and Wang respectively for measuring semantic similarities
@@ -16,9 +16,9 @@ class RDose(RPackage):
        implemented for discovering disease associations of high-throughput
        biological data."""
 
-    homepage = "https://bioconductor.org/packages/DOSE"
-    git      = "https://git.bioconductor.org/packages/DOSE.git"
+    bioc = "DOSE"
 
+    version('3.20.1', commit='bf434f24d035217822cb1b0ab08a486b9a53edb4')
     version('3.16.0', commit='a534a4f2ef1e54e8b92079cf1bbedb5042fd90cd')
     version('3.10.2', commit='5ea51a2e2a04b4f3cc974cecb4537e14efd6a7e3')
     version('3.8.2', commit='4d3d1ca710aa7e4288a412c8d52b054b86a57639')
@@ -27,8 +27,8 @@ class RDose(RPackage):
     version('3.2.0', commit='71f563fc39d02dfdf65184c94e0890a63b96b86b')
 
     depends_on('r@3.3.1:', type=('build', 'run'))
-    depends_on('r@3.4.0:', when='@3.6.1:', type=('build', 'run'))
-    depends_on('r@3.5.0:', when='@3.16.0:', type=('build', 'run'))
+    depends_on('r@3.4.0:', type=('build', 'run'), when='@3.6.1:')
+    depends_on('r@3.5.0:', type=('build', 'run'), when='@3.16.0:')
     depends_on('r-annotationdbi', type=('build', 'run'))
     depends_on('r-biocparallel', type=('build', 'run'))
     depends_on('r-do-db', type=('build', 'run'))
@@ -37,7 +37,8 @@ class RDose(RPackage):
     depends_on('r-gosemsim@2.0.0:', type=('build', 'run'))
     depends_on('r-qvalue', type=('build', 'run'))
     depends_on('r-reshape2', type=('build', 'run'))
-    depends_on('r-s4vectors', when='@:3.10.2', type=('build', 'run'))
-    depends_on('r-scales', when='@3.2.0:3.4.0', type=('build', 'run'))
-    depends_on('r-rvcheck', when='@3.4.0', type=('build', 'run'))
-    depends_on('r-igraph', when='@3.2.0:3.4.0', type=('build', 'run'))
+
+    depends_on('r-s4vectors', type=('build', 'run'), when='@:3.10.2')
+    depends_on('r-scales', type=('build', 'run'), when='@3.2.0:3.4.0')
+    depends_on('r-rvcheck', type=('build', 'run'), when='@3.4.0')
+    depends_on('r-igraph', type=('build', 'run'), when='@3.2.0:3.4.0')
diff --git a/var/spack/repos/builtin/packages/r-dss/package.py b/var/spack/repos/builtin/packages/r-dss/package.py
index b8b4c3dab5..666509197b 100644
--- a/var/spack/repos/builtin/packages/r-dss/package.py
+++ b/var/spack/repos/builtin/packages/r-dss/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RDss(RPackage):
-    """Dispersion shrinkage for sequencing data
+    """Dispersion shrinkage for sequencing data.
 
     DSS is an R library performing differntial analysis for count-based
     sequencing data. It detectes differentially expressed genes (DEGs) from
@@ -16,9 +16,9 @@ class RDss(RPackage):
     shrinkage method for estimating the dispersion parameter from Gamma-Poisson
     or Beta-Binomial distributions."""
 
-    homepage = "https://bioconductor.org/packages/DSS/"
-    git      = "https://git.bioconductor.org/packages/DSS"
+    bioc = "DSS"
 
+    version('2.42.0', commit='33e87450fbb64bb3e321688ff613e83cd40efe48')
     version('2.38.0', commit='82e65b92e6e227f1f99620362db8b03059e07e98')
     version('2.36.0', commit='841c7ed')
     version('2.34.0', commit='f9819c7')
@@ -26,6 +26,6 @@ class RDss(RPackage):
 
     depends_on('r@3.3:', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
-    depends_on('r-biocparallel', when='@2.36.0:', type=('build', 'run'))
+    depends_on('r-biocparallel', type=('build', 'run'), when='@2.36.0:')
     depends_on('r-bsseq', type=('build', 'run'))
-    depends_on('r-delayedarray', when='@2.36.0:', type=('build', 'run'))
+    depends_on('r-delayedarray', type=('build', 'run'), when='@2.36.0:')
diff --git a/var/spack/repos/builtin/packages/r-edger/package.py b/var/spack/repos/builtin/packages/r-edger/package.py
index 34334a832c..63506ad9e0 100644
--- a/var/spack/repos/builtin/packages/r-edger/package.py
+++ b/var/spack/repos/builtin/packages/r-edger/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class REdger(RPackage):
-    """Empirical Analysis of Digital Gene Expression Data in R
+    """Empirical Analysis of Digital Gene Expression Data in R.
 
        Differential expression analysis of RNA-seq expression profiles with
        biological replication. Implements a range of statistical methodology
@@ -17,9 +17,9 @@ class REdger(RPackage):
        of other types of genomic data that produce counts, including ChIP-seq,
        Bisulfite-seq, SAGE and CAGE."""
 
-    homepage = "https://bioconductor.org/packages/edgeR"
-    git      = "https://git.bioconductor.org/packages/edgeR.git"
+    bioc = "edgeR"
 
+    version('3.36.0', commit='c7db03addfc42138a1901834409c02da9d873026')
     version('3.32.1', commit='b881d801d60e5b38413d27f149384c218621c55a')
     version('3.26.8', commit='836809e043535f2264e5db8b5c0eabcffe85613f')
     version('3.24.3', commit='d1260a2aeba67b9ab7a9b8b197b746814ad0716d')
@@ -28,9 +28,9 @@ class REdger(RPackage):
     version('3.18.1', commit='101106f3fdd9e2c45d4a670c88f64c12e97a0495')
 
     depends_on('r@2.15.0:', type=('build', 'run'))
-    depends_on('r@3.6.0:', when='@3.26.8:', type=('build', 'run'))
+    depends_on('r@3.6.0:', type=('build', 'run'), when='@3.26.8:')
     depends_on('r-limma', type=('build', 'run'))
-    depends_on('r-limma@3.34.5:', when='@3.20.9:', type=('build', 'run'))
-    depends_on('r-limma@3.41.5:', when='@3.32.1:', type=('build', 'run'))
+    depends_on('r-limma@3.34.5:', type=('build', 'run'), when='@3.20.9:')
+    depends_on('r-limma@3.41.5:', type=('build', 'run'), when='@3.32.1:')
     depends_on('r-locfit', type=('build', 'run'))
-    depends_on('r-rcpp', when='@3.20.9:', type=('build', 'run'))
+    depends_on('r-rcpp', type=('build', 'run'), when='@3.20.9:')
diff --git a/var/spack/repos/builtin/packages/r-enrichplot/package.py b/var/spack/repos/builtin/packages/r-enrichplot/package.py
index 767e8b6f8a..bee8538666 100644
--- a/var/spack/repos/builtin/packages/r-enrichplot/package.py
+++ b/var/spack/repos/builtin/packages/r-enrichplot/package.py
@@ -7,40 +7,46 @@ from spack import *
 
 
 class REnrichplot(RPackage):
-    """Visualization of Functional Enrichment Result
+    """Visualization of Functional Enrichment Result.
 
        The 'enrichplot' package implements several visualization methods for
        interpreting functional enrichment results obtained from ORA or GSEA
        analysis. All the visualization methods are developed based on 'ggplot2'
        graphics."""
 
-    homepage = "https://bioconductor.org/packages/enrichplot"
-    git      = "https://git.bioconductor.org/packages/enrichplot.git"
+    bioc = "enrichplot"
 
+    version('1.14.1', commit='ccf3a6d9b7cd9cffd8de6d6263efdffe59d2ec36')
     version('1.10.2', commit='77ee04f60a07cc31151f8f47f8ee64f3a43c9760')
     version('1.4.0', commit='6ffe5d9c5dbe5cbea29f2e0941595475bbbcea0e')
     version('1.2.0', commit='2eeaafb571d35a106eba8ae7df014f3201066e8b')
     version('1.0.2', commit='ba7726fa0d4b581b7514dcbb04889cdbdd75ff29')
 
     depends_on('r@3.4.0:', type=('build', 'run'))
-    depends_on('r@3.5.0:', when='@1.10.2:', type=('build', 'run'))
-    depends_on('r-cowplot', type=('build', 'run'))
-    depends_on('r-dose', type=('build', 'run'))
-    depends_on('r-dose@3.5.1:', when='@:1.4.0', type=('build', 'run'))
+    depends_on('r@3.5.0:', type=('build', 'run'), when='@1.10.2:')
+    depends_on('r-aplot', type=('build', 'run'), when='@1.14.1:')
+    depends_on('r-dose@3.5.1:', type=('build', 'run'))
+    depends_on('r-dose@3.13.1:', type=('build', 'run'), when='@1.8.1:')
+    depends_on('r-dose@3.16.0:', type=('build', 'run'), when='@1.12.3:')
     depends_on('r-ggplot2', type=('build', 'run'))
     depends_on('r-ggraph', type=('build', 'run'))
     depends_on('r-igraph', type=('build', 'run'))
-    depends_on('r-plyr', when='@1.10.2:', type=('build', 'run'))
-    depends_on('r-purrr', when='@1.2.0:', type=('build', 'run'))
-    depends_on('r-rcolorbrewer', when='@1.2.0:', type=('build', 'run'))
+    depends_on('r-plyr', type=('build', 'run'), when='@1.10.2:')
+    depends_on('r-purrr', type=('build', 'run'), when='@1.2.0:')
+    depends_on('r-rcolorbrewer', type=('build', 'run'), when='@1.2.0:')
     depends_on('r-reshape2', type=('build', 'run'))
-    depends_on('r-scatterpie', when='@1.10.2:', type=('build', 'run'))
-    depends_on('r-shadowtext', when='@1.10.2:', type=('build', 'run'))
+    depends_on('r-scatterpie', type=('build', 'run'), when='@1.10.2:')
+    depends_on('r-shadowtext', type=('build', 'run'), when='@1.10.2:')
     depends_on('r-gosemsim', type=('build', 'run'))
-    depends_on('r-magrittr', when='@1.10.2:', type=('build', 'run'))
-    depends_on('r-ggridges', when='@:1.4.0', type=('build', 'run'))
-    depends_on('r-upsetr', when='@:1.4.0', type=('build', 'run'))
-    depends_on('r-annotationdbi', when='@:1.4.0', type=('build', 'run'))
-    depends_on('r-europepmc', when='@1.2.0:1.4.0', type=('build', 'run'))
-    depends_on('r-ggplotify', when='@1.2.0:1.4.0', type=('build', 'run'))
-    depends_on('r-gridextra', when='@1.2.0:1.4.0', type=('build', 'run'))
+    depends_on('r-magrittr', type=('build', 'run'), when='@1.10.2:')
+    depends_on('r-ggtree', type=('build', 'run'), when='@1.14.1:')
+    depends_on('r-yulab-utils@0.0.4:', type=('build', 'run'), when='@1.14.1:')
+
+    depends_on('r-ggridges', type=('build', 'run'), when='@:1.4.0')
+    depends_on('r-upsetr', type=('build', 'run'), when='@:1.4.0')
+    depends_on('r-annotationdbi', type=('build', 'run'), when='@:1.4.0')
+    depends_on('r-europepmc', type=('build', 'run'), when='@1.2.0:1.4.0')
+    depends_on('r-ggplotify', type=('build', 'run'), when='@1.2.0:1.4.0')
+    depends_on('r-gridextra', type=('build', 'run'), when='@1.2.0:1.4.0')
+
+    depends_on('r-cowplot', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ensembldb/package.py b/var/spack/repos/builtin/packages/r-ensembldb/package.py
index e6e9228f31..22605bb67d 100644
--- a/var/spack/repos/builtin/packages/r-ensembldb/package.py
+++ b/var/spack/repos/builtin/packages/r-ensembldb/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class REnsembldb(RPackage):
-    """Utilities to create and use Ensembl-based annotation databases
+    """Utilities to create and use Ensembl-based annotation databases.
 
        The package provides functions to create and use transcript centric
        annotation databases/packages. The annotation for the databases are
@@ -22,9 +22,9 @@ class REnsembldb(RPackage):
        encoding transcripts. Finally, ensembldb provides functions to map
        between genomic, transcript and protein coordinates."""
 
-    homepage = "https://bioconductor.org/packages/ensembldb"
-    git      = "https://git.bioconductor.org/packages/ensembldb.git"
+    bioc = "ensembldb"
 
+    version('2.18.3', commit='e2fcfc0c7700110df070a171d2d542b37ec098f3')
     version('2.14.0', commit='c7150519ed4ef38e5eac1043209863dbc7be43a1')
     version('2.8.1', commit='a4d8d89c143dca86b364d59dff8e46cc81c41ac0')
     version('2.6.8', commit='c2c4f41b4ecc81d5328ce1d380065dfcb5e0c54c')
@@ -34,12 +34,12 @@ class REnsembldb(RPackage):
 
     depends_on('r-biocgenerics@0.15.10:', type=('build', 'run'))
     depends_on('r-genomicranges@1.23.21:', type=('build', 'run'))
-    depends_on('r-genomicranges@1.31.18:', when='@2.4.1:', type=('build', 'run'))
+    depends_on('r-genomicranges@1.31.18:', type=('build', 'run'), when='@2.4.1:')
     depends_on('r-genomicfeatures@1.23.18:', type=('build', 'run'))
-    depends_on('r-genomicfeatures@1.29.10:', when='@2.2.2:', type=('build', 'run'))
+    depends_on('r-genomicfeatures@1.29.10:', type=('build', 'run'), when='@2.2.2:')
     depends_on('r-annotationfilter@0.99.7:', type=('build', 'run'))
-    depends_on('r-annotationfilter@1.1.9:', when='@2.2.2:', type=('build', 'run'))
-    depends_on('r-annotationfilter@1.5.2:', when='@2.6.8:', type=('build', 'run'))
+    depends_on('r-annotationfilter@1.1.9:', type=('build', 'run'), when='@2.2.2:')
+    depends_on('r-annotationfilter@1.5.2:', type=('build', 'run'), when='@2.6.8:')
     depends_on('r-rsqlite@1.1:', type=('build', 'run'))
     depends_on('r-dbi', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
@@ -47,13 +47,14 @@ class REnsembldb(RPackage):
     depends_on('r-annotationdbi@1.31.19:', type=('build', 'run'))
     depends_on('r-rtracklayer', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
-    depends_on('r-s4vectors@0.23.10:', when='@2.14.0:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.23.10:', type=('build', 'run'), when='@2.14.0:')
     depends_on('r-rsamtools', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
-    depends_on('r-iranges@2.11.16:', when='@2.2.2:', type=('build', 'run'))
-    depends_on('r-iranges@2.13.24:', when='@2.4.1:', type=('build', 'run'))
+    depends_on('r-iranges@2.11.16:', type=('build', 'run'), when='@2.2.2:')
+    depends_on('r-iranges@2.13.24:', type=('build', 'run'), when='@2.4.1:')
     depends_on('r-protgenerics', type=('build', 'run'))
     depends_on('r-biostrings', type=('build', 'run'))
-    depends_on('r-biostrings@2.47.9:', when='@2.4.1:', type=('build', 'run'))
+    depends_on('r-biostrings@2.47.9:', type=('build', 'run'), when='@2.4.1:')
     depends_on('r-curl', type=('build', 'run'))
-    depends_on('r-annotationhub', when='@2.0.4:2.2.2', type=('build', 'run'))
+
+    depends_on('r-annotationhub', type=('build', 'run'), when='@2.0.4:2.2.2')
diff --git a/var/spack/repos/builtin/packages/r-exomecopy/package.py b/var/spack/repos/builtin/packages/r-exomecopy/package.py
index 151ac64b67..9d2d5a74bf 100644
--- a/var/spack/repos/builtin/packages/r-exomecopy/package.py
+++ b/var/spack/repos/builtin/packages/r-exomecopy/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RExomecopy(RPackage):
-    """Copy number variant detection from exome sequencing read depth
+    """Copy number variant detection from exome sequencing read depth.
 
     Detection of copy number variants (CNV) from exome sequencing samples,
     including unpaired samples. The package implements a hidden Markov model
@@ -15,9 +15,9 @@ class RExomecopy(RPackage):
     GC-content, to simultaneously normalize and segment the samples into
     regions of constant copy count."""
 
-    homepage = "https://www.bioconductor.org/packages/release/bioc/html/exomeCopy.html"
-    git      = "https://git.bioconductor.org/packages/exomeCopy"
+    bioc = "exomeCopy"
 
+    version('1.40.0', commit='ebde39be67baace2c326359421fd17f4a02fd4fe')
     version('1.36.0', commit='cbe3134acbbc9b7d5426ae2f142dc64cadb3fc26')
     version('1.32.0', commit='c9a884427d91b6d62ddc16a939bd808e389d3ea6')
 
diff --git a/var/spack/repos/builtin/packages/r-experimenthub/package.py b/var/spack/repos/builtin/packages/r-experimenthub/package.py
index 4e7b6da0b4..a63002b205 100644
--- a/var/spack/repos/builtin/packages/r-experimenthub/package.py
+++ b/var/spack/repos/builtin/packages/r-experimenthub/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RExperimenthub(RPackage):
-    """Client to access ExperimentHub resources:
+    """Client to access ExperimentHub resources.
 
     This package provides a client for the Bioconductor ExperimentHub web
     resource. ExperimentHub provides a central location where curated data from
@@ -16,8 +16,9 @@ class RExperimenthub(RPackage):
     creates and manages a local cache of files retrieved enabling quick and
     reproducible access."""
 
-    bioc     = "ExperimentHub"
+    bioc = "ExperimentHub"
 
+    version('2.2.1', commit='4e10686fa72baefef5d2990f41a7c44c527a7a7d')
     version('1.16.1', commit='61d51b7ca968d6cc1befe299e0784d9a19ca51f6')
 
     depends_on('r-biocgenerics@0.15.10:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg18/package.py b/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg18/package.py
index a27e47205a..a312f23c07 100644
--- a/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg18/package.py
+++ b/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg18/package.py
@@ -7,13 +7,13 @@ from spack import *
 
 
 class RFdbInfiniummethylationHg18(RPackage):
-    """Annotation package for Illumina Infinium DNA methylation probes
+    """Annotation package for Illumina Infinium DNA methylation probes.
 
     Compiled HumanMethylation27 and HumanMethylation450 annotations"""
 
     # This is a bioconductor package but there is no available git repository
-    homepage = "https://bioconductor.org/packages/release/data/annotation/html/FDb.InfiniumMethylation.hg18.html"
-    url      = "https://bioconductor.org/packages/release/data/annotation/src/contrib/FDb.InfiniumMethylation.hg18_2.2.0.tar.gz"
+    bioc = "FDb.InfiniumMethylation.hg18"
+    url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/FDb.InfiniumMethylation.hg18_2.2.0.tar.gz"
 
     version('2.2.0', sha256='4a9028ac03c11fffbab731ea750bc7f9b0884fc43c6a8dac6eb2c644e4c79f6f')
 
diff --git a/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg19/package.py b/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg19/package.py
index cf999ca104..07d91ead8f 100644
--- a/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg19/package.py
+++ b/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg19/package.py
@@ -7,13 +7,13 @@ from spack import *
 
 
 class RFdbInfiniummethylationHg19(RPackage):
-    """Annotation package for Illumina Infinium DNA methylation probes
+    """Annotation package for Illumina Infinium DNA methylation probes.
 
     Compiled HumanMethylation27 and HumanMethylation450 annotations."""
 
     # No available git repository
-    homepage = "https://bioconductor.org/packages/release/data/annotation/html/FDb.InfiniumMethylation.hg19.html"
-    url      = "https://bioconductor.org/packages/release/data/annotation/src/contrib/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz"
+    bioc = "FDb.InfiniumMethylation.hg19"
+    url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz"
 
     version('2.2.0', sha256='605aa3643588a2f40a942fa760b92662060a0dfedb26b4e4cd6f1a78b703093f')
 
diff --git a/var/spack/repos/builtin/packages/r-fgsea/package.py b/var/spack/repos/builtin/packages/r-fgsea/package.py
index af1538cfb3..9722ed89ce 100644
--- a/var/spack/repos/builtin/packages/r-fgsea/package.py
+++ b/var/spack/repos/builtin/packages/r-fgsea/package.py
@@ -7,16 +7,16 @@ from spack import *
 
 
 class RFgsea(RPackage):
-    """Fast Gene Set Enrichment Analysis
+    """Fast Gene Set Enrichment Analysis.
 
        The package implements an algorithm for fast gene set enrichment
        analysis. Using the fast algorithm allows to make more permutations and
        get more fine grained p-values, which allows to use accurate stantard
        approaches to multiple hypothesis correction."""
 
-    homepage = "https://bioconductor.org/packages/fgsea"
-    git      = "https://git.bioconductor.org/packages/fgsea.git"
+    bioc = "fgsea"
 
+    version('1.20.0', commit='b704f81687dc16afdaafc6d30108c62a067856b2')
     version('1.16.0', commit='9d9df596c7e160afa18e067b7637cfc465494318')
     version('1.10.1', commit='fb06a6ebfb4a195e77e37226d100a2148b90c5f3')
     version('1.8.0', commit='bb2898aca9fb23e90770671a83fe23f79bb1841b')
@@ -31,5 +31,5 @@ class RFgsea(RPackage):
     depends_on('r-ggplot2@2.2.0:', type=('build', 'run'))
     depends_on('r-gridextra', type=('build', 'run'))
     depends_on('r-fastmatch', type=('build', 'run'))
-    depends_on('r-matrix', when='@1.6.0:', type=('build', 'run'))
-    depends_on('r-bh', when='@1.10.1:', type=('build', 'run'))
+    depends_on('r-matrix', type=('build', 'run'), when='@1.6.0:')
+    depends_on('r-bh', type=('build', 'run'), when='@1.10.1:')
diff --git a/var/spack/repos/builtin/packages/r-gcrma/package.py b/var/spack/repos/builtin/packages/r-gcrma/package.py
index 81672f24f9..7540ffa53c 100644
--- a/var/spack/repos/builtin/packages/r-gcrma/package.py
+++ b/var/spack/repos/builtin/packages/r-gcrma/package.py
@@ -7,13 +7,13 @@ from spack import *
 
 
 class RGcrma(RPackage):
-    """Background Adjustment Using Sequence Information
+    """Background Adjustment Using Sequence Information.
 
     Background adjustment using sequence information."""
 
-    homepage = "https://bioconductor.org/packages/gcrma"
-    git      = "https://git.bioconductor.org/packages/gcrma.git"
+    bioc = "gcrma"
 
+    version('2.66.0', commit='ba134b392def89d36b5639a187e0c25a4353457b')
     version('2.62.0', commit='b91bdf5bf4e875defedb4d4e3e1e75867773287a')
     version('2.56.0', commit='1f37bbfb4d3ed542b1e90704ab0fa8914d5e0224')
     version('2.54.0', commit='9515fdbbc766a2a3b2ec61cf530c57bbded77ccc')
@@ -27,5 +27,6 @@ class RGcrma(RPackage):
     depends_on('r-affyio@1.13.3:', type=('build', 'run'))
     depends_on('r-xvector', type=('build', 'run'))
     depends_on('r-biostrings@2.11.32:', type=('build', 'run'))
-    depends_on('r-biocmanager', when='@2.54.0:', type=('build', 'run'))
-    depends_on('r-biocinstaller', when='@:2.52.0', type=('build', 'run'))
+    depends_on('r-biocmanager', type=('build', 'run'), when='@2.54.0:')
+
+    depends_on('r-biocinstaller', type=('build', 'run'), when='@:2.52.0')
diff --git a/var/spack/repos/builtin/packages/r-gdsfmt/package.py b/var/spack/repos/builtin/packages/r-gdsfmt/package.py
index 38edbfae95..bc852366f4 100644
--- a/var/spack/repos/builtin/packages/r-gdsfmt/package.py
+++ b/var/spack/repos/builtin/packages/r-gdsfmt/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RGdsfmt(RPackage):
-    """R Interface to CoreArray Genomic Data Structure (GDS) Files
+    """R Interface to CoreArray Genomic Data Structure (GDS) Files.
 
        This package provides a high-level R interface to CoreArray Genomic Data
        Structure (GDS) data files, which are portable across platforms with
@@ -22,9 +22,9 @@ class RGdsfmt(RPackage):
        GDS file in parallel with multiple R processes supported by the package
        parallel."""
 
-    homepage = "https://bioconductor.org/packages/gdsfmt"
-    git      = "https://git.bioconductor.org/packages/gdsfmt.git"
+    bioc = "gdsfmt"
 
+    version('1.30.0', commit='d27dde6a70bb2295f5bbc8961152b45ccee7a652')
     version('1.26.1', commit='bd180b21b1ace120035f0da255cbf6f13088f069')
     version('1.20.0', commit='b1fbaba0a5ace3dc45daecc85168651cd85dce00')
     version('1.18.1', commit='b911b953e9db7988e93ec2010b0ab1e384d073c9')
diff --git a/var/spack/repos/builtin/packages/r-genefilter/package.py b/var/spack/repos/builtin/packages/r-genefilter/package.py
index fb165fbc33..8b0a7b3175 100644
--- a/var/spack/repos/builtin/packages/r-genefilter/package.py
+++ b/var/spack/repos/builtin/packages/r-genefilter/package.py
@@ -7,13 +7,13 @@ from spack import *
 
 
 class RGenefilter(RPackage):
-    """genefilter: methods for filtering genes from high-throughput experiments
+    """Methods for filtering genes from high-throughput experiments.
 
     Some basic functions for filtering genes."""
 
-    homepage = "https://bioconductor.org/packages/genefilter"
-    git      = "https://git.bioconductor.org/packages/genefilter.git"
+    bioc = "genefilter"
 
+    version('1.76.0', commit='8d630fd25f0d2a4101e05e123c3959591203a7ea')
     version('1.72.1', commit='b01b00a766982ef7d80b90a252085c8c4f085e1b')
     version('1.72.0', commit='8cb0b2e73531a417d53e5625bcf436265cdbe101')
     version('1.66.0', commit='1c4c471ccca873bf92dcf0b50f611eaa64c4f0cf')
@@ -22,9 +22,10 @@ class RGenefilter(RPackage):
     version('1.60.0', commit='c98f695253c330a9380b2b4ffa27f3b7d66773e4')
     version('1.58.1', commit='ace2556049677f60882adfe91f8cc96791556fc2')
 
-    depends_on('r-biocgenerics@0.31.2:', when='@1.68.0:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.31.2:', type=('build', 'run'), when='@1.68.0:')
     depends_on('r-annotationdbi', type=('build', 'run'))
     depends_on('r-annotate', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-survival', type=('build', 'run'))
-    depends_on('r-s4vectors@0.9.42:', when='@:1.66.0', type=('build', 'run'))
+
+    depends_on('r-s4vectors@0.9.42:', type=('build', 'run'), when='@:1.66.0')
diff --git a/var/spack/repos/builtin/packages/r-genelendatabase/package.py b/var/spack/repos/builtin/packages/r-genelendatabase/package.py
index 82df752120..84402eeece 100644
--- a/var/spack/repos/builtin/packages/r-genelendatabase/package.py
+++ b/var/spack/repos/builtin/packages/r-genelendatabase/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RGenelendatabase(RPackage):
-    """Lengths of mRNA transcripts for a number of genomes
+    """Lengths of mRNA transcripts for a number of genomes.
 
        Length of mRNA transcripts for a number of genomes and gene ID formats,
        largely based on UCSC table browser"""
 
-    homepage = "https://bioconductor.org/packages/geneLenDataBase"
-    git      = "https://git.bioconductor.org/packages/geneLenDataBase.git"
+    bioc = "geneLenDataBase"
 
+    version('1.30.0', commit='b3cc755f1ffcbb2eacd9ea45e11f39f1639782b1')
     version('1.26.0', commit='2724715ae23a6647d1c0c6e934720aad9377d65e')
     version('1.20.0', commit='70a1abed00ee68f7bfa07c42c011f9edae9915e4')
     version('1.18.0', commit='77db87e5a4819bf94761fabef0d2ff741a1c5d07')
diff --git a/var/spack/repos/builtin/packages/r-genemeta/package.py b/var/spack/repos/builtin/packages/r-genemeta/package.py
index 97acead0f7..a0f8b4f9b8 100644
--- a/var/spack/repos/builtin/packages/r-genemeta/package.py
+++ b/var/spack/repos/builtin/packages/r-genemeta/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RGenemeta(RPackage):
-    """MetaAnalysis for High Throughput Experiments
+    """MetaAnalysis for High Throughput Experiments.
 
        A collection of meta-analysis tools for analysing high throughput
        experimental data"""
 
-    homepage = "https://bioconductor.org/packages/GeneMeta"
-    git      = "https://git.bioconductor.org/packages/GeneMeta.git"
+    bioc = "GeneMeta"
 
+    version('1.66.0', commit='c16eb09492f08f6cc0f253fafa3fa5dce35dcdba')
     version('1.62.0', commit='eb4273ff5867e39592f50b97b454fa5e32b4a9bf')
     version('1.56.0', commit='cb2c9e353d34ea9f3db06cb236c7a89674f2682d')
     version('1.54.0', commit='932553cd8df82b7df804fccda9bfd4b0f36d79d7')
diff --git a/var/spack/repos/builtin/packages/r-geneplotter/package.py b/var/spack/repos/builtin/packages/r-geneplotter/package.py
index 7ce29e0de8..34cbc67874 100644
--- a/var/spack/repos/builtin/packages/r-geneplotter/package.py
+++ b/var/spack/repos/builtin/packages/r-geneplotter/package.py
@@ -7,13 +7,13 @@ from spack import *
 
 
 class RGeneplotter(RPackage):
-    """Graphics related functions for Bioconductor
+    """Graphics related functions for Bioconductor.
 
     Functions for plotting genomic data."""
 
-    homepage = "https://bioconductor.org/packages/geneplotter"
-    git      = "https://git.bioconductor.org/packages/geneplotter.git"
+    bioc = "geneplotter"
 
+    version('1.72.0', commit='57a1d830ba7844fda5236af0153d5b5587634f96')
     version('1.68.0', commit='f1fea7e468fb24fdfa93ef4493600a4d8d183f69')
     version('1.62.0', commit='1fbaddde11014b453b131860409f89cd784e8e48')
     version('1.60.0', commit='6723a9fc0730e146187e79c2ddab6a68186dc5ad')
diff --git a/var/spack/repos/builtin/packages/r-genie3/package.py b/var/spack/repos/builtin/packages/r-genie3/package.py
index 9c7ffa2bb3..86cb2613f5 100644
--- a/var/spack/repos/builtin/packages/r-genie3/package.py
+++ b/var/spack/repos/builtin/packages/r-genie3/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RGenie3(RPackage):
-    """GEne Network Inference with Ensemble of trees
+    """GEne Network Inference with Ensemble of trees.
 
        This package implements the GENIE3 algorithm for inferring gene
        regulatory networks from expression data."""
 
-    homepage = "https://bioconductor.org/packages/GENIE3"
-    git      = "https://git.bioconductor.org/packages/GENIE3.git"
+    bioc = "GENIE3"
 
+    version('1.16.0', commit='5543b1b883d3a1c92e955de6668444278edc2bdf')
     version('1.12.0', commit='14289cee9bed113ab35ba03bcaac4a30e5784497')
     version('1.6.0', commit='d6a49182e098342afe77f01c322dfc7b72450502')
     version('1.4.3', commit='ae719c759f23f09d28fcf1acc45b860cd7761f08')
@@ -22,3 +22,4 @@ class RGenie3(RPackage):
     version('1.0.0', commit='eb7c95ed12ea50d61e8fa20bc2b25ae9d74c302f')
 
     depends_on('r-reshape2', type=('build', 'run'))
+    depends_on('r-dplyr', type=('build', 'run'), when='@1.16.0:')
diff --git a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py
index e599b5386b..99dc82df12 100644
--- a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py
+++ b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py
@@ -8,16 +8,16 @@ from spack import *
 
 class RGenomeinfodb(RPackage):
     """Utilities for manipulating chromosome names, including modifying them to
-       follow a particular naming style
+       follow a particular naming style.
 
        Contains data and functions that define and allow translation between
        different chromosome sequence naming conventions (e.g., "chr1" versus
        "1"), including a function that attempts to place sequence names in
        their natural, rather than lexicographic, order."""
 
-    homepage = "https://bioconductor.org/packages/GenomeInfoDb"
-    git      = "https://git.bioconductor.org/packages/GenomeInfoDb.git"
+    bioc = "GenomeInfoDb"
 
+    version('1.30.1', commit='bf8b385a2ffcecf9b41e581794056f267895863d')
     version('1.26.2', commit='96dd27a7e3ef476790b1475aab50dbbed7df67a2')
     version('1.20.0', commit='ea771e3b429ef17fb912fb37333556c6f77f2265')
     version('1.18.2', commit='557b75ea7734749a2650d30f5c5d52c57a6bcc6f')
@@ -26,11 +26,13 @@ class RGenomeinfodb(RPackage):
     version('1.12.3', commit='2deef3f0571b7f622483257bc22d2509ab5a0369')
 
     depends_on('r@3.1:', type=('build', 'run'))
+    depends_on('r@4.0.0:', type=('build', 'run'), when='@1.30.1:')
     depends_on('r-biocgenerics@0.13.8:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.37.0:', type=('build', 'run'), when='@1.30.1:')
     depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.17.25:', when='@1.16.0:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.25.12:', when='@1.26.2:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.25:', type=('build', 'run'), when='@1.16.0:')
+    depends_on('r-s4vectors@0.25.12:', type=('build', 'run'), when='@1.26.2:')
     depends_on('r-iranges@1.99.26:', type=('build', 'run'))
-    depends_on('r-iranges@2.13.12:', when='@1.16.0:', type=('build', 'run'))
+    depends_on('r-iranges@2.13.12:', type=('build', 'run'), when='@1.16.0:')
     depends_on('r-rcurl', type=('build', 'run'))
     depends_on('r-genomeinfodbdata', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py b/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py
index bc301016f8..4c682a4a56 100644
--- a/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py
+++ b/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py
@@ -10,8 +10,8 @@ class RGenomeinfodbdata(RPackage):
     """for mapping between NCBI taxonomy ID and species. Used by functions
        in the GenomeInfoDb package."""
 
-    homepage = "https://bioconductor.org/packages/GenomeInfoDbData/"
-    url      = "https://bioconductor.org/packages/release/data/annotation/src/contrib/GenomeInfoDbData_0.99.0.tar.gz"
+    bioc = "GenomeInfoDbData"
+    url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/GenomeInfoDbData_0.99.0.tar.gz"
 
     version('1.2.7',
             url='https://bioconductor.org/packages/3.14/data/annotation/src/contrib/GenomeInfoDbData_1.2.7.tar.gz',
diff --git a/var/spack/repos/builtin/packages/r-genomicalignments/package.py b/var/spack/repos/builtin/packages/r-genomicalignments/package.py
index c42ba27e85..a0afca41d7 100644
--- a/var/spack/repos/builtin/packages/r-genomicalignments/package.py
+++ b/var/spack/repos/builtin/packages/r-genomicalignments/package.py
@@ -7,16 +7,16 @@ from spack import *
 
 
 class RGenomicalignments(RPackage):
-    """Representation and manipulation of short genomic alignments
+    """Representation and manipulation of short genomic alignments.
 
        Provides efficient containers for storing and manipulating short genomic
        alignments (typically obtained by aligning short reads to a reference
        genome). This includes read counting, computing the coverage, junction
        detection, and working with the nucleotide content of the alignments."""
 
-    homepage = "https://bioconductor.org/packages/GenomicAlignments"
-    git      = "https://git.bioconductor.org/packages/GenomicAlignments.git"
+    bioc = "GenomicAlignments"
 
+    version('1.30.0', commit='2d2c5fce3529c2962fdcefd736d8b7f7c0ec2d54')
     version('1.26.0', commit='6c74c74ee53efcd880171126366fee4bd72357bc')
     version('1.20.1', commit='9dce402071e4cd945de7ff82ea574c79993625fd')
     version('1.18.1', commit='8ac41e5981cf343076044f451a984afb651688ab')
@@ -25,28 +25,30 @@ class RGenomicalignments(RPackage):
     version('1.12.2', commit='b5d6f19e4a89b6c1c3e9e58e5ea4eb13870874ef')
 
     depends_on('r@2.10:', type=('build', 'run'))
+    depends_on('r@4.0.0:', type=('build', 'run'), when='@1.30.0:')
     depends_on('r-biocgenerics@0.15.3:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.37.0:', type=('build', 'run'), when='@1.30.0:')
     depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.17.28:', when='@1.16.0:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.19.11:', when='@1.18.1:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.27.12:', when='@1.26.0:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.28:', type=('build', 'run'), when='@1.16.0:')
+    depends_on('r-s4vectors@0.19.11:', type=('build', 'run'), when='@1.18.1:')
+    depends_on('r-s4vectors@0.27.12:', type=('build', 'run'), when='@1.26.0:')
     depends_on('r-iranges@2.5.36:', type=('build', 'run'))
-    depends_on('r-iranges@2.11.16:', when='@1.14.2:', type=('build', 'run'))
-    depends_on('r-iranges@2.13.25:', when='@1.16.0:', type=('build', 'run'))
-    depends_on('r-iranges@2.15.12:', when='@1.18.1:', type=('build', 'run'))
-    depends_on('r-iranges@2.23.9:', when='@1.26.0:', type=('build', 'run'))
+    depends_on('r-iranges@2.11.16:', type=('build', 'run'), when='@1.14.2:')
+    depends_on('r-iranges@2.13.25:', type=('build', 'run'), when='@1.16.0:')
+    depends_on('r-iranges@2.15.12:', type=('build', 'run'), when='@1.18.1:')
+    depends_on('r-iranges@2.23.9:', type=('build', 'run'), when='@1.26.0:')
     depends_on('r-genomeinfodb@1.11.5:', type=('build', 'run'))
-    depends_on('r-genomeinfodb@1.13.1:', when='@1.14.2:', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.13.1:', type=('build', 'run'), when='@1.14.2:')
     depends_on('r-genomicranges@1.27.19:', type=('build', 'run'))
-    depends_on('r-genomicranges@1.29.14:', when='@1.14.2:', type=('build', 'run'))
-    depends_on('r-genomicranges@1.31.19:', when='@1.16.0:', type=('build', 'run'))
-    depends_on('r-genomicranges@1.33.4:', when='@1.18.1:', type=('build', 'run'))
-    depends_on('r-genomicranges@1.41.5:', when='@1.26.0:', type=('build', 'run'))
+    depends_on('r-genomicranges@1.29.14:', type=('build', 'run'), when='@1.14.2:')
+    depends_on('r-genomicranges@1.31.19:', type=('build', 'run'), when='@1.16.0:')
+    depends_on('r-genomicranges@1.33.4:', type=('build', 'run'), when='@1.18.1:')
+    depends_on('r-genomicranges@1.41.5:', type=('build', 'run'), when='@1.26.0:')
     depends_on('r-summarizedexperiment@1.5.3:', type=('build', 'run'))
-    depends_on('r-summarizedexperiment@1.9.13:', when='@1.16.0:', type=('build', 'run'))
+    depends_on('r-summarizedexperiment@1.9.13:', type=('build', 'run'), when='@1.16.0:')
     depends_on('r-biostrings@2.37.1:', type=('build', 'run'))
-    depends_on('r-biostrings@2.47.6:', when='@1.16.0:', type=('build', 'run'))
-    depends_on('r-biostrings@2.55.7:', when='@1.26.0:', type=('build', 'run'))
+    depends_on('r-biostrings@2.47.6:', type=('build', 'run'), when='@1.16.0:')
+    depends_on('r-biostrings@2.55.7:', type=('build', 'run'), when='@1.26.0:')
     depends_on('r-rsamtools@1.21.4:', type=('build', 'run'))
-    depends_on('r-rsamtools@1.31.2:', when='@1.16.0:', type=('build', 'run'))
+    depends_on('r-rsamtools@1.31.2:', type=('build', 'run'), when='@1.16.0:')
     depends_on('r-biocparallel', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-genomicfeatures/package.py b/var/spack/repos/builtin/packages/r-genomicfeatures/package.py
index cba53196e0..96e310a1a2 100644
--- a/var/spack/repos/builtin/packages/r-genomicfeatures/package.py
+++ b/var/spack/repos/builtin/packages/r-genomicfeatures/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RGenomicfeatures(RPackage):
-    """Conveniently import and query gene models
+    """Conveniently import and query gene models.
 
        A set of tools and methods for making and manipulating transcript
        centric annotations. With these tools the user can easily download the
@@ -18,9 +18,9 @@ class RGenomicfeatures(RPackage):
        exons, cds and genes. Flexible methods are provided for extracting the
        desired features in a convenient format."""
 
-    homepage = "https://bioconductor.org/packages/GenomicFeatures"
-    git      = "https://git.bioconductor.org/packages/GenomicFeatures.git"
+    bioc = "GenomicFeatures"
 
+    version('1.46.4', commit='d3ab6fd069624904ce7fcdf75dad884473f97975')
     version('1.42.1', commit='2e82891974138b0e976799d64a8938f0be61284d')
     version('1.36.4', commit='28082ec465c91ccaec6881ff348b380edac1b555')
     version('1.34.8', commit='c798b3bb111f4de30632303540074ec1875c1387')
@@ -30,28 +30,31 @@ class RGenomicfeatures(RPackage):
 
     depends_on('r-biocgenerics@0.1.0:', type=('build', 'run'))
     depends_on('r-s4vectors@0.9.47:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.17.29:', when='@1.32.3:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.29:', type=('build', 'run'), when='@1.32.3:')
     depends_on('r-iranges@2.9.19:', type=('build', 'run'))
-    depends_on('r-iranges@2.11.16:', when='@1.30.3:', type=('build', 'run'))
-    depends_on('r-iranges@2.13.23:', when='@1.32.3:', type=('build', 'run'))
+    depends_on('r-iranges@2.11.16:', type=('build', 'run'), when='@1.30.3:')
+    depends_on('r-iranges@2.13.23:', type=('build', 'run'), when='@1.32.3:')
     depends_on('r-genomeinfodb@1.11.4:', type=('build', 'run'))
-    depends_on('r-genomeinfodb@1.13.1:', when='@1.30.3:', type=('build', 'run'))
-    depends_on('r-genomeinfodb@1.15.4:', when='@1.32.3:', type=('build', 'run'))
-    depends_on('r-genomeinfodb@1.25.7:', when='@1.42.1:', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.13.1:', type=('build', 'run'), when='@1.30.3:')
+    depends_on('r-genomeinfodb@1.15.4:', type=('build', 'run'), when='@1.32.3:')
+    depends_on('r-genomeinfodb@1.25.7:', type=('build', 'run'), when='@1.42.1:')
     depends_on('r-genomicranges@1.27.6:', type=('build', 'run'))
-    depends_on('r-genomicranges@1.29.14:', when='@1.30.3:', type=('build', 'run'))
-    depends_on('r-genomicranges@1.31.17:', when='@1.32.3:', type=('build', 'run'))
+    depends_on('r-genomicranges@1.29.14:', type=('build', 'run'), when='@1.30.3:')
+    depends_on('r-genomicranges@1.31.17:', type=('build', 'run'), when='@1.32.3:')
     depends_on('r-annotationdbi@1.33.15:', type=('build', 'run'))
-    depends_on('r-annotationdbi@1.41.4:', when='@1.32.3:', type=('build', 'run'))
+    depends_on('r-annotationdbi@1.41.4:', type=('build', 'run'), when='@1.32.3:')
     depends_on('r-dbi', type=('build', 'run'))
     depends_on('r-rsqlite@2.0:', type=('build', 'run'))
     depends_on('r-rcurl', type=('build', 'run'))
     depends_on('r-xvector', type=('build', 'run'))
-    depends_on('r-xvector@0.19.7:', when='@1.32.3:', type=('build', 'run'))
+    depends_on('r-xvector@0.19.7:', type=('build', 'run'), when='@1.32.3:')
     depends_on('r-biostrings@2.23.3:', type=('build', 'run'))
-    depends_on('r-biostrings@2.47.6:', when='@1.32.3:', type=('build', 'run'))
+    depends_on('r-biostrings@2.47.6:', type=('build', 'run'), when='@1.32.3:')
+    depends_on('r-biocio', type=('build', 'run'), when='@1.46.4:')
     depends_on('r-rtracklayer@1.29.24:', type=('build', 'run'))
-    depends_on('r-rtracklayer@1.39.7:', when='@1.32.3:', type=('build', 'run'))
+    depends_on('r-rtracklayer@1.39.7:', type=('build', 'run'), when='@1.32.3:')
+    depends_on('r-rtracklayer@1.51.5:', type=('build', 'run'), when='@1.46.4:')
     depends_on('r-biomart@2.17.1:', type=('build', 'run'))
     depends_on('r-biobase@2.15.1:', type=('build', 'run'))
-    depends_on('r-rmysql', when='@1.30.3', type=('build', 'run'))
+
+    depends_on('r-rmysql', type=('build', 'run'), when='@1.30.3')
diff --git a/var/spack/repos/builtin/packages/r-genomicranges/package.py b/var/spack/repos/builtin/packages/r-genomicranges/package.py
index a05ef0301c..1a8549fafe 100644
--- a/var/spack/repos/builtin/packages/r-genomicranges/package.py
+++ b/var/spack/repos/builtin/packages/r-genomicranges/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RGenomicranges(RPackage):
-    """Representation and manipulation of genomic intervals
+    """Representation and manipulation of genomic intervals.
 
        The ability to efficiently represent and manipulate genomic annotations
        and alignments is playing a central role when it comes to analyzing
@@ -20,9 +20,9 @@ class RGenomicranges(RPackage):
        respectively. Both packages build on top of the GenomicRanges
        infrastructure."""
 
-    homepage = "https://bioconductor.org/packages/GenomicRanges"
-    git      = "https://git.bioconductor.org/packages/GenomicRanges.git"
+    bioc = "GenomicRanges"
 
+    version('1.46.1', commit='e422642f64815cdfee8fc340681ad87a7eafc3bb')
     version('1.42.0', commit='32baca734b599d60fa13bdbe31c5712e648f538d')
     version('1.36.1', commit='418e7e5647dd54d81b804455ddfcbc027fd0164a')
     version('1.34.0', commit='ebaad5ca61abb67c2c30c132e07531ba4257bccd')
@@ -31,21 +31,23 @@ class RGenomicranges(RPackage):
     version('1.28.6', commit='197472d618f3ed04c795dc6ed435500c29619563')
 
     depends_on('r@2.10:', type=('build', 'run'))
+    depends_on('r@4.0.0:', type=('build', 'run'), when='@1.46.1:')
     depends_on('r-biocgenerics@0.21.2:', type=('build', 'run'))
-    depends_on('r-biocgenerics@0.25.3:', when='@1.32.7:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.25.3:', type=('build', 'run'), when='@1.32.7:')
+    depends_on('r-biocgenerics@0.37.0:', type=('build', 'run'), when='@1.46.1:')
     depends_on('r-s4vectors@0.9.47:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.17.32:', when='@1.32.7:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.19.11:', when='@1.34.0:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.27.12:', when='@1.42.0:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.32:', type=('build', 'run'), when='@1.32.7:')
+    depends_on('r-s4vectors@0.19.11:', type=('build', 'run'), when='@1.34.0:')
+    depends_on('r-s4vectors@0.27.12:', type=('build', 'run'), when='@1.42.0:')
     depends_on('r-iranges@2.9.11:', type=('build', 'run'))
-    depends_on('r-iranges@2.11.16:', when='@1.30.3:', type=('build', 'run'))
-    depends_on('r-iranges@2.14.4:', when='@1.32.7:', type=('build', 'run'))
-    depends_on('r-iranges@2.15.12:', when='@1.34.0:', type=('build', 'run'))
-    depends_on('r-iranges@2.17.1:', when='@1.36.1:', type=('build', 'run'))
-    depends_on('r-iranges@2.23.9:', when='@1.42.0:', type=('build', 'run'))
+    depends_on('r-iranges@2.11.16:', type=('build', 'run'), when='@1.30.3:')
+    depends_on('r-iranges@2.14.4:', type=('build', 'run'), when='@1.32.7:')
+    depends_on('r-iranges@2.15.12:', type=('build', 'run'), when='@1.34.0:')
+    depends_on('r-iranges@2.17.1:', type=('build', 'run'), when='@1.36.1:')
+    depends_on('r-iranges@2.23.9:', type=('build', 'run'), when='@1.42.0:')
     depends_on('r-genomeinfodb@1.11.5:', type=('build', 'run'))
-    depends_on('r-genomeinfodb@1.13.1:', when='@1.30.3:', type=('build', 'run'))
-    depends_on('r-genomeinfodb@1.15.2:', when='@1.32.7:', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.13.1:', type=('build', 'run'), when='@1.30.3:')
+    depends_on('r-genomeinfodb@1.15.2:', type=('build', 'run'), when='@1.32.7:')
     depends_on('r-xvector', type=('build', 'run'))
-    depends_on('r-xvector@0.19.8:', when='@1.32.7:', type=('build', 'run'))
-    depends_on('r-xvector@0.29.2:', when='@1.42.0:', type=('build', 'run'))
+    depends_on('r-xvector@0.19.8:', type=('build', 'run'), when='@1.32.7:')
+    depends_on('r-xvector@0.29.2:', type=('build', 'run'), when='@1.42.0:')
diff --git a/var/spack/repos/builtin/packages/r-geoquery/package.py b/var/spack/repos/builtin/packages/r-geoquery/package.py
index 78d4b62870..efbde50ef9 100644
--- a/var/spack/repos/builtin/packages/r-geoquery/package.py
+++ b/var/spack/repos/builtin/packages/r-geoquery/package.py
@@ -7,16 +7,16 @@ from spack import *
 
 
 class RGeoquery(RPackage):
-    """Get data from NCBI Gene Expression Omnibus (GEO)
+    """Get data from NCBI Gene Expression Omnibus (GEO).
 
        The NCBI Gene Expression Omnibus (GEO) is a public repository of
        microarray data. Given the rich and varied nature of this resource, it
        is only natural to want to apply BioConductor tools to these data.
        GEOquery is the bridge between GEO and BioConductor."""
 
-    homepage = "https://bioconductor.org/packages/GEOquery"
-    git      = "https://git.bioconductor.org/packages/GEOquery.git"
+    bioc = "GEOquery"
 
+    version('2.62.2', commit='1966c108fe8a58ac39ef53c3c452fd160efa526e')
     version('2.58.0', commit='6332ca3791ddcfb233b9ad75b5904b3d60f49b93')
     version('2.52.0', commit='3059331eb82ad4947c2d1bef86ff9526e70af643')
     version('2.50.5', commit='135c17f8fe535acda14f95a37d1be1ff2bd80f97')
@@ -26,12 +26,15 @@ class RGeoquery(RPackage):
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-httr', type=('build', 'run'))
-    depends_on('r-readr', when='@2.46.15:', type=('build', 'run'))
-    depends_on('r-readr@1.3.1:', when='@2.50.5:', type=('build', 'run'))
-    depends_on('r-xml2', when='@2.46.15:', type=('build', 'run'))
-    depends_on('r-dplyr', when='@2.46.15:', type=('build', 'run'))
-    depends_on('r-tidyr', when='@2.46.15:', type=('build', 'run'))
-    depends_on('r-magrittr', when='@2.46.15:', type=('build', 'run'))
-    depends_on('r-limma', when='@2.46.15:', type=('build', 'run'))
-    depends_on('r-xml', when='@2.42.0', type=('build', 'run'))
-    depends_on('r-rcurl', when='@2.42.0', type=('build', 'run'))
+    depends_on('r-readr', type=('build', 'run'), when='@2.46.15:')
+    depends_on('r-readr@1.3.1:', type=('build', 'run'), when='@2.50.5:')
+    depends_on('r-xml2', type=('build', 'run'), when='@2.46.15:')
+    depends_on('r-dplyr', type=('build', 'run'), when='@2.46.15:')
+    depends_on('r-data-table', type=('build', 'run'), when='@2.62.2:')
+    depends_on('r-tidyr', type=('build', 'run'), when='@2.46.15:')
+    depends_on('r-magrittr', type=('build', 'run'), when='@2.46.15:')
+    depends_on('r-r-utils', type=('build', 'run'), when='@2.62.2:')
+    depends_on('r-limma', type=('build', 'run'), when='@2.46.15:')
+
+    depends_on('r-xml', type=('build', 'run'), when='@2.42.0')
+    depends_on('r-rcurl', type=('build', 'run'), when='@2.42.0')
diff --git a/var/spack/repos/builtin/packages/r-ggbio/package.py b/var/spack/repos/builtin/packages/r-ggbio/package.py
index 6c0d43b6dd..67d6f04a1b 100644
--- a/var/spack/repos/builtin/packages/r-ggbio/package.py
+++ b/var/spack/repos/builtin/packages/r-ggbio/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RGgbio(RPackage):
-    """Visualization tools for genomic data
+    """Visualization tools for genomic data.
 
        The ggbio package extends and specializes the grammar of graphics for
        biological data. The graphics are designed to answer common scientific
@@ -19,9 +19,9 @@ class RGgbio(RPackage):
        fragment length, edge-linked interval to data view, mismatch pileup, and
        several splicing summaries."""
 
-    homepage = "https://bioconductor.org/packages/ggbio"
-    git      = "https://git.bioconductor.org/packages/ggbio.git"
+    bioc = "ggbio"
 
+    version('1.42.0', commit='3540047ef018957d59fba8af7d3c58e4659f8e26')
     version('1.38.0', commit='c39c51993f419cfc2f094e664477f25f5212a242')
     version('1.32.0', commit='04bd12fbe0b1c5c6b721a5f927e1352765f9bf88')
     version('1.30.0', commit='8b05258b089b06a743352e92058edda06c24cfb7')
@@ -37,15 +37,15 @@ class RGgbio(RPackage):
     depends_on('r-gtable', type=('build', 'run'))
     depends_on('r-hmisc', type=('build', 'run'))
     depends_on('r-biovizbase@1.23.3:', type=('build', 'run'))
-    depends_on('r-biovizbase@1.28.2:', when='@1.28.5:', type=('build', 'run'))
-    depends_on('r-biovizbase@1.29.2:', when='@1.30.0:', type=('build', 'run'))
+    depends_on('r-biovizbase@1.28.2:', type=('build', 'run'), when='@1.28.5:')
+    depends_on('r-biovizbase@1.29.2:', type=('build', 'run'), when='@1.30.0:')
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
-    depends_on('r-iranges@2.11.16:', when='@1.26.1:', type=('build', 'run'))
+    depends_on('r-iranges@2.11.16:', type=('build', 'run'), when='@1.26.1:')
     depends_on('r-genomeinfodb@1.1.3:', type=('build', 'run'))
     depends_on('r-genomicranges@1.21.10:', type=('build', 'run'))
-    depends_on('r-genomicranges@1.29.14:', when='@1.26.1:', type=('build', 'run'))
+    depends_on('r-genomicranges@1.29.14:', type=('build', 'run'), when='@1.26.1:')
     depends_on('r-summarizedexperiment', type=('build', 'run'))
     depends_on('r-biostrings', type=('build', 'run'))
     depends_on('r-rsamtools@1.17.28:', type=('build', 'run'))
@@ -54,10 +54,10 @@ class RGgbio(RPackage):
     depends_on('r-variantannotation@1.11.4:', type=('build', 'run'))
     depends_on('r-rtracklayer@1.25.16:', type=('build', 'run'))
     depends_on('r-genomicfeatures@1.17.13:', type=('build', 'run'))
-    depends_on('r-genomicfeatures@1.29.11:', when='@1.26.1:', type=('build', 'run'))
+    depends_on('r-genomicfeatures@1.29.11:', type=('build', 'run'), when='@1.26.1:')
     depends_on('r-organismdbi', type=('build', 'run'))
     depends_on('r-ggally', type=('build', 'run'))
     depends_on('r-ensembldb@1.99.13:', type=('build', 'run'))
     depends_on('r-annotationdbi', type=('build', 'run'))
     depends_on('r-annotationfilter', type=('build', 'run'))
-    depends_on('r-rlang', when='@1.28.5:', type=('build', 'run'))
+    depends_on('r-rlang', type=('build', 'run'), when='@1.28.5:')
diff --git a/var/spack/repos/builtin/packages/r-ggtree/package.py b/var/spack/repos/builtin/packages/r-ggtree/package.py
new file mode 100644
index 0000000000..b3836e724f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ggtree/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RGgtree(RPackage):
+    """an R package for visualization of tree and annotation data.
+
+    'ggtree' extends the 'ggplot2' plotting system which implemented the
+    grammar of graphics. 'ggtree' is designed for visualization and annotation
+    of phylogenetic trees and other tree-like structures with their annotation
+    data."""
+
+    bioc = "ggtree"
+
+    version('3.2.1', commit='d3747e636fe1a6a9e09b56a3a3899208ebd05547')
+
+    depends_on('r@3.5.0:', type=('build', 'run'))
+    depends_on('r-ape', type=('build', 'run'))
+    depends_on('r-aplot@0.0.4:', type=('build', 'run'))
+    depends_on('r-dplyr', type=('build', 'run'))
+    depends_on('r-ggplot2@3.0.0:', type=('build', 'run'))
+    depends_on('r-magrittr', type=('build', 'run'))
+    depends_on('r-purrr', type=('build', 'run'))
+    depends_on('r-rlang', type=('build', 'run'))
+    depends_on('r-ggfun', type=('build', 'run'))
+    depends_on('r-yulab-utils', type=('build', 'run'))
+    depends_on('r-tidyr', type=('build', 'run'))
+    depends_on('r-tidytree@0.2.6:', type=('build', 'run'))
+    depends_on('r-treeio@1.8.0:', type=('build', 'run'))
+    depends_on('r-scales', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-glimma/package.py b/var/spack/repos/builtin/packages/r-glimma/package.py
index ca1adb43d2..ac5fa1b5e3 100644
--- a/var/spack/repos/builtin/packages/r-glimma/package.py
+++ b/var/spack/repos/builtin/packages/r-glimma/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RGlimma(RPackage):
-    """Interactive HTML graphics
+    """Interactive HTML graphics.
 
        This package generates interactive visualisations for analysis of RNA-
        sequencing data using output from limma, edgeR or DESeq2 packages in an
@@ -15,9 +15,9 @@ class RGlimma(RPackage):
        representations of analysis results in order to provide additional
        information."""
 
-    homepage = "https://bioconductor.org/packages/Glimma"
-    git      = "https://git.bioconductor.org/packages/Glimma.git"
+    bioc = "Glimma"
 
+    version('2.4.0', commit='caa270e44ec6994035d2e915c0f68a14ccbb58db')
     version('2.0.0', commit='40bebaa79e8c87c5686cff7285def4461c11bca9')
     version('1.12.0', commit='d02174239fe0b47983d6947ed42a1a53b24caecb')
     version('1.10.1', commit='ffc7abc36190396598fadec5e9c653441e47be72')
@@ -26,14 +26,15 @@ class RGlimma(RPackage):
     version('1.4.0', commit='c613c5334ed7868f36d5716b97fdb6234fb291f8')
 
     depends_on('r@3.3.0:', type=('build', 'run'))
-    depends_on('r@3.4.0:', when='@1.6.0:', type=('build', 'run'))
-    depends_on('r@4.0.0:', when='@2.0.0:', type=('build', 'run'))
-    depends_on('r-htmlwidgets', when='@2.0.0:', type=('build', 'run'))
+    depends_on('r@3.4.0:', type=('build', 'run'), when='@1.6.0:')
+    depends_on('r@4.0.0:', type=('build', 'run'), when='@2.0.0:')
+    depends_on('r-htmlwidgets', type=('build', 'run'), when='@2.0.0:')
     depends_on('r-edger', type=('build', 'run'))
-    depends_on('r-deseq2', when='@2.0.0:', type=('build', 'run'))
-    depends_on('r-limma', when='@2.0.0:', type=('build', 'run'))
-    depends_on('r-summarizedexperiment', when='@2.0.0:', type=('build', 'run'))
+    depends_on('r-deseq2', type=('build', 'run'), when='@2.0.0:')
+    depends_on('r-limma', type=('build', 'run'), when='@2.0.0:')
+    depends_on('r-summarizedexperiment', type=('build', 'run'), when='@2.0.0:')
     depends_on('r-jsonlite', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
-    depends_on('r-biobase', when='@1.4.0:1.6.0', type=('build', 'run'))
-    depends_on('r-scater', when='@1.4.0', type=('build', 'run'))
+
+    depends_on('r-biobase', type=('build', 'run'), when='@1.4.0:1.6.0')
+    depends_on('r-scater', type=('build', 'run'), when='@1.4.0')
diff --git a/var/spack/repos/builtin/packages/r-globaltest/package.py b/var/spack/repos/builtin/packages/r-globaltest/package.py
index ff024d53d3..0288a9a226 100644
--- a/var/spack/repos/builtin/packages/r-globaltest/package.py
+++ b/var/spack/repos/builtin/packages/r-globaltest/package.py
@@ -8,7 +8,7 @@ from spack import *
 
 class RGlobaltest(RPackage):
     """Testing Groups of Covariates/Features for Association with a Response
-    Variable, with Applications to Gene Set Testing:
+    Variable, with Applications to Gene Set Testing.
 
     The global test tests groups of covariates (or features) for association
     with a response variable. This package implements the test with diagnostic
@@ -16,8 +16,9 @@ class RGlobaltest(RPackage):
     facilitate the use of this test for gene set testing of GO and KEGG
     terms."""
 
-    bioc     = "globaltest"
+    bioc = "globaltest"
 
+    version('5.48.0', commit='86c2c8f35734dcbc8c8ca791d8a190dc525beac9')
     version('5.44.0', commit='571933d5c779a241740be913ff49ecdd59bcbc45')
 
     depends_on('r-survival', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-go-db/package.py b/var/spack/repos/builtin/packages/r-go-db/package.py
index cebbae210f..27143c2433 100644
--- a/var/spack/repos/builtin/packages/r-go-db/package.py
+++ b/var/spack/repos/builtin/packages/r-go-db/package.py
@@ -7,14 +7,17 @@ from spack import *
 
 
 class RGoDb(RPackage):
-    """A set of annotation maps describing the entire Gene Ontology
+    """A set of annotation maps describing the entire Gene Ontology.
 
     A set of annotation maps describing the entire Gene
     Ontology assembled using data from GO."""
 
-    homepage = "https://www.bioconductor.org/packages/GO.db/"
-    url      = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/GO.db_3.4.1.tar.gz"
+    bioc = "GO.db"
+    url = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/GO.db_3.4.1.tar.gz"
 
+    version('3.14.0',
+            sha256='45d0a681a662667d45b2472d160b72f7058ad0a28dd0ca24742e11ddfd87d8e7',
+            url='https://bioconductor.org/packages/3.14/data/annotation/src/contrib/GO.db_3.14.0.tar.gz')
     version('3.12.1',
             sha256='e0316959d3d32096f9432c897413dff74fce53e15ead7917a7724467d971dab9',
             url='https://bioconductor.org/packages/3.12/data/annotation/src/contrib/GO.db_3.12.1.tar.gz')
@@ -24,4 +27,5 @@ class RGoDb(RPackage):
 
     depends_on('r@2.7.0:', type=('build', 'run'))
     depends_on('r-annotationdbi@1.37.4:', type=('build', 'run'))
-    depends_on('r-annotationdbi@1.51.3:', when='@3.12.1:', type=('build', 'run'))
+    depends_on('r-annotationdbi@1.51.3:', type=('build', 'run'), when='@3.12.1:')
+    depends_on('r-annotationdbi@1.55.1:', type=('build', 'run'), when='@3.14.0:')
diff --git a/var/spack/repos/builtin/packages/r-gofuncr/package.py b/var/spack/repos/builtin/packages/r-gofuncr/package.py
index c5413ca1e6..77351853e7 100644
--- a/var/spack/repos/builtin/packages/r-gofuncr/package.py
+++ b/var/spack/repos/builtin/packages/r-gofuncr/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RGofuncr(RPackage):
-    """Gene ontology enrichment using FUNC
+    """Gene ontology enrichment using FUNC.
 
        GOfuncR performs a gene ontology enrichment analysis based on the
        ontology enrichment software FUNC. GO-annotations are obtained from
@@ -26,9 +26,9 @@ class RGofuncr(RPackage):
        genes into account. It is also possible to provide custom gene
        coordinates, annotations and ontologies."""
 
-    homepage = "https://bioconductor.org/packages/GOfuncR"
-    git      = "https://git.bioconductor.org/packages/GOfuncR.git"
+    bioc = "GOfuncR"
 
+    version('1.14.0', commit='b3d445acf95851241d1fdb673d108ee115bdc17b')
     version('1.10.0', commit='51b01a2b9afa03fde2e1628036096cbeafaa2ef4')
     version('1.4.0', commit='2f633dc28e3faeddc5346fcdcadf1c29e3fcf709')
     version('1.2.0', commit='140a3cea4fe34d32fef9be756f85e337ce3deded')
@@ -41,5 +41,5 @@ class RGofuncr(RPackage):
     depends_on('r-mapplots@1.5:', type=('build', 'run'))
     depends_on('r-gtools@3.5.0:', type=('build', 'run'))
     depends_on('r-genomicranges@1.28.4:', type=('build', 'run'))
-    depends_on('r-iranges', when='@1.2.0:', type=('build', 'run'))
+    depends_on('r-iranges', type=('build', 'run'), when='@1.2.0:')
     depends_on('r-annotationdbi', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-gosemsim/package.py b/var/spack/repos/builtin/packages/r-gosemsim/package.py
index e2dcdd1b69..66ea0ad631 100644
--- a/var/spack/repos/builtin/packages/r-gosemsim/package.py
+++ b/var/spack/repos/builtin/packages/r-gosemsim/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RGosemsim(RPackage):
-    """GO-terms Semantic Similarity Measures
+    """GO-terms Semantic Similarity Measures.
 
        The semantic comparisons of Gene Ontology (GO) annotations provide
        quantitative ways to compute similarities between genes and gene groups,
@@ -17,9 +17,9 @@ class RGosemsim(RPackage):
        GOSemSim implemented five methods proposed by Resnik, Schlicker, Jiang,
        Lin and Wang respectively."""
 
-    homepage = "https://bioconductor.org/packages/GOSemSim"
-    git      = "https://git.bioconductor.org/packages/GOSemSim.git"
+    bioc = "GOSemSim"
 
+    version('2.20.0', commit='fa82442aaa4ad1a8dacc05ee2c54f5e5e770a794')
     version('2.16.1', commit='92f1d567f3584fe488f434abce87c2e1950081c0')
     version('2.10.0', commit='5db1ecbf2f8d870430d6e587609327d05ba3ad7b')
     version('2.8.0', commit='c8c985b2a814cc2365c7f05b2509205e1b6b7f58')
@@ -28,8 +28,8 @@ class RGosemsim(RPackage):
     version('2.2.0', commit='247434790e6c8cf99e5643f569390362b8c87c52')
 
     depends_on('r@3.3.2:', type=('build', 'run'))
-    depends_on('r@3.4.0:', when='@2.8.0:', type=('build', 'run'))
-    depends_on('r@3.5.0:', when='@2.16.1:', type=('build', 'run'))
+    depends_on('r@3.4.0:', type=('build', 'run'), when='@2.8.0:')
+    depends_on('r@3.5.0:', type=('build', 'run'), when='@2.16.1:')
     depends_on('r-annotationdbi', type=('build', 'run'))
     depends_on('r-go-db', type=('build', 'run'))
     depends_on('r-rcpp', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-goseq/package.py b/var/spack/repos/builtin/packages/r-goseq/package.py
index 359591879d..b34c5c38cc 100644
--- a/var/spack/repos/builtin/packages/r-goseq/package.py
+++ b/var/spack/repos/builtin/packages/r-goseq/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RGoseq(RPackage):
-    """Gene Ontology analyser for RNA-seq and other length biased data
+    """Gene Ontology analyser for RNA-seq and other length biased data.
 
        Detects Gene Ontology and/or other user defined categories which are
        over/under represented in RNA-seq data"""
 
-    homepage = "https://bioconductor.org/packages/goseq"
-    git      = "https://git.bioconductor.org/packages/goseq.git"
+    bioc = "goseq"
 
+    version('1.46.0', commit='1fb5626cc80f595499af511a830322ed12bbe144')
     version('1.42.0', commit='8164b90e7505bbc1035105fdc15219c764ef8b8d')
     version('1.36.0', commit='26c9f7de18889afeee1b571ca1c4ab4d2877ab80')
     version('1.34.1', commit='bad217b42cc34423698fbcf701d4e3591aac4474')
diff --git a/var/spack/repos/builtin/packages/r-gostats/package.py b/var/spack/repos/builtin/packages/r-gostats/package.py
index d7e5b11634..e54f0669aa 100644
--- a/var/spack/repos/builtin/packages/r-gostats/package.py
+++ b/var/spack/repos/builtin/packages/r-gostats/package.py
@@ -7,15 +7,15 @@ from spack import *
 
 
 class RGostats(RPackage):
-    """Tools for manipulating GO and microarrays
+    """Tools for manipulating GO and microarrays.
 
        A set of tools for interacting with GO and microarray data. A variety of
        basic manipulation tools for graphs, hypothesis testing and other simple
        calculations."""
 
-    homepage = "https://bioconductor.org/packages/GOstats"
-    git      = "https://git.bioconductor.org/packages/GOstats.git"
+    bioc = "GOstats"
 
+    version('2.60.0', commit='a20055cc1c04a91b0291a918dadd9ea912c187ce')
     version('2.56.0', commit='8f988c3b4b1ce7e05626aae8956004c7bbdd6f3a')
     version('2.50.0', commit='ee13f84341988d537a5485dcdcfb71f69e6e4930')
     version('2.48.0', commit='5db7020f4bab725cd729b32bd1d5e819b31f2485')
@@ -27,12 +27,12 @@ class RGostats(RPackage):
     depends_on('r@2.10:', type=('build', 'run'))
     depends_on('r-biobase@1.15.29:', type=('build', 'run'))
     depends_on('r-category@2.3.26:', type=('build', 'run'))
-    depends_on('r-category@2.43.2:', when='@2.44.0:', type=('build', 'run'))
-    depends_on('r-graph@1.15.15:', when='@2.42.0', type=('build', 'run'))
-    depends_on('r-graph', when='@2.44.0:', type=('build', 'run'))
+    depends_on('r-category@2.43.2:', type=('build', 'run'), when='@2.44.0:')
+    depends_on('r-graph', type=('build', 'run'), when='@2.44.0:')
+    depends_on('r-graph@1.15.15:', type=('build', 'run'), when='@2.42.0')
     depends_on('r-annotationdbi@0.0.89:', type=('build', 'run'))
     depends_on('r-go-db@1.13.0:', type=('build', 'run'))
     depends_on('r-rbgl', type=('build', 'run'))
     depends_on('r-annotate@1.13.2:', type=('build', 'run'))
     depends_on('r-annotationforge', type=('build', 'run'))
-    depends_on('r-rgraphviz', when='@2.44.0:', type=('build', 'run'))
+    depends_on('r-rgraphviz', type=('build', 'run'), when='@2.44.0:')
diff --git a/var/spack/repos/builtin/packages/r-graph/package.py b/var/spack/repos/builtin/packages/r-graph/package.py
index c93e163db2..4a41f2793a 100644
--- a/var/spack/repos/builtin/packages/r-graph/package.py
+++ b/var/spack/repos/builtin/packages/r-graph/package.py
@@ -7,13 +7,13 @@ from spack import *
 
 
 class RGraph(RPackage):
-    """graph: A package to handle graph data structures
+    """A package to handle graph data structures.
 
        A package that implements some simple graph handling capabilities."""
 
-    homepage = "https://bioconductor.org/packages/graph"
-    git      = "https://git.bioconductor.org/packages/graph.git"
+    bioc = "graph"
 
+    version('1.72.0', commit='7afbd26ecd76e55e6bbd74915a561d7a9b15f907')
     version('1.68.0', commit='03ad9ed088095605e317510b8234501318994e94')
     version('1.62.0', commit='95223bd63ceb66cfe8d881f992a441de8b8c89a3')
     version('1.60.0', commit='e2aecb0a862f32091b16e0036f53367d3edf4c1d')
diff --git a/var/spack/repos/builtin/packages/r-gseabase/package.py b/var/spack/repos/builtin/packages/r-gseabase/package.py
index ab25e569f4..829f317cb5 100644
--- a/var/spack/repos/builtin/packages/r-gseabase/package.py
+++ b/var/spack/repos/builtin/packages/r-gseabase/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RGseabase(RPackage):
-    """Gene set enrichment data structures and methods
+    """Gene set enrichment data structures and methods.
 
        This package provides classes and methods to support Gene Set Enrichment
        Analysis (GSEA)."""
 
-    homepage = "https://bioconductor.org/packages/GSEABase"
-    git      = "https://git.bioconductor.org/packages/GSEABase.git"
+    bioc = "GSEABase"
 
+    version('1.56.0', commit='ee7c3ca4ad0f1f3e9b9162db1515413802860ecc')
     version('1.52.1', commit='257dfccbc5b507d82099fac6b06bb03825e995e8')
     version('1.46.0', commit='edce83a9256a0c03206c2bce7c90ada0d90f6622')
     version('1.44.0', commit='7042ff64a98b05b9572231ee1b4f3ae4fc9c768e')
diff --git a/var/spack/repos/builtin/packages/r-gtrellis/package.py b/var/spack/repos/builtin/packages/r-gtrellis/package.py
index 687dc18f94..b9c06d4b04 100644
--- a/var/spack/repos/builtin/packages/r-gtrellis/package.py
+++ b/var/spack/repos/builtin/packages/r-gtrellis/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RGtrellis(RPackage):
-    """Genome Level Trellis Layout
+    """Genome Level Trellis Layout.
 
        Genome level Trellis graph visualizes genomic data conditioned by
        genomic categories (e.g. chromosomes). For each genomic category,
@@ -16,9 +16,9 @@ class RGtrellis(RPackage):
        flexibility to arrange genomic categories and to add self-defined
        graphics in the plot."""
 
-    homepage = "https://bioconductor.org/packages/gtrellis"
-    git      = "https://git.bioconductor.org/packages/gtrellis.git"
+    bioc = "gtrellis"
 
+    version('1.26.0', commit='f2c3121b31ad1b422e2cf503435d0590e903ff3f')
     version('1.22.0', commit='c071c5631f3dedda212aed87d9c02954b5ed6611')
     version('1.16.1', commit='a9003ededc8f2a48c78d4545e2f214023c13a7da')
     version('1.14.0', commit='93935fb34211d12b250e22291712e18a31b0208d')
@@ -30,5 +30,5 @@ class RGtrellis(RPackage):
     depends_on('r-iranges', type=('build', 'run'))
     depends_on('r-genomicranges', type=('build', 'run'))
     depends_on('r-circlize@0.3.3:', type=('build', 'run'))
-    depends_on('r-circlize@0.4.8:', when='@1.16.1', type=('build', 'run'))
+    depends_on('r-circlize@0.4.8:', type=('build', 'run'), when='@1.16.1')
     depends_on('r-getoptlong', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-gviz/package.py b/var/spack/repos/builtin/packages/r-gviz/package.py
index 515f0df108..98d8c1e096 100644
--- a/var/spack/repos/builtin/packages/r-gviz/package.py
+++ b/var/spack/repos/builtin/packages/r-gviz/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RGviz(RPackage):
-    """Plotting data and annotation information along genomic coordinates
+    """Plotting data and annotation information along genomic coordinates.
 
        Genomic data analyses requires integrated visualization of known genomic
        information and new experimental data. Gviz uses the biomaRt and the
@@ -16,9 +16,9 @@ class RGviz(RPackage):
        of the grid graphics package. This results in genomic information
        plotted together with your data."""
 
-    homepage = "https://bioconductor.org/packages/Gviz"
-    git      = "https://git.bioconductor.org/packages/Gviz.git"
+    bioc = "Gviz"
 
+    version('1.38.3', commit='c4b352a16455a5744533c511e59354977814cb9e')
     version('1.34.0', commit='445fadff2aedd8734580fa908aa47ff1216a8182')
     version('1.28.3', commit='20b9825af144cfc888629c34aa980b5bbd65bf86')
     version('1.26.5', commit='430310b9d2e098f9757a71d26a2f69871071f30c')
@@ -27,7 +27,8 @@ class RGviz(RPackage):
     version('1.20.0', commit='299b8255e1b03932cebe287c3690d58c88f5ba5c')
 
     depends_on('r@2.10.0:', type=('build', 'run'))
-    depends_on('r@4.0:', when='@1.34.0:', type=('build', 'run'))
+    depends_on('r@4.0:', type=('build', 'run'), when='@1.34.0:')
+    depends_on('r@4.1:', type=('build', 'run'), when='@1.38.3:')
     depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
     depends_on('r-iranges@1.99.18:', type=('build', 'run'))
     depends_on('r-genomicranges@1.17.20:', type=('build', 'run'))
@@ -39,7 +40,7 @@ class RGviz(RPackage):
     depends_on('r-annotationdbi@1.27.5:', type=('build', 'run'))
     depends_on('r-biobase@2.15.3:', type=('build', 'run'))
     depends_on('r-genomicfeatures@1.17.22:', type=('build', 'run'))
-    depends_on('r-ensembldb@2.11.3:', when='@1.34.0:', type=('build', 'run'))
+    depends_on('r-ensembldb@2.11.3:', type=('build', 'run'), when='@1.34.0:')
     depends_on('r-bsgenome@1.33.1:', type=('build', 'run'))
     depends_on('r-biostrings@2.33.11:', type=('build', 'run'))
     depends_on('r-biovizbase@1.13.8:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-hdf5array/package.py b/var/spack/repos/builtin/packages/r-hdf5array/package.py
index 4b39cc23ca..99837921f9 100644
--- a/var/spack/repos/builtin/packages/r-hdf5array/package.py
+++ b/var/spack/repos/builtin/packages/r-hdf5array/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RHdf5array(RPackage):
-    """HDF5 backend for DelayedArray objects
+    """HDF5 backend for DelayedArray objects.
 
        Implements the HDF5Array and TENxMatrix classes, 2 convenient and
        memory-efficient array-like containers for on-disk representation of
@@ -18,9 +18,9 @@ class RHdf5array(RPackage):
        extensions, they support all operations supported by DelayedArray
        objects. These operations can be either delayed or block-processed."""
 
-    homepage = "https://bioconductor.org/packages/HDF5Array"
-    git      = "https://git.bioconductor.org/packages/HDF5Array.git"
+    bioc = "HDF5Array"
 
+    version('1.22.1', commit='b3f091fbc159609e8e0792d2bf9fbef52c6ceede')
     version('1.18.0', commit='d5bd55d170cb384fdebdf60751e1e28483782caa')
     version('1.12.3', commit='21c6077f3f789748a18f2e579110576c5522e975')
     version('1.10.1', commit='0b8ae1dfb56e4203dd8e14781850370df46a5e2c')
@@ -30,21 +30,22 @@ class RHdf5array(RPackage):
 
     depends_on('r@3.4:', type=('build', 'run'))
     depends_on('r-delayedarray@0.2.4:', type=('build', 'run'))
-    depends_on('r-delayedarray@0.3.18:', when='@1.6.0:', type=('build', 'run'))
-    depends_on('r-delayedarray@0.5.32:', when='@1.8.1:', type=('build', 'run'))
-    depends_on('r-delayedarray@0.7.41:', when='@1.10.1:', type=('build', 'run'))
-    depends_on('r-delayedarray@0.9.3:', when='@1.12.3:', type=('build', 'run'))
-    depends_on('r-delayedarray@0.15.16:', when='@1.18.0:', type=('build', 'run'))
+    depends_on('r-delayedarray@0.3.18:', type=('build', 'run'), when='@1.6.0:')
+    depends_on('r-delayedarray@0.5.32:', type=('build', 'run'), when='@1.8.1:')
+    depends_on('r-delayedarray@0.7.41:', type=('build', 'run'), when='@1.10.1:')
+    depends_on('r-delayedarray@0.9.3:', type=('build', 'run'), when='@1.12.3:')
+    depends_on('r-delayedarray@0.15.16:', type=('build', 'run'), when='@1.18.0:')
     depends_on('r-rhdf5', type=('build', 'run'))
-    depends_on('r-rhdf5@2.25.6:', when='@1.10.1:', type=('build', 'run'))
-    depends_on('r-rhdf5@2.31.6:', when='@1.18.0:', type=('build', 'run'))
-    depends_on('r-matrix', when='@1.18.0:', type=('build', 'run'))
+    depends_on('r-rhdf5@2.25.6:', type=('build', 'run'), when='@1.10.1:')
+    depends_on('r-rhdf5@2.31.6:', type=('build', 'run'), when='@1.18.0:')
+    depends_on('r-matrix', type=('build', 'run'), when='@1.18.0:')
+    depends_on('r-rhdf5filters', type=('build', 'run'), when='@1.22.1:')
     depends_on('r-biocgenerics', type=('build', 'run'))
-    depends_on('r-biocgenerics@0.25.1:', when='@1.8.1:', type=('build', 'run'))
-    depends_on('r-biocgenerics@0.31.5:', when='@1.18.0:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.25.1:', type=('build', 'run'), when='@1.8.1:')
+    depends_on('r-biocgenerics@0.31.5:', type=('build', 'run'), when='@1.18.0:')
     depends_on('r-s4vectors', type=('build', 'run'))
-    depends_on('r-s4vectors@0.21.6:', when='@1.12.3:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.27.13:', when='@1.18.0:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.21.6:', type=('build', 'run'), when='@1.12.3:')
+    depends_on('r-s4vectors@0.27.13:', type=('build', 'run'), when='@1.18.0:')
     depends_on('r-iranges', type=('build', 'run'))
-    depends_on('r-rhdf5lib', when='@1.12.3:', type=('build', 'run'))
+    depends_on('r-rhdf5lib', type=('build', 'run'), when='@1.12.3:')
     depends_on('gmake', type='build')
diff --git a/var/spack/repos/builtin/packages/r-hypergraph/package.py b/var/spack/repos/builtin/packages/r-hypergraph/package.py
index 2c0a9c645b..f412aa949d 100644
--- a/var/spack/repos/builtin/packages/r-hypergraph/package.py
+++ b/var/spack/repos/builtin/packages/r-hypergraph/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RHypergraph(RPackage):
-    """A package providing hypergraph data structures
+    """A package providing hypergraph data structures.
 
        A package that implements some simple capabilities for representing and
        manipulating hypergraphs."""
 
-    homepage = "https://bioconductor.org/packages/hypergraph"
-    git      = "https://git.bioconductor.org/packages/hypergraph.git"
+    bioc = "hypergraph"
 
+    version('1.66.0', commit='e9c47336df6409006622818f541f258103163a39')
     version('1.62.0', commit='a286bbb70289e9f3cdf41407d52e5976bd6ed11e')
     version('1.56.0', commit='f8b977fe068f15ecea49d30e77a871a35afcb97b')
     version('1.54.0', commit='cf134b9221e9b5f6329a6786a366f57426c49e7c')
diff --git a/var/spack/repos/builtin/packages/r-illumina450probevariants-db/package.py b/var/spack/repos/builtin/packages/r-illumina450probevariants-db/package.py
index 0e024821f0..2d5c3f8a86 100644
--- a/var/spack/repos/builtin/packages/r-illumina450probevariants-db/package.py
+++ b/var/spack/repos/builtin/packages/r-illumina450probevariants-db/package.py
@@ -8,13 +8,14 @@ from spack import *
 
 class RIllumina450probevariantsDb(RPackage):
     """Annotation Package combining variant data from 1000 Genomes Project for
-    Illumina HumanMethylation450 Bead Chip probes:
+    Illumina HumanMethylation450 Bead Chip probes.
 
     Includes details on variants for each probe on the 450k bead chip for each
     of the four populations (Asian, American, African and European)."""
 
-    bioc     = "Illumina450ProbeVariants.db"
+    bioc = "Illumina450ProbeVariants.db"
 
+    version('1.30.0', commit='ba1296b4aafc287dea61f5f37c6c99fd553e52a2')
     version('1.26.0', commit='fffe6033cc8d87354078c14de1e29976eaedd611')
 
     depends_on('r@3.0.1:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kanno-ilmn12-hg19/package.py b/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kanno-ilmn12-hg19/package.py
index d490a9d4c7..971bb47e79 100644
--- a/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kanno-ilmn12-hg19/package.py
+++ b/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kanno-ilmn12-hg19/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RIlluminahumanmethylation450kannoIlmn12Hg19(RPackage):
-    """Annotation for Illumina's 450k methylation arrays
+    """Annotation for Illumina's 450k methylation arrays.
 
     Manifests and annotation for Illumina's 450k array data."""
 
     # This package is available via bioconductor but there is no available git
     # repository.
-    homepage = "https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylation450kanno.ilmn12.hg19.html"
-    url      = "https://bioconductor.org/packages/release/data/annotation/src/contrib/IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0.tar.gz"
+    bioc = "IlluminaHumanMethylation450kanno.ilmn12.hg19"
+    url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0.tar.gz"
 
     version('0.6.0', sha256='249b8fd62add3c95b5047b597cff0868d26a98862a47cebd656edcd175a73b15')
 
diff --git a/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kmanifest/package.py b/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kmanifest/package.py
index 00e241aafe..cc217f85d1 100644
--- a/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kmanifest/package.py
+++ b/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kmanifest/package.py
@@ -7,10 +7,10 @@ from spack import *
 
 
 class RIlluminahumanmethylation450kmanifest(RPackage):
-    """Annotation for Illumina's 450k methylation arrays"""
+    """Annotation for Illumina's 450k methylation arrays."""
 
-    url      = "https://bioconductor.org/packages/release/data/annotation/src/contrib/IlluminaHumanMethylation450kmanifest_0.4.0.tar.gz"
-    bioc     = "IlluminaHumanMethylation450kmanifest"
+    bioc = "IlluminaHumanMethylation450kmanifest"
+    url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/IlluminaHumanMethylation450kmanifest_0.4.0.tar.gz"
 
     version('0.4.0', sha256='41b2e54bac3feafc7646fe40bce3aa2b92c10871b0a13657c5736517792fa763')
 
diff --git a/var/spack/repos/builtin/packages/r-illuminahumanmethylationepicanno-ilm10b4-hg19/package.py b/var/spack/repos/builtin/packages/r-illuminahumanmethylationepicanno-ilm10b4-hg19/package.py
index eff3f09d04..f2bc5755d4 100644
--- a/var/spack/repos/builtin/packages/r-illuminahumanmethylationepicanno-ilm10b4-hg19/package.py
+++ b/var/spack/repos/builtin/packages/r-illuminahumanmethylationepicanno-ilm10b4-hg19/package.py
@@ -7,10 +7,10 @@ from spack import *
 
 
 class RIlluminahumanmethylationepicannoIlm10b4Hg19(RPackage):
-    """Annotation for Illumina's EPIC methylation arrays"""
+    """Annotation for Illumina's EPIC methylation arrays."""
 
-    url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0.tar.gz"
     bioc = "IlluminaHumanMethylationEPICanno.ilm10b4.hg19"
+    url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0.tar.gz"
 
     version('0.6.0', sha256='2c8128126b63e7fa805a5f3b02449367dca9c3be3eb5f6300acc718826590719')
 
diff --git a/var/spack/repos/builtin/packages/r-illuminahumanmethylationepicmanifest/package.py b/var/spack/repos/builtin/packages/r-illuminahumanmethylationepicmanifest/package.py
index 12571f6744..8e40918a1e 100644
--- a/var/spack/repos/builtin/packages/r-illuminahumanmethylationepicmanifest/package.py
+++ b/var/spack/repos/builtin/packages/r-illuminahumanmethylationepicmanifest/package.py
@@ -7,10 +7,10 @@ from spack import *
 
 
 class RIlluminahumanmethylationepicmanifest(RPackage):
-    """Manifest for Illumina's EPIC methylation arrays"""
+    """Manifest for Illumina's EPIC methylation arrays."""
 
-    url      = "https://bioconductor.org/packages/release/data/annotation/src/contrib/IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz"
-    bioc     = "IlluminaHumanMethylationEPICmanifest"
+    bioc = "IlluminaHumanMethylationEPICmanifest"
+    url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz"
 
     version('0.3.0', sha256='e39a69d98486cec981e97c56f45bbe47d2ccb5bbb66a1b16fa0685575493902a')
 
diff --git a/var/spack/repos/builtin/packages/r-illuminaio/package.py b/var/spack/repos/builtin/packages/r-illuminaio/package.py
index 895c4a77ea..a654d24be7 100644
--- a/var/spack/repos/builtin/packages/r-illuminaio/package.py
+++ b/var/spack/repos/builtin/packages/r-illuminaio/package.py
@@ -7,13 +7,13 @@ from spack import *
 
 
 class RIlluminaio(RPackage):
-    """Parsing Illumina Microarray Output Files
+    """Parsing Illumina Microarray Output Files.
 
        Tools for parsing Illumina's microarray output files, including IDAT."""
 
-    homepage = "https://bioconductor.org/packages/illuminaio"
-    git      = "https://git.bioconductor.org/packages/illuminaio.git"
+    bioc = "illuminaio"
 
+    version('0.36.0', commit='c5b6e9164b73c650c0a9f055f4fd0580ac64fae7')
     version('0.32.0', commit='e1322c781dd475a5e8ff6c0422bebb3deb47fa80')
     version('0.26.0', commit='40c2f94df2ea64d745d25aadd2bfb33ac3e02f81')
     version('0.24.0', commit='47953c77713c2da00a610f39308f86c5b44f6c59')
diff --git a/var/spack/repos/builtin/packages/r-impute/package.py b/var/spack/repos/builtin/packages/r-impute/package.py
index 62b8fac60c..79f872f5a4 100644
--- a/var/spack/repos/builtin/packages/r-impute/package.py
+++ b/var/spack/repos/builtin/packages/r-impute/package.py
@@ -7,13 +7,13 @@ from spack import *
 
 
 class RImpute(RPackage):
-    """impute: Imputation for microarray data
+    """impute: Imputation for microarray data.
 
        Imputation for microarray data (currently KNN only)"""
 
-    homepage = "https://bioconductor.org/packages/impute"
-    git      = "https://git.bioconductor.org/packages/impute.git"
+    bioc = "impute"
 
+    version('1.68.0', commit='fa4e4d883e609633c49d865a44acd6a79954eaac')
     version('1.64.0', commit='31a5636f4dfbb1fd61386738786a0de048a620c2')
     version('1.58.0', commit='dc17173df08d965a0d0aac9fa4ad519bd99d127e')
     version('1.56.0', commit='6c037ed4dffabafceae684265f86f2a18751b559')
diff --git a/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py b/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py
index 8471b9ce48..503947b1cc 100644
--- a/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py
+++ b/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py
@@ -8,15 +8,15 @@ from spack import *
 
 class RInteractivedisplaybase(RPackage):
     """Base package for enabling powerful shiny web displays of Bioconductor
-       objects
+       objects.
 
        The interactiveDisplayBase package contains the the basic methods needed
        to generate interactive Shiny based display methods for Bioconductor
        objects."""
 
-    homepage = "https://bioconductor.org/packages/interactiveDisplayBase"
-    git      = "https://git.bioconductor.org/packages/interactiveDisplayBase.git"
+    bioc = "interactiveDisplayBase"
 
+    version('1.32.0', commit='0f88b2ac3689d51abb6ac0045b3207ca77963a5a')
     version('1.28.0', commit='a74c02c971c4f9c7086e14abd23f1a4190da4599')
     version('1.22.0', commit='4ce3cde1dabc01375c153ad614d77a5e28b96916')
     version('1.20.0', commit='f40912c8af7afbaaf68c003a6e148d81cbe84df6')
@@ -27,4 +27,4 @@ class RInteractivedisplaybase(RPackage):
     depends_on('r@2.10:', type=('build', 'run'))
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-shiny', type=('build', 'run'))
-    depends_on('r-dt', when='@1.28.0:', type=('build', 'run'))
+    depends_on('r-dt', type=('build', 'run'), when='@1.28.0:')
diff --git a/var/spack/repos/builtin/packages/r-iranges/package.py b/var/spack/repos/builtin/packages/r-iranges/package.py
index 3230f6d159..7648efc3a4 100644
--- a/var/spack/repos/builtin/packages/r-iranges/package.py
+++ b/var/spack/repos/builtin/packages/r-iranges/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RIranges(RPackage):
-    """Foundation of integer range manipulation in Bioconductor
+    """Foundation of integer range manipulation in Bioconductor.
 
        Provides efficient low-level and highly reusable S4 classes for storing,
        manipulating and aggregating over annotated ranges of integers.
@@ -16,9 +16,9 @@ class RIranges(RPackage):
        list-like classes for storing, transforming and aggregating large
        grouped data, i.e., collections of atomic vectors and DataFrames."""
 
-    homepage = "https://bioconductor.org/packages/IRanges"
-    git      = "https://git.bioconductor.org/packages/IRanges.git"
+    bioc = "IRanges"
 
+    version('2.28.0', commit='d85ee908a379e12d1e32599e999c71ab37c25e57')
     version('2.24.1', commit='6c61fddf4c5830f69a0f7f108888c67cd0a12b19')
     version('2.22.2', commit='8c5e991')
     version('2.18.3', commit='c98a7ba074e72f2e5ec98252dffe9d3392711972')
@@ -28,15 +28,17 @@ class RIranges(RPackage):
     version('2.10.5', commit='b00d1d5025e3c480d17c13100f0da5a0132b1614')
 
     depends_on('r@3.1.0:', type=('build', 'run'))
-    depends_on('r@4.0.0:', when='@2.24.1:', type=('build', 'run'))
+    depends_on('r@4.0.0:', type=('build', 'run'), when='@2.24.1:')
     depends_on('r-biocgenerics@0.21.1:', type=('build', 'run'))
-    depends_on('r-biocgenerics@0.23.3:', when='@2.12.0:', type=('build', 'run'))
-    depends_on('r-biocgenerics@0.25.3:', when='@2.14.12:', type=('build', 'run'))
-    depends_on('r-biocgenerics@0.36.0:', when='@2.24.1:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.23.3:', type=('build', 'run'), when='@2.12.0:')
+    depends_on('r-biocgenerics@0.25.3:', type=('build', 'run'), when='@2.14.12:')
+    depends_on('r-biocgenerics@0.36.0:', type=('build', 'run'), when='@2.24.1:')
+    depends_on('r-biocgenerics@0.39.2:', type=('build', 'run'), when='@2.28.0:')
     depends_on('r-s4vectors@0.13.17:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.15.5:', when='@2.12.0:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.18.2:', when='@2.14.12:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.19.11:', when='@2.16.0:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.21.9:', when='@2.18.3:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.25.14:', when='@2.22.2:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.27.12:', when='@2.24.1:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.15.5:', type=('build', 'run'), when='@2.12.0:')
+    depends_on('r-s4vectors@0.18.2:', type=('build', 'run'), when='@2.14.12:')
+    depends_on('r-s4vectors@0.19.11:', type=('build', 'run'), when='@2.16.0:')
+    depends_on('r-s4vectors@0.21.9:', type=('build', 'run'), when='@2.18.3:')
+    depends_on('r-s4vectors@0.25.14:', type=('build', 'run'), when='@2.22.2:')
+    depends_on('r-s4vectors@0.27.12:', type=('build', 'run'), when='@2.24.1:')
+    depends_on('r-s4vectors@0.29.19:', type=('build', 'run'), when='@2.28.0:')
diff --git a/var/spack/repos/builtin/packages/r-jaspar2018/package.py b/var/spack/repos/builtin/packages/r-jaspar2018/package.py
index 3b7a35a626..91051bef81 100644
--- a/var/spack/repos/builtin/packages/r-jaspar2018/package.py
+++ b/var/spack/repos/builtin/packages/r-jaspar2018/package.py
@@ -12,8 +12,7 @@ class RJaspar2018(RPackage):
        Data package for JASPAR 2018. To search this databases, please use the
        package TFBSTools (>= 1.15.6)."""
 
-    homepage = "https://bioconductor.org/packages/JASPAR2018"
-    git      = "https://git.bioconductor.org/packages/JASPAR2018.git"
+    bioc = "JASPAR2018"
 
     version('1.1.0', commit='cf8598d3c9054d85c43655cf82be17f74d800fa5')
     version('1.0.0', commit='4c84092b3737bb1c57ab56f4321f2f5e4b0efeaa')
diff --git a/var/spack/repos/builtin/packages/r-kegg-db/package.py b/var/spack/repos/builtin/packages/r-kegg-db/package.py
index ab3eb2c293..761d5fde9c 100644
--- a/var/spack/repos/builtin/packages/r-kegg-db/package.py
+++ b/var/spack/repos/builtin/packages/r-kegg-db/package.py
@@ -7,13 +7,13 @@ from spack import *
 
 
 class RKeggDb(RPackage):
-    """A set of annotation maps for KEGG
+    """A set of annotation maps for KEGG.
 
     A set of annotation maps for KEGG assembled using data from KEGG."""
 
     # NOTE: The KEGG.db package was removed in Bioconductor-3.13
 
-    homepage = "https://www.bioconductor.org/packages/KEGG.db/"
+    bioc = "KEGG.db"
     url = "https://www.bioconductor.org/packages/release/data/annotation/src/contrib/KEGG.db_3.2.3.tar.gz"
 
     version('3.2.4',
diff --git a/var/spack/repos/builtin/packages/r-kegggraph/package.py b/var/spack/repos/builtin/packages/r-kegggraph/package.py
index b0eacb090d..edb3f9dc63 100644
--- a/var/spack/repos/builtin/packages/r-kegggraph/package.py
+++ b/var/spack/repos/builtin/packages/r-kegggraph/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RKegggraph(RPackage):
-    """KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
+    """KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor.
 
        KEGGGraph is an interface between KEGG pathway and graph object as well
        as a collection of tools to analyze, dissect and visualize these graphs.
@@ -16,9 +16,9 @@ class RKegggraph(RPackage):
        functionalities including parsing, graph operation, visualization and
        etc."""
 
-    homepage = "https://bioconductor.org/packages/KEGGgraph"
-    git      = "https://git.bioconductor.org/packages/KEGGgraph.git"
+    bioc = "KEGGgraph"
 
+    version('1.54.0', commit='135ee3dad30ca208e21acd0a2d81120b74b64079')
     version('1.50.0', commit='3335e85cdba264c04e6e36378578cf6c83a30eb8')
     version('1.44.0', commit='2c24e8ec53fe34c72ea65f34e3c09905ab2e5c62')
     version('1.42.0', commit='7d907e22a3ad7b4829a7cbaba5a8f8dc8013a609')
@@ -27,6 +27,8 @@ class RKegggraph(RPackage):
     version('1.38.1', commit='dd31665beb36d5aad8ed09ed56c603633b6b2292')
 
     depends_on('r@2.10.0:', type=('build', 'run'))
+    depends_on('r@3.5.0:', type=('build', 'run'), when='@1.54.0:')
     depends_on('r-xml@2.3-0:', type=('build', 'run'))
     depends_on('r-graph', type=('build', 'run'))
-    depends_on('r-rcurl', when='@1.44.0:', type=('build', 'run'))
+    depends_on('r-rcurl', type=('build', 'run'), when='@1.44.0:')
+    depends_on('r-rgraphviz', type=('build', 'run'), when='@1.54.0:')
diff --git a/var/spack/repos/builtin/packages/r-keggrest/package.py b/var/spack/repos/builtin/packages/r-keggrest/package.py
index 45d581ef2d..dfe235b0ab 100644
--- a/var/spack/repos/builtin/packages/r-keggrest/package.py
+++ b/var/spack/repos/builtin/packages/r-keggrest/package.py
@@ -7,15 +7,15 @@ from spack import *
 
 
 class RKeggrest(RPackage):
-    """Client-side REST access to KEGG
+    """Client-side REST access to KEGG.
 
        A package that provides a client interface to the KEGG REST server.
        Based on KEGGSOAP by J. Zhang, R. Gentleman, and Marc Carlson, and KEGG
        (python package) by Aurelien Mazurie."""
 
-    homepage = "https://bioconductor.org/packages/KEGGREST"
-    git      = "https://git.bioconductor.org/packages/KEGGREST.git"
+    bioc = "KEGGREST"
 
+    version('1.34.0', commit='2056750dc202fa04a34b84c6c712e884c7cad2bd')
     version('1.30.1', commit='fd9970ea9df117d625257b8c6351cf85098cfbc1')
     version('1.24.1', commit='bbc3ef476e02147aad8e1f33178136cc797c1b3f')
     version('1.22.0', commit='4374507376be811d29416d0cbbfd9115a50494d9')
diff --git a/var/spack/repos/builtin/packages/r-ksamples/package.py b/var/spack/repos/builtin/packages/r-ksamples/package.py
new file mode 100644
index 0000000000..a5b9f0bd0e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ksamples/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RKsamples(RPackage):
+    """K-Sample Rank Tests and their Combinations.
+
+    Compares k samples using the Anderson-Darling test, Kruskal-Wallis type
+    tests with different rank score criteria, Steel's multiple comparison test,
+    and the Jonckheere-Terpstra (JT) test. It computes asymptotic, simulated or
+    (limited) exact P-values, all valid under randomization, with or without
+    ties, or conditionally under random sampling from populations, given the
+    observed tie pattern. Except for Steel's test and the JT test it also
+    combines these tests across several blocks of samples. Also analyzed are 2
+    x t contingency tables and their blocked combinations using the
+    Kruskal-Wallis criterion. Steel's test is inverted to provide simultaneous
+    confidence bounds for shift parameters. A plotting function compares tail
+    probabilities obtained under asymptotic approximation with those obtained
+    via simulation or exact calculations."""
+
+    cran = "kSamples"
+
+    version('1.2-9', sha256='ba3ec4af3dfcf7cf12f0b784ef67bfea565e16985647ead904629886cc1542ff')
+
+    depends_on('r-suppdists', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-limma/package.py b/var/spack/repos/builtin/packages/r-limma/package.py
index 33332afd6d..f850822f2d 100644
--- a/var/spack/repos/builtin/packages/r-limma/package.py
+++ b/var/spack/repos/builtin/packages/r-limma/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RLimma(RPackage):
-    """Linear Models for Microarray Data
+    """Linear Models for Microarray Data.
 
        Data analysis, linear models and differential expression for microarray
        data."""
 
-    homepage = "https://bioconductor.org/packages/limma"
-    git      = "https://git.bioconductor.org/packages/limma.git"
+    bioc = "limma"
 
+    version('3.50.0', commit='657b19bbc33c5c941af79aeb68967bf42ea40e23')
     version('3.46.0', commit='ff03542231827f39ebde6464cdbba0110e24364e')
     version('3.40.6', commit='3ae0767ecf7a764030e7b7d0b1d0f292c0b24055')
     version('3.38.3', commit='77b292eb150cdedaa1db704bcfb01f0bb29e9849')
@@ -23,4 +23,4 @@ class RLimma(RPackage):
     version('3.32.10', commit='593edf28e21fe054d64137ae271b8a52ab05bc60')
 
     depends_on('r@2.3.0:', type=('build', 'run'))
-    depends_on('r@3.6.0:', when='@3.40.6:', type=('build', 'run'))
+    depends_on('r@3.6.0:', type=('build', 'run'), when='@3.40.6:')
diff --git a/var/spack/repos/builtin/packages/r-lumi/package.py b/var/spack/repos/builtin/packages/r-lumi/package.py
index c07669ca94..5f8cc57d84 100644
--- a/var/spack/repos/builtin/packages/r-lumi/package.py
+++ b/var/spack/repos/builtin/packages/r-lumi/package.py
@@ -8,7 +8,7 @@ from spack import *
 
 class RLumi(RPackage):
     """BeadArray Specific Methods for Illumina Methylation and Expression
-    Microarrays
+    Microarrays.
 
     The lumi package provides an integrated solution for the Illumina
     microarray data analysis. It includes functions of Illumina BeadStudio
@@ -17,9 +17,9 @@ class RLumi(RPackage):
     also includes the functions of processing Illumina methylation microarrays,
     especially Illumina Infinium methylation microarrays."""
 
-    homepage = "https://bioconductor.org/packages/release/bioc/html/lumi.html"
-    git      = "https://git.bioconductor.org/packages/lumi"
+    bioc = "lumi"
 
+    version('2.46.0', commit='a68932c17a61c99e58ebbd8008d078bec6adb4e7')
     version('2.42.0', commit='a643b3ba46fee951b8566ddd8216af7e6c92f6f6')
     version('2.38.0', commit='321d480d44ce9a0c02ce5af1bddc1f549abdea59')
 
diff --git a/var/spack/repos/builtin/packages/r-makecdfenv/package.py b/var/spack/repos/builtin/packages/r-makecdfenv/package.py
index 4a272e5de7..4c316e6c3a 100644
--- a/var/spack/repos/builtin/packages/r-makecdfenv/package.py
+++ b/var/spack/repos/builtin/packages/r-makecdfenv/package.py
@@ -7,16 +7,16 @@ from spack import *
 
 
 class RMakecdfenv(RPackage):
-    """CDF Environment Maker
+    """CDF Environment Maker.
 
        This package has two functions. One reads a Affymetrix chip description
        file (CDF) and creates a hash table environment containing the
        location/probe set membership mapping. The other creates a package that
        automatically loads that environment."""
 
-    homepage = "https://bioconductor.org/packages/makecdfenv"
-    git      = "https://git.bioconductor.org/packages/makecdfenv.git"
+    bioc = "makecdfenv"
 
+    version('1.70.0', commit='82ecd0fa8ac401e4ac8f1e9139556d2be4a3c4f3')
     version('1.66.0', commit='02aa975d543089f5495cb3b4e8edbcf0ff05148a')
     version('1.60.0', commit='900ece3ecd7a0ade9f8a0374e5a03def4e079cb3')
     version('1.58.0', commit='6f513e39c4920a6da10d22718fc3bf278fe5ffe2')
diff --git a/var/spack/repos/builtin/packages/r-marray/package.py b/var/spack/repos/builtin/packages/r-marray/package.py
index d654461fb9..55095efa3a 100644
--- a/var/spack/repos/builtin/packages/r-marray/package.py
+++ b/var/spack/repos/builtin/packages/r-marray/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RMarray(RPackage):
-    """Exploratory analysis for two-color spotted microarray data:
+    """Exploratory analysis for two-color spotted microarray data.
 
     Class definitions for two-color spotted microarray data. Fuctions for data
     input, diagnostic plots, normalization and quality checking."""
 
-    homepage = "https://www.maths.usyd.edu.au/u/jeany/"
-    bioc     = "marray"
+    bioc = "marray"
 
+    version('1.72.0', commit='da35e8b8d2c9ef17e779013a5d252f38a1c66633')
     version('1.68.0', commit='67b3080486abdba7dd19fccd7fb731b0e8b5b3f9')
 
     depends_on('r@2.10.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-matrixgenerics/package.py b/var/spack/repos/builtin/packages/r-matrixgenerics/package.py
index 491049b2d9..5d31908371 100644
--- a/var/spack/repos/builtin/packages/r-matrixgenerics/package.py
+++ b/var/spack/repos/builtin/packages/r-matrixgenerics/package.py
@@ -7,7 +7,8 @@ from spack import *
 
 
 class RMatrixgenerics(RPackage):
-    """S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
+    """S4 Generic Summary Statistic Functions that Operate on Matrix-Like
+    Objects.
 
     S4 generic functions modeled after the 'matrixStats' API for alternative
     matrix implementations. Packages with alternative matrix implementation can
@@ -16,9 +17,10 @@ class RMatrixgenerics(RPackage):
     developers can import this package and handle a different matrix
     implementations without worrying about incompatibilities."""
 
-    homepage = "https://bioconductor.org/packages/MatrixGenerics"
-    git      = "https://git.bioconductor.org/packages/MatrixGenerics"
+    bioc = "MatrixGenerics"
 
+    version('1.6.0', commit='4588a60e5cc691424c17faa281bdd7d99d83ec34')
     version('1.2.1', commit='abcc9ca0504e0b915cd7933a3169a8e9e5bd2fe9')
 
     depends_on('r-matrixstats@0.57.1:', type=('build', 'run'))
+    depends_on('r-matrixstats@0.60.1:', type=('build', 'run'), when='@1.6.0:')
diff --git a/var/spack/repos/builtin/packages/r-mergemaid/package.py b/var/spack/repos/builtin/packages/r-mergemaid/package.py
index 51bba220f8..6c44fe1925 100644
--- a/var/spack/repos/builtin/packages/r-mergemaid/package.py
+++ b/var/spack/repos/builtin/packages/r-mergemaid/package.py
@@ -20,8 +20,7 @@ class RMergemaid(RPackage):
        from 'modelOutcome' to graphically display the results and cross-
        validate associations of gene expression data with survival."""
 
-    homepage = "https://bioconductor.org/packages/MergeMaid"
-    git      = "https://git.bioconductor.org/packages/MergeMaid.git"
+    bioc = "MergeMaid"
 
     version('2.56.0', commit='c510d1d85bb39476e8397b24c4bc127780a17686')
     version('2.54.0', commit='8e79bd2bd06b25138b3c5107681c89d714a3b194')
diff --git a/var/spack/repos/builtin/packages/r-methylumi/package.py b/var/spack/repos/builtin/packages/r-methylumi/package.py
index d247b01336..c16967e00e 100644
--- a/var/spack/repos/builtin/packages/r-methylumi/package.py
+++ b/var/spack/repos/builtin/packages/r-methylumi/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RMethylumi(RPackage):
-    """Handle Illumina methylation data
+    """Handle Illumina methylation data.
 
     This package provides classes for holding and manipulating Illumina
     methylation data. Based on eSet, it can contain MIAME information, sample
@@ -18,9 +18,9 @@ class RMethylumi(RPackage):
     background correction, and quality control features for GoldenGate,
     Infinium, and Infinium HD arrays are also included."""
 
-    homepage = "https://bioconductor.org/packages/release/bioc/html/methylumi.html"
-    git      = "https://git.bioconductor.org/packages/methylumi"
+    bioc = "methylumi"
 
+    version('2.40.1', commit='211039225ca6fca9af75b8266f656161912ce10f')
     version('2.36.0', commit='5fb0b609f9c9181ac99f902745958774e5489606')
     version('2.32.0', commit='e2a29c1b214c0d43c7325d176f9ce41dcf8e2f9d')
 
@@ -33,7 +33,7 @@ class RMethylumi(RPackage):
     depends_on('r-fdb-infiniummethylation-hg19@2.2.0:', type=('build', 'run'))
     depends_on('r-minfi', type=('build', 'run'))
     depends_on('r-biocgenerics', type=('build', 'run'))
-    depends_on('r-s4vectors', when='@2.36.0:', type=('build', 'run'))
+    depends_on('r-s4vectors', type=('build', 'run'), when='@2.36.0:')
     depends_on('r-iranges', type=('build', 'run'))
     depends_on('r-genomeinfodb', type=('build', 'run'))
     depends_on('r-genomicranges', type=('build', 'run'))
@@ -43,3 +43,4 @@ class RMethylumi(RPackage):
     depends_on('r-genefilter', type=('build', 'run'))
     depends_on('r-annotationdbi', type=('build', 'run'))
     depends_on('r-illuminaio', type=('build', 'run'))
+    depends_on('r-genomicfeatures', type=('build', 'run'), when='@2.40.1:')
diff --git a/var/spack/repos/builtin/packages/r-minfi/package.py b/var/spack/repos/builtin/packages/r-minfi/package.py
index 5469cd268e..99ff0c72c0 100644
--- a/var/spack/repos/builtin/packages/r-minfi/package.py
+++ b/var/spack/repos/builtin/packages/r-minfi/package.py
@@ -7,13 +7,13 @@ from spack import *
 
 
 class RMinfi(RPackage):
-    """Analyze Illumina Infinium DNA methylation arrays
+    """Analyze Illumina Infinium DNA methylation arrays.
 
        Tools to analyze & visualize Illumina Infinium methylation arrays."""
 
-    homepage = "https://bioconductor.org/packages/minfi"
-    git      = "https://git.bioconductor.org/packages/minfi.git"
+    bioc = "minfi"
 
+    version('1.40.0', commit='17fa2b5d6cdbef6cbfb690242bd3f660731431f1')
     version('1.36.0', commit='94301da343226be7cd878c2a6c1bb529564785d6')
     version('1.30.0', commit='a4c28e9388fe3b35e7d21a9669e39250ed6dcbcd')
     version('1.28.4', commit='b5125b2f3e05d37d519eeb6fd44a60efdad388e7')
@@ -38,9 +38,9 @@ class RMinfi(RPackage):
     depends_on('r-limma', type=('build', 'run'))
     depends_on('r-preprocesscore', type=('build', 'run'))
     depends_on('r-illuminaio', type=('build', 'run'))
-    depends_on('r-illuminaio@0.23.2:', when='@1.28.4:', type=('build', 'run'))
-    depends_on('r-delayedmatrixstats', when='@1.26.2:', type=('build', 'run'))
-    depends_on('r-delayedmatrixstats@1.3.4:', when='@1.28.4:', type=('build', 'run'))
+    depends_on('r-illuminaio@0.23.2:', type=('build', 'run'), when='@1.28.4:')
+    depends_on('r-delayedmatrixstats', type=('build', 'run'), when='@1.26.2:')
+    depends_on('r-delayedmatrixstats@1.3.4:', type=('build', 'run'), when='@1.28.4:')
     depends_on('r-mclust', type=('build', 'run'))
     depends_on('r-genefilter', type=('build', 'run'))
     depends_on('r-nlme', type=('build', 'run'))
@@ -49,10 +49,11 @@ class RMinfi(RPackage):
     depends_on('r-quadprog', type=('build', 'run'))
     depends_on('r-data-table', type=('build', 'run'))
     depends_on('r-geoquery', type=('build', 'run'))
-    depends_on('r-delayedarray@0.5.23:', when='@1.26.2:', type=('build', 'run'))
-    depends_on('r-delayedarray@0.7.38:', when='@1.28.4:', type=('build', 'run'))
-    depends_on('r-delayedarray@0.9.8:', when='@1.30.0:', type=('build', 'run'))
-    depends_on('r-delayedarray@0.15.16:', when='@1.36.0:', type=('build', 'run'))
-    depends_on('r-hdf5array', when='@1.26.2:', type=('build', 'run'))
-    depends_on('r-biocparallel', when='@1.26.2:', type=('build', 'run'))
-    depends_on('r-matrixstats@0.50.0:', when='@:1.30.0', type=('build', 'run'))
+    depends_on('r-delayedarray@0.5.23:', type=('build', 'run'), when='@1.26.2:')
+    depends_on('r-delayedarray@0.7.38:', type=('build', 'run'), when='@1.28.4:')
+    depends_on('r-delayedarray@0.9.8:', type=('build', 'run'), when='@1.30.0:')
+    depends_on('r-delayedarray@0.15.16:', type=('build', 'run'), when='@1.36.0:')
+    depends_on('r-hdf5array', type=('build', 'run'), when='@1.26.2:')
+    depends_on('r-biocparallel', type=('build', 'run'), when='@1.26.2:')
+
+    depends_on('r-matrixstats@0.50.0:', type=('build', 'run'), when='@:1.30.0')
diff --git a/var/spack/repos/builtin/packages/r-missmethyl/package.py b/var/spack/repos/builtin/packages/r-missmethyl/package.py
index a54e78ec40..51f2245e3a 100644
--- a/var/spack/repos/builtin/packages/r-missmethyl/package.py
+++ b/var/spack/repos/builtin/packages/r-missmethyl/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RMissmethyl(RPackage):
-    """Analysing Illumina HumanMethylation BeadChip Data:
+    """Analysing Illumina HumanMethylation BeadChip Data.
 
     Normalisation, testing for differential variability and differential
     methylation and gene set testing for data from Illumina's Infinium
@@ -21,8 +21,9 @@ class RMissmethyl(RPackage):
     taking into account the number of probes per gene on the array, as well as
     taking into account multi-gene associated probes."""
 
-    bioc     = "missMethyl"
+    bioc = "missMethyl"
 
+    version('1.28.0', commit='6a36aee28837736291ac630c1da3909f0e9c8d6a')
     version('1.24.0', commit='f6c86048911dc0e302fb593b7d0623f6e77ac332')
 
     depends_on('r@3.6.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-mlinterfaces/package.py b/var/spack/repos/builtin/packages/r-mlinterfaces/package.py
index 084d37d24c..ce1d932f75 100644
--- a/var/spack/repos/builtin/packages/r-mlinterfaces/package.py
+++ b/var/spack/repos/builtin/packages/r-mlinterfaces/package.py
@@ -8,14 +8,14 @@ from spack import *
 
 class RMlinterfaces(RPackage):
     """Uniform interfaces to R machine learning procedures for data in
-       Bioconductor containers
+       Bioconductor containers.
 
        This package provides uniform interfaces to machine learning code for
        data in R and Bioconductor containers."""
 
-    homepage = "https://bioconductor.org/packages/MLInterfaces"
-    git      = "https://git.bioconductor.org/packages/MLInterfaces.git"
+    bioc = "MLInterfaces"
 
+    version('1.74.0', commit='5ee73b6491b1d68d7b49ddce6483df98ad880946')
     version('1.70.0', commit='7b076c3e85314dd5fd5bd8a98e8123d08d9acd3b')
     version('1.64.1', commit='0b081112d87771248bc33b3b82d5ca4685f986a1')
     version('1.62.1', commit='6cf59a90b14779cf57a0b36f1087304082ae50fe')
@@ -24,8 +24,8 @@ class RMlinterfaces(RPackage):
     version('1.56.0', commit='31fe6fb20d859fcb01d5552f42bca6bab16cc67f')
 
     depends_on('r@2.9:', type=('build', 'run'))
-    depends_on('r@3.5:', when='@1.60.1:', type=('build', 'run'))
-    depends_on('r-rcpp', when='@1.70.0:', type=('build', 'run'))
+    depends_on('r@3.5:', type=('build', 'run'), when='@1.60.1:')
+    depends_on('r-rcpp', type=('build', 'run'), when='@1.70.0:')
     depends_on('r-biocgenerics@0.13.11:', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-annotate', type=('build', 'run'))
@@ -44,4 +44,6 @@ class RMlinterfaces(RPackage):
     depends_on('r-hwriter', type=('build', 'run'))
     depends_on('r-threejs@0.2.2:', type=('build', 'run'))
     depends_on('r-mlbench', type=('build', 'run'))
-    depends_on('r-rda', when='@:1.64.1', type=('build', 'run'))
+    depends_on('r-magrittr', type=('build', 'run'), when='@1.74.0:')
+
+    depends_on('r-rda', type=('build', 'run'), when='@:1.64.1')
diff --git a/var/spack/repos/builtin/packages/r-mscoreutils/package.py b/var/spack/repos/builtin/packages/r-mscoreutils/package.py
new file mode 100644
index 0000000000..9d1e4f7dd8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mscoreutils/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMscoreutils(RPackage):
+    """Core Utils for Mass Spectrometry Data.
+
+    MsCoreUtils defines low-level functions for mass spectrometry data and is
+    independent of any high-level data structures. These functions include mass
+    spectra processing functions (noise estimation, smoothing, binning),
+    quantitative aggregation functions (median polish, robust summarisation,
+    ...), missing data imputation, data normalisation (quantiles, vsn, ...) as
+    well as misc helper functions, that are used across high-level data
+    structure within the R for Mass Spectrometry packages."""
+
+    bioc = "MsCoreUtils"
+
+    version('1.6.0', commit='9ed95b2d20dacaa83567fadd04349c81db9127ef')
+
+    depends_on('r@3.6.0:', type=('build', 'run'))
+    depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-mass', type=('build', 'run'))
+    depends_on('r-clue', type=('build', 'run'))
+    depends_on('r-rcpp', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-msnbase/package.py b/var/spack/repos/builtin/packages/r-msnbase/package.py
index 9b31bb3d96..09cd1eec72 100644
--- a/var/spack/repos/builtin/packages/r-msnbase/package.py
+++ b/var/spack/repos/builtin/packages/r-msnbase/package.py
@@ -7,15 +7,15 @@ from spack import *
 
 
 class RMsnbase(RPackage):
-    """Base Functions and Classes for Mass Spectrometry and Proteomics
+    """Base Functions and Classes for Mass Spectrometry and Proteomics.
 
        MSnbase provides infrastructure for manipulation, processing and
        visualisation of mass spectrometry and proteomics data, ranging from raw
        to quantitative and annotated data."""
 
-    homepage = "https://bioconductor.org/packages/MSnbase"
-    git      = "https://git.bioconductor.org/packages/MSnbase.git"
+    bioc = "MSnbase"
 
+    version('2.20.4', commit='c86ac8b341832f2b577f2153258c1abf064e6448')
     version('2.16.1', commit='4d88b4edd1af59474462b1b06ad0ec5831f3a878')
     version('2.10.1', commit='4d5899bc9c714f0b1a70cddd537cd4621b2b53b0')
     version('2.8.3', commit='ef883752c5e92d445647bc5b5d23d5df320db415')
@@ -24,23 +24,24 @@ class RMsnbase(RPackage):
     version('2.2.0', commit='d6e8fb7f106d05096fa9074da0f829ac8f02c197')
 
     depends_on('r@3.1:', type=('build', 'run'))
-    depends_on('r@3.5:', when='@2.16.1:', type=('build', 'run'))
+    depends_on('r@3.5:', type=('build', 'run'), when='@2.16.1:')
     depends_on('r-biocgenerics@0.7.1:', type=('build', 'run'))
     depends_on('r-biobase@2.15.2:', type=('build', 'run'))
     depends_on('r-mzr@2.7.6:', type=('build', 'run'))
-    depends_on('r-mzr@2.11.11:', when='@2.4.2:', type=('build', 'run'))
-    depends_on('r-mzr@2.13.6:', when='@2.6.4:', type=('build', 'run'))
-    depends_on('r-mzr@2.15.1:', when='@2.8.3:', type=('build', 'run'))
-    depends_on('r-mzr@2.17.3:', when='@2.10.1:', type=('build', 'run'))
-    depends_on('r-mzr@2.19.6:', when='@2.16.1:', type=('build', 'run'))
+    depends_on('r-mzr@2.11.11:', type=('build', 'run'), when='@2.4.2:')
+    depends_on('r-mzr@2.13.6:', type=('build', 'run'), when='@2.6.4:')
+    depends_on('r-mzr@2.15.1:', type=('build', 'run'), when='@2.8.3:')
+    depends_on('r-mzr@2.17.3:', type=('build', 'run'), when='@2.10.1:')
+    depends_on('r-mzr@2.19.6:', type=('build', 'run'), when='@2.16.1:')
     depends_on('r-s4vectors', type=('build', 'run'))
     depends_on('r-protgenerics@1.5.1:', type=('build', 'run'))
-    depends_on('r-protgenerics@1.19.3:', when='@2.16.1:', type=('build', 'run'))
+    depends_on('r-protgenerics@1.19.3:', type=('build', 'run'), when='@2.16.1:')
+    depends_on('r-protgenerics@1.25.1:', type=('build', 'run'), when='@2.20.4:')
+    depends_on('r-mscoreutils', type=('build', 'run'), when='@2.20.4:')
     depends_on('r-biocparallel', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
-    depends_on('r-iranges@2.13.28:', when='@2.6.4:', type=('build', 'run'))
+    depends_on('r-iranges@2.13.28:', type=('build', 'run'), when='@2.6.4:')
     depends_on('r-plyr', type=('build', 'run'))
-    depends_on('r-preprocesscore', type=('build', 'run'))
     depends_on('r-vsn', type=('build', 'run'))
     depends_on('r-affy', type=('build', 'run'))
     depends_on('r-impute', type=('build', 'run'))
@@ -51,6 +52,8 @@ class RMsnbase(RPackage):
     depends_on('r-lattice', type=('build', 'run'))
     depends_on('r-ggplot2', type=('build', 'run'))
     depends_on('r-xml', type=('build', 'run'))
-    depends_on('r-scales', when='@2.6.4:', type=('build', 'run'))
-    depends_on('r-mass', when='@2.6.4:', type=('build', 'run'))
+    depends_on('r-scales', type=('build', 'run'), when='@2.6.4:')
+    depends_on('r-mass', type=('build', 'run'), when='@2.6.4:')
     depends_on('r-rcpp', type=('build', 'run'))
+
+    depends_on('r-preprocesscore', type=('build', 'run'), when='@:2.16.1')
diff --git a/var/spack/repos/builtin/packages/r-multcompview/package.py b/var/spack/repos/builtin/packages/r-multcompview/package.py
new file mode 100644
index 0000000000..e79a509a66
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-multcompview/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMultcompview(RPackage):
+    """Visualizations of Paired Comparisons.
+
+    Convert a logical vector or a vector of p-values or a correlation,
+    difference, or distance matrix into a display identifying the pairs for
+    which the differences were not significantly different. Designed for use in
+    conjunction with the output of functions like TukeyHSD, dist{stats},
+    simint, simtest, csimint, csimtest{multcomp}, friedmanmc,
+    kruskalmc{pgirmess}."""
+
+    cran = "multcompView"
+
+    version('0.1-8', sha256='123d539172ad6fc63d83d1fc7f356a5ed7b691e7803827480118bebc374fd8e5')
diff --git a/var/spack/repos/builtin/packages/r-multtest/package.py b/var/spack/repos/builtin/packages/r-multtest/package.py
index 1f8f5c7cbc..793f2cc756 100644
--- a/var/spack/repos/builtin/packages/r-multtest/package.py
+++ b/var/spack/repos/builtin/packages/r-multtest/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RMulttest(RPackage):
-    """Resampling-based multiple hypothesis testing
+    """Resampling-based multiple hypothesis testing.
 
        Non-parametric bootstrap and permutation resampling-based multiple
        testing procedures (including empirical Bayes methods) for controlling
@@ -27,9 +27,9 @@ class RMulttest(RPackage):
        identifying differentially expressed genes in DNA microarray
        experiments."""
 
-    homepage = "https://bioconductor.org/packages/multtest"
-    git      = "https://git.bioconductor.org/packages/multtest.git"
+    bioc = "multtest"
 
+    version('2.50.0', commit='1de96649a942b115d3d554394514745e86eb3fd3')
     version('2.46.0', commit='c4dd27b333c80313a88668b59d0299988c6478a2')
     version('2.40.0', commit='5f00017c2d3a31e05e1cfe06d9f7afdee19f8473')
     version('2.38.0', commit='4dfe71cecfb298a94521088fb7bd83c5498d2915')
diff --git a/var/spack/repos/builtin/packages/r-mzid/package.py b/var/spack/repos/builtin/packages/r-mzid/package.py
index d7de28ad92..0ea0a9c30b 100644
--- a/var/spack/repos/builtin/packages/r-mzid/package.py
+++ b/var/spack/repos/builtin/packages/r-mzid/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RMzid(RPackage):
-    """An mzIdentML parser for R
+    """An mzIdentML parser for R.
 
        A parser for mzIdentML files implemented using the XML package. The
        parser tries to be general and able to handle all types of mzIdentML
@@ -15,9 +15,9 @@ class RMzid(RPackage):
        specific parser. Please contact the maintainer with any problems and
        supply an mzIdentML file so the problems can be fixed quickly."""
 
-    homepage = "https://bioconductor.org/packages/mzID"
-    git      = "https://git.bioconductor.org/packages/mzID.git"
+    bioc = "mzID"
 
+    version('1.32.0', commit='d4146385b54f4d8361e23fc2c2aef79e952f4730')
     version('1.28.0', commit='cd006631c8222ce5b4af0577a7401b39cc58fd9c')
     version('1.22.0', commit='382d9cf11f0cba996911a9d79e193d28f3ac6042')
     version('1.20.1', commit='819582646944440ddd9ed3724ae964841573e54c')
diff --git a/var/spack/repos/builtin/packages/r-mzr/package.py b/var/spack/repos/builtin/packages/r-mzr/package.py
index f34043a1fd..3f091378a1 100644
--- a/var/spack/repos/builtin/packages/r-mzr/package.py
+++ b/var/spack/repos/builtin/packages/r-mzr/package.py
@@ -8,7 +8,7 @@ from spack import *
 
 class RMzr(RPackage):
     """parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass
-       spectrometry data)
+       spectrometry data).
 
        mzR provides a unified API to the common file formats and parsers
        available for mass spectrometry data. It comes with a wrapper for the
@@ -17,9 +17,9 @@ class RMzr(RPackage):
        subset of the proteowizard library for mzML and mzIdentML. The netCDF
        reading code has previously been used in XCMS."""
 
-    homepage = "https://bioconductor.org/packages/mzR"
-    git      = "https://git.bioconductor.org/packages/mzR.git"
+    bioc = "mzR"
 
+    version('2.28.0', commit='bee7d6fb5f99e1fab5444ae1ad27b0bc6e83be9e')
     version('2.24.1', commit='e1d4de8761e6729fd45320d842691c8fe9116b7b')
     version('2.18.1', commit='13f9f9b1149859c3e29cfce941d958cc4f680546')
     version('2.16.2', commit='22d7dad98f46b5bed7f6f7b3a703dcdf5997f709')
@@ -31,9 +31,9 @@ class RMzr(RPackage):
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-biocgenerics@0.13.6:', type=('build', 'run'))
     depends_on('r-protgenerics', type=('build', 'run'))
-    depends_on('r-protgenerics@1.9.1:', when='@2.12.0:', type=('build', 'run'))
-    depends_on('r-protgenerics@1.17.3:', when='@2.24.1:', type=('build', 'run'))
-    depends_on('r-ncdf4', when='@2.16.2:', type=('build', 'run'))
+    depends_on('r-protgenerics@1.9.1:', type=('build', 'run'), when='@2.12.0:')
+    depends_on('r-protgenerics@1.17.3:', type=('build', 'run'), when='@2.24.1:')
+    depends_on('r-ncdf4', type=('build', 'run'), when='@2.16.2:')
     depends_on('r-zlibbioc', type=('build', 'run'))
-    depends_on('r-rhdf5lib@1.1.4:', when='@2.14.0:', type=('build', 'run'))
+    depends_on('r-rhdf5lib@1.1.4:', type=('build', 'run'), when='@2.14.0:')
     depends_on('gmake', type='build')
diff --git a/var/spack/repos/builtin/packages/r-oligoclasses/package.py b/var/spack/repos/builtin/packages/r-oligoclasses/package.py
index 403f120010..2f6e9e18c5 100644
--- a/var/spack/repos/builtin/packages/r-oligoclasses/package.py
+++ b/var/spack/repos/builtin/packages/r-oligoclasses/package.py
@@ -7,15 +7,15 @@ from spack import *
 
 
 class ROligoclasses(RPackage):
-    """Classes for high-throughput arrays supported by oligo and crlmm
+    """Classes for high-throughput arrays supported by oligo and crlmm.
 
        This package contains class definitions, validity checks, and
        initialization methods for classes used by the oligo and crlmm
        packages."""
 
-    homepage = "https://bioconductor.org/packages/oligoClasses"
-    git      = "https://git.bioconductor.org/packages/oligoClasses.git"
+    bioc = "oligoClasses"
 
+    version('1.56.0', commit='6e6c7b4ba54095d1d3c44c081839f57af9261cbf')
     version('1.52.0', commit='7995efbd2d26b8fa950830d62db92bdaf5cbeeea')
     version('1.46.0', commit='325684f66fc92f778098f24bcfbef0ce3da9717c')
     version('1.44.0', commit='d3e1134cdbea5f95b83215dc66e5f7b6a1cd0638')
@@ -25,7 +25,7 @@ class ROligoclasses(RPackage):
 
     depends_on('r@2.14:', type=('build', 'run'))
     depends_on('r-biocgenerics@0.3.2:', type=('build', 'run'))
-    depends_on('r-biocgenerics@0.27.1:', when='@1.44.0:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.27.1:', type=('build', 'run'), when='@1.44.0:')
     depends_on('r-biobase@2.17.8:', type=('build', 'run'))
     depends_on('r-iranges@2.5.17:', type=('build', 'run'))
     depends_on('r-genomicranges@1.23.7:', type=('build', 'run'))
@@ -33,9 +33,10 @@ class ROligoclasses(RPackage):
     depends_on('r-biostrings@2.23.6:', type=('build', 'run'))
     depends_on('r-affyio@1.23.2:', type=('build', 'run'))
     depends_on('r-foreach', type=('build', 'run'))
-    depends_on('r-biocmanager', when='@1.44.0:', type=('build', 'run'))
+    depends_on('r-biocmanager', type=('build', 'run'), when='@1.44.0:')
     depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
     depends_on('r-rsqlite', type=('build', 'run'))
-    depends_on('r-dbi', when='@1.40.0:', type=('build', 'run'))
+    depends_on('r-dbi', type=('build', 'run'), when='@1.40.0:')
     depends_on('r-ff', type=('build', 'run'))
-    depends_on('r-biocinstaller', when='@:1.42.0', type=('build', 'run'))
+
+    depends_on('r-biocinstaller', type=('build', 'run'), when='@:1.42.0')
diff --git a/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py b/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py
index 69da594ef5..178bb144dc 100644
--- a/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py
+++ b/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py
@@ -7,14 +7,17 @@ from spack import *
 
 
 class ROrgHsEgDb(RPackage):
-    """Genome wide annotation for Human
+    """Genome wide annotation for Human.
 
     Genome wide annotation for Human, primarily based on mapping using Entrez
     Gene identifiers."""
 
-    homepage = "https://bioconductor.org/packages/org.Hs.eg.db/"
-    url      = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/org.Hs.eg.db_3.4.1.tar.gz"
+    bioc = "org.Hs.eg.db"
+    url  = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/org.Hs.eg.db_3.4.1.tar.gz"
 
+    version('3.14.0',
+            sha256='0f87b3f1925a1d7007e5ad9200bdf511788bd1d7cb76f1121feeb109889c2b00',
+            url='https://www.bioconductor.org/packages/3.14/data/annotation/src/contrib/org.Hs.eg.db_3.14.0.tar.gz')
     version('3.12.0',
             sha256='48a1ab5347ec7a8602c555d9aba233102b61ffa2765826e5c8890ff0003249bb',
             url='https://www.bioconductor.org/packages/3.12/data/annotation/src/contrib/org.Hs.eg.db_3.12.0.tar.gz')
@@ -27,5 +30,6 @@ class ROrgHsEgDb(RPackage):
 
     depends_on('r@2.7.0:', type=('build', 'run'))
     depends_on('r-annotationdbi@1.37.4:', type=('build', 'run'))
-    depends_on('r-annotationdbi@1.43.1:', when='@3.8.2:', type=('build', 'run'))
-    depends_on('r-annotationdbi@1.51.3:', when='@3.12.0:', type=('build', 'run'))
+    depends_on('r-annotationdbi@1.43.1:', type=('build', 'run'), when='@3.8.2:')
+    depends_on('r-annotationdbi@1.51.3:', type=('build', 'run'), when='@3.12.0:')
+    depends_on('r-annotationdbi@1.55.1:', type=('build', 'run'), when='@3.14.0:')
diff --git a/var/spack/repos/builtin/packages/r-organismdbi/package.py b/var/spack/repos/builtin/packages/r-organismdbi/package.py
index 377ee406c4..017b9ea5e3 100644
--- a/var/spack/repos/builtin/packages/r-organismdbi/package.py
+++ b/var/spack/repos/builtin/packages/r-organismdbi/package.py
@@ -8,15 +8,15 @@ from spack import *
 
 class ROrganismdbi(RPackage):
     """Software to enable the smooth interfacing of different database
-       packages
+       packages.
 
        The package enables a simple unified interface to several annotation
        packages each of which has its own schema by taking advantage of the
        fact that each of these packages implements a select methods."""
 
-    homepage = "https://bioconductor.org/packages/OrganismDbi"
-    git      = "https://git.bioconductor.org/packages/OrganismDbi.git"
+    bioc = "OrganismDbi"
 
+    version('1.36.0', commit='3e7a90d248ff09f05ccd381ff921e12373a4b330')
     version('1.32.0', commit='c8100c4fea17bf1b10d4efacc73a7e2866d649e3')
     version('1.26.0', commit='495b4a8f8264d06d827537d43b3c6cc705244bb5')
     version('1.24.0', commit='3428952dc0f267a01e256a1c0873656cfbfde7f8')
@@ -28,14 +28,15 @@ class ROrganismdbi(RPackage):
     depends_on('r-biocgenerics@0.15.10:', type=('build', 'run'))
     depends_on('r-annotationdbi@1.33.15:', type=('build', 'run'))
     depends_on('r-genomicfeatures@1.23.31:', type=('build', 'run'))
-    depends_on('r-genomicfeatures@1.39.4:', when='@1.32.0:', type=('build', 'run'))
+    depends_on('r-genomicfeatures@1.39.4:', type=('build', 'run'), when='@1.32.0:')
     depends_on('r-biobase', type=('build', 'run'))
-    depends_on('r-biocmanager', when='@1.24.0:', type=('build', 'run'))
+    depends_on('r-biocmanager', type=('build', 'run'), when='@1.24.0:')
     depends_on('r-genomicranges', type=('build', 'run'))
-    depends_on('r-genomicranges@1.31.13:', when='@1.22.0:', type=('build', 'run'))
+    depends_on('r-genomicranges@1.31.13:', type=('build', 'run'), when='@1.22.0:')
     depends_on('r-graph', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
     depends_on('r-rbgl', type=('build', 'run'))
     depends_on('r-dbi', type=('build', 'run'))
     depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
-    depends_on('r-biocinstaller', when='@:1.22.0', type=('build', 'run'))
+
+    depends_on('r-biocinstaller', type=('build', 'run'), when='@:1.22.0')
diff --git a/var/spack/repos/builtin/packages/r-pathview/package.py b/var/spack/repos/builtin/packages/r-pathview/package.py
index 01e113701b..91903fb433 100644
--- a/var/spack/repos/builtin/packages/r-pathview/package.py
+++ b/var/spack/repos/builtin/packages/r-pathview/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RPathview(RPackage):
-    """a tool set for pathway based data integration and visualization
+    """a tool set for pathway based data integration and visualization.
 
        Pathview is a tool set for pathway based data integration and
        visualization. It maps and renders a wide variety of biological data on
@@ -18,9 +18,9 @@ class RPathview(RPackage):
        seamlessly integrates with pathway and gene set (enrichment) analysis
        tools for large-scale and fully automated analysis."""
 
-    homepage = "https://bioconductor.org/packages/pathview"
-    git      = "https://git.bioconductor.org/packages/pathview.git"
+    bioc = "pathview"
 
+    version('1.34.0', commit='a8788902a3bb047f8ee785966e57f84596076bbd')
     version('1.30.1', commit='a6a32395db408798cb076894678e90148bae6bf4')
     version('1.24.0', commit='e4401c1425c980ce2e6e478a4602a9f6d36ccd8d')
     version('1.22.3', commit='ff86f9e166a5b03bbed1a0ad276778958c3045ce')
diff --git a/var/spack/repos/builtin/packages/r-pcamethods/package.py b/var/spack/repos/builtin/packages/r-pcamethods/package.py
index 738f898433..4c9f0dc079 100644
--- a/var/spack/repos/builtin/packages/r-pcamethods/package.py
+++ b/var/spack/repos/builtin/packages/r-pcamethods/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RPcamethods(RPackage):
-    """A collection of PCA methods
+    """A collection of PCA methods.
 
        Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear
        PCA and the conventional SVD PCA. A cluster based method for missing
@@ -19,9 +19,9 @@ class RPcamethods(RPackage):
        Initiated at the Max-Planck Institute for Molecular Plant Physiology,
        Golm, Germany."""
 
-    homepage = "https://bioconductor.org/packages/pcaMethods"
-    git      = "https://git.bioconductor.org/packages/pcaMethods.git"
+    bioc = "pcaMethods"
 
+    version('1.86.0', commit='9419cfa18c18dfbd1e1194127fd120ab456c3657')
     version('1.82.0', commit='d500b3363308f1f8ca70625c5cd10cce59b27641')
     version('1.76.0', commit='5db995330ced37dfd5ddad6ad1d90b4815d3127a')
     version('1.74.0', commit='1b8f0a5cdfe3664119d0d7e926a2e0fe7320133c')
diff --git a/var/spack/repos/builtin/packages/r-pfam-db/package.py b/var/spack/repos/builtin/packages/r-pfam-db/package.py
index bdd532213b..77383836c2 100644
--- a/var/spack/repos/builtin/packages/r-pfam-db/package.py
+++ b/var/spack/repos/builtin/packages/r-pfam-db/package.py
@@ -7,14 +7,17 @@ from spack import *
 
 
 class RPfamDb(RPackage):
-    """A set of protein ID mappings for PFAM
+    """A set of protein ID mappings for PFAM.
 
     A set of protein ID mappings for PFAM assembled using data from
     public repositories."""
 
-    homepage = "https://www.bioconductor.org/packages/PFAM.db/"
-    url      = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/PFAM.db_3.4.1.tar.gz"
+    bioc = "PFAM.db"
+    url = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/PFAM.db_3.4.1.tar.gz"
 
+    version('3.14.0',
+            sha256='25c1915079e8f93d04e2cc1ab791f7f47813aaab5ac394feaf57520bb292d616',
+            url='https://bioconductor.org/packages/3.14/data/annotation/src/contrib/PFAM.db_3.14.0.tar.gz')
     version('3.12.0',
             sha256='ec42d067522baf2d7d3ca78d4f8cc0dac08a4b98f1d890f52424e5d5b16f2fe9',
             url='https://bioconductor.org/packages/3.12/data/annotation/src/contrib/PFAM.db_3.12.0.tar.gz')
@@ -26,6 +29,7 @@ class RPfamDb(RPackage):
             url='https://bioconductor.org/packages/3.5/data/annotation/src/contrib/PFAM.db_3.4.1.tar.gz')
 
     depends_on('r@2.7.0:', when='@3.4.1:', type=('build', 'run'))
-    depends_on('r-annotationdbi@1.37.4:', when='@3.4.1:', type=('build', 'run'))
-    depends_on('r-annotationdbi@1.47.1:', when='@3.10.0:', type=('build', 'run'))
-    depends_on('r-annotationdbi@1.51.3:', when='@3.12.0:', type=('build', 'run'))
+    depends_on('r-annotationdbi@1.37.4:', type=('build', 'run'), when='@3.4.1:')
+    depends_on('r-annotationdbi@1.47.1:', type=('build', 'run'), when='@3.10.0:')
+    depends_on('r-annotationdbi@1.51.3:', type=('build', 'run'), when='@3.12.0:')
+    depends_on('r-annotationdbi@1.55.1:', type=('build', 'run'), when='@3.14.0:')
diff --git a/var/spack/repos/builtin/packages/r-phyloseq/package.py b/var/spack/repos/builtin/packages/r-phyloseq/package.py
index 4eeb573557..339db4c4fa 100644
--- a/var/spack/repos/builtin/packages/r-phyloseq/package.py
+++ b/var/spack/repos/builtin/packages/r-phyloseq/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RPhyloseq(RPackage):
-    """Handling and analysis of high-throughput microbiome census data
+    """Handling and analysis of high-throughput microbiome census data.
 
        phyloseq provides a set of classes and tools to facilitate the import,
        storage, analysis, and graphical display of microbiome census data."""
 
-    homepage = "https://bioconductor.org/packages/phyloseq"
-    git      = "https://git.bioconductor.org/packages/phyloseq.git"
+    bioc = "phyloseq"
 
+    version('1.38.0', commit='1e2409a6ed3c23e308275098c2dc9fdba9d5e5f6')
     version('1.34.0', commit='cbed93ead5528fe9024d646c597dab9fc95952d3')
     version('1.28.0', commit='a86ed1e0a650fdf80bee5a0a5a82aaa5a276178d')
     version('1.26.1', commit='a084072bc9e057b90adfbd59e27db2a1ecee151c')
@@ -23,19 +23,19 @@ class RPhyloseq(RPackage):
     version('1.20.0', commit='107d1d5e3437a6e33982c06a548d3cc91df2a7e0')
 
     depends_on('r@3.3.0:', type=('build', 'run'))
-    depends_on('r@3.4.0:', when='@1.22.3', type=('build', 'run'))
+    depends_on('r@3.4.0:', type=('build', 'run'), when='@1.22.3')
     depends_on('r-ade4@1.7.4:', type=('build', 'run'))
     depends_on('r-ape@3.4:', type=('build', 'run'))
-    depends_on('r-ape@5.0:', when='@1.22.3:', type=('build', 'run'))
+    depends_on('r-ape@5.0:', type=('build', 'run'), when='@1.22.3:')
     depends_on('r-biobase', type=('build', 'run'))
-    depends_on('r-biobase@2.36.2:', when='@1.22.3:', type=('build', 'run'))
+    depends_on('r-biobase@2.36.2:', type=('build', 'run'), when='@1.22.3:')
     depends_on('r-biocgenerics@0.18.0:', type=('build', 'run'))
-    depends_on('r-biocgenerics@0.22.0:', when='@1.22.3:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.22.0:', type=('build', 'run'), when='@1.22.3:')
     depends_on('r-biomformat@1.0.0:', type=('build', 'run'))
     depends_on('r-biostrings@2.40.0:', type=('build', 'run'))
     depends_on('r-cluster@2.0.4:', type=('build', 'run'))
     depends_on('r-data-table@1.9.6:', type=('build', 'run'))
-    depends_on('r-data-table@1.10.4:', when='@1.22.3:', type=('build', 'run'))
+    depends_on('r-data-table@1.10.4:', type=('build', 'run'), when='@1.22.3:')
     depends_on('r-foreach@1.4.3:', type=('build', 'run'))
     depends_on('r-ggplot2@2.1.0:', type=('build', 'run'))
     depends_on('r-igraph@1.0.1:', type=('build', 'run'))
@@ -44,5 +44,5 @@ class RPhyloseq(RPackage):
     depends_on('r-reshape2@1.4.1:', type=('build', 'run'))
     depends_on('r-scales@0.4.0:', type=('build', 'run'))
     depends_on('r-vegan@2.3.5:', type=('build', 'run'))
-    depends_on('r-vegan@2.4:', when='@1.22.3:', type=('build', 'run'))
-    depends_on('r-vegan@2.5:', when='@1.24.2:', type=('build', 'run'))
+    depends_on('r-vegan@2.4:', type=('build', 'run'), when='@1.22.3:')
+    depends_on('r-vegan@2.5:', type=('build', 'run'), when='@1.24.2:')
diff --git a/var/spack/repos/builtin/packages/r-pmcmrplus/package.py b/var/spack/repos/builtin/packages/r-pmcmrplus/package.py
new file mode 100644
index 0000000000..f726daae43
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-pmcmrplus/package.py
@@ -0,0 +1,51 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPmcmrplus(RPackage):
+    """Calculate Pairwise Multiple Comparisons of Mean Rank Sums Extended.
+
+    For one-way layout experiments the one-way ANOVA can be performed as an
+    omnibus test. All-pairs multiple comparisons tests (Tukey-Kramer test,
+    Scheffe test, LSD-test) and many-to-one tests (Dunnett test) for normally
+    distributed residuals and equal within variance are available. Furthermore,
+    all-pairs tests (Games-Howell test, Tamhane's T2 test, Dunnett T3 test,
+    Ury-Wiggins-Hochberg test) and many-to-one (Tamhane-Dunnett Test) for
+    normally distributed residuals and heterogeneous variances are provided.
+    Van der Waerden's normal scores test for omnibus, all-pairs and many-to-one
+    tests is provided for non-normally distributed residuals and homogeneous
+    variances. The Kruskal-Wallis, BWS and Anderson-Darling omnibus test and
+    all-pairs tests (Nemenyi test, Dunn test, Conover test,
+    Dwass-Steele-Critchlow- Fligner test) as well as many-to-one (Nemenyi test,
+    Dunn test, U-test) are given for the analysis of variance by ranks.
+    Non-parametric trend tests (Jonckheere test, Cuzick test, Johnson-Mehrotra
+    test, Spearman test) are included.  In addition, a Friedman-test for
+    one-way ANOVA with repeated measures on ranks (CRBD) and Skillings-Mack
+    test for unbalanced CRBD is provided with consequent all-pairs tests
+    (Nemenyi test, Siegel test, Miller test, Conover test, Exact test) and
+    many-to-one tests (Nemenyi test, Demsar test, Exact test).  A trend can be
+    tested with Pages's test. Durbin's test for a two-way balanced incomplete
+    block design (BIBD) is given in this package as well as Gore's test for
+    CRBD with multiple observations per cell is given.  Outlier tests, Mandel's
+    k- and h statistic as well as functions for Type I error and Power analysis
+    as well as generic summary, print and plot methods are provided."""
+
+    cran = "PMCMRplus"
+
+    version('1.9.3', sha256='76baba60f57343fa5bb6f6d2ea27aab77178e02b0d2f9d5d74abde7d18994f03')
+
+    depends_on('r@3.5.0:', type=('build', 'run'))
+    depends_on('r-mvtnorm@1.0:', type=('build', 'run'))
+    depends_on('r-multcompview', type=('build', 'run'))
+    depends_on('r-gmp', type=('build', 'run'))
+    depends_on('r-rmpfr', type=('build', 'run'))
+    depends_on('r-suppdists', type=('build', 'run'))
+    depends_on('r-ksamples@1.2.7:', type=('build', 'run'))
+    depends_on('r-bwstest@0.2.1:', type=('build', 'run'))
+    depends_on('r-mass', type=('build', 'run'))
+    depends_on('gmp@4.2.3:')
+    depends_on('mpfr@3.0.0:')
diff --git a/var/spack/repos/builtin/packages/r-preprocesscore/package.py b/var/spack/repos/builtin/packages/r-preprocesscore/package.py
index 07ecc41c48..d635e04b26 100644
--- a/var/spack/repos/builtin/packages/r-preprocesscore/package.py
+++ b/var/spack/repos/builtin/packages/r-preprocesscore/package.py
@@ -7,13 +7,13 @@ from spack import *
 
 
 class RPreprocesscore(RPackage):
-    """A collection of pre-processing functions
+    """A collection of pre-processing functions.
 
        A library of core preprocessing routines."""
 
-    homepage = "https://bioconductor.org/packages/preprocessCore"
-    git      = "https://git.bioconductor.org/packages/preprocessCore.git"
+    bioc = "preprocessCore"
 
+    version('1.56.0', commit='8f3272219507aa85e0c876fb434dc3b926c22c5d')
     version('1.52.1', commit='91de4ab67315dc2af68554ae3c48823f4b1ea8ac')
     version('1.46.0', commit='8cfc3938c1b08424587f437ed6cd2ec43512500e')
     version('1.44.0', commit='dc1dc61fc562aaff3fd9b11ab0d48c2d6b3a5b81')
diff --git a/var/spack/repos/builtin/packages/r-protgenerics/package.py b/var/spack/repos/builtin/packages/r-protgenerics/package.py
index b6f880e59a..3084e927a4 100644
--- a/var/spack/repos/builtin/packages/r-protgenerics/package.py
+++ b/var/spack/repos/builtin/packages/r-protgenerics/package.py
@@ -7,13 +7,13 @@ from spack import *
 
 
 class RProtgenerics(RPackage):
-    """S4 generic functions for Bioconductor proteomics infrastructure
+    """S4 generic functions for Bioconductor proteomics infrastructure.
 
        S4 generic functions needed by Bioconductor proteomics packages."""
 
-    homepage = "https://bioconductor.org/packages/ProtGenerics"
-    git      = "https://git.bioconductor.org/packages/ProtGenerics.git"
+    bioc = "ProtGenerics"
 
+    version('1.26.0', commit='2033289ab928034b86c321e56c37e502e557c7a1')
     version('1.22.0', commit='2bb3011fb0d79536e1c50251084a7057004449c6')
     version('1.16.0', commit='960a5fdc586898513b5ae9c48fffba5c5d703723')
     version('1.14.0', commit='c85940b70a16ad69275c4facb3ef673d20a1c998')
diff --git a/var/spack/repos/builtin/packages/r-quantro/package.py b/var/spack/repos/builtin/packages/r-quantro/package.py
index 659ba05889..9b152a8dda 100644
--- a/var/spack/repos/builtin/packages/r-quantro/package.py
+++ b/var/spack/repos/builtin/packages/r-quantro/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RQuantro(RPackage):
-    """A test for when to use quantile normalization
+    """A test for when to use quantile normalization.
 
        A data-driven test for the assumptions of quantile normalization using
        raw data such as objects that inherit eSets (e.g. ExpressionSet,
@@ -16,9 +16,9 @@ class RQuantro(RPackage):
        are global differences in the distributions between the user-defined
        groups."""
 
-    homepage = "https://bioconductor.org/packages/quantro"
-    git      = "https://git.bioconductor.org/packages/quantro.git"
+    bioc = "quantro"
 
+    version('1.28.0', commit='109e7452a349f273e10d2ffb79d5624260b67dd5')
     version('1.24.0', commit='c7c0180292156a01722d91b353da44324e72d68f')
     version('1.18.0', commit='f6553c2296289eed31e4b2f32a082e990bdb8359')
     version('1.16.0', commit='cfc2e853bdc3cc90fd35e153fe243892d50d61c6')
@@ -27,7 +27,7 @@ class RQuantro(RPackage):
     version('1.10.0', commit='111337c0aba052aa49c3d2e2d3042794b28858c9')
 
     depends_on('r@3.1.3:', type=('build', 'run'))
-    depends_on('r@4.0:', when='@1.24.0:', type=('build', 'run'))
+    depends_on('r@4.0:', type=('build', 'run'), when='@1.24.0:')
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-minfi', type=('build', 'run'))
     depends_on('r-doparallel', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-qvalue/package.py b/var/spack/repos/builtin/packages/r-qvalue/package.py
index abeacf2706..040b9eefda 100644
--- a/var/spack/repos/builtin/packages/r-qvalue/package.py
+++ b/var/spack/repos/builtin/packages/r-qvalue/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RQvalue(RPackage):
-    """Q-value estimation for false discovery rate control
+    """Q-value estimation for false discovery rate control.
 
        This package takes a list of p-values resulting from the simultaneous
        testing of many hypotheses and estimates their q-values and local FDR
@@ -21,9 +21,9 @@ class RQvalue(RPackage):
        software can be applied to problems in genomics, brain imaging,
        astrophysics, and data mining."""
 
-    homepage = "https://bioconductor.org/packages/qvalue"
-    git      = "https://git.bioconductor.org/packages/qvalue.git"
+    bioc = "qvalue"
 
+    version('2.26.0', commit='6d7410d4b8673bcf9065e054670c1fbcb917a27e')
     version('2.22.0', commit='b4bde8198252737b287fd7f9a4ed697f57fad92c')
     version('2.16.0', commit='5efbe20ef522a45a7a04b681f72bb9a12e2747ae')
     version('2.14.1', commit='b694e4b264f25250eb1d1115e70c07f65767c20e')
diff --git a/var/spack/repos/builtin/packages/r-rbgl/package.py b/var/spack/repos/builtin/packages/r-rbgl/package.py
index 6529dd1284..5b1e4fb16e 100644
--- a/var/spack/repos/builtin/packages/r-rbgl/package.py
+++ b/var/spack/repos/builtin/packages/r-rbgl/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RRbgl(RPackage):
-    """An interface to the BOOST graph library
+    """An interface to the BOOST graph library.
 
        A fairly extensive and comprehensive interface to the graph algorithms
        contained in the BOOST library."""
 
-    homepage = "https://bioconductor.org/packages/RBGL"
-    git      = "https://git.bioconductor.org/packages/RBGL.git"
+    bioc = "RBGL"
 
+    version('1.70.0', commit='9cfd5fdad4f1f438ff748317f32e822aede8921b')
     version('1.66.0', commit='bf0c111dbc231de6d3423c28e115b54fb010e1ea')
     version('1.60.0', commit='ef24c17c411659b8f030602bd9781c534d6ec93b')
     version('1.58.2', commit='086ad0c6bab7be29311b6ae14fd39df7a21331a6')
@@ -23,4 +23,4 @@ class RRbgl(RPackage):
     version('1.52.0', commit='93e8fcfafec8f1cd5638fe30dc0f9506d15b49c0')
 
     depends_on('r-graph', type=('build', 'run'))
-    depends_on('r-bh', when='@1.60.0:', type=('build', 'run'))
+    depends_on('r-bh', type=('build', 'run'), when='@1.60.0:')
diff --git a/var/spack/repos/builtin/packages/r-rcppgsl/package.py b/var/spack/repos/builtin/packages/r-rcppgsl/package.py
new file mode 100644
index 0000000000..7eb9983371
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rcppgsl/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRcppgsl(RPackage):
+    """'Rcpp' Integration for 'GNU GSL' Vectors and Matrices.
+
+    'Rcpp' integration for 'GNU GSL' vectors and matrices The 'GNU Scientific
+    Library' (or 'GSL') is a collection of numerical routines for scientific
+    computing. It is particularly useful for C and C++ programs as it provides
+    a standard C interface to a wide range of mathematical routines. There are
+    over 1000 functions in total with an extensive test suite. The 'RcppGSL'
+    package provides an easy-to-use interface between 'GSL' data structures and
+    R using concepts from 'Rcpp' which is itself a package that eases the
+    interfaces between R and C++. This package also serves as a prime example
+    of how to build a package that uses 'Rcpp' to connect to another
+    third-party library. The 'autoconf' script, 'inline' plugin and example
+    package can all be used as a stanza to write a similar package against
+    another library."""
+
+    cran = "RcppGSL"
+
+    version('0.3.10', sha256='8612087da02fb791f427fed310c23d0482a8eb60fb089119f018878143f95451')
+
+    depends_on('r-rcpp@0.11.0:', type=('build', 'run'))
+    depends_on('gsl')
diff --git a/var/spack/repos/builtin/packages/r-rcppziggurat/package.py b/var/spack/repos/builtin/packages/r-rcppziggurat/package.py
new file mode 100644
index 0000000000..d043ec20a7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rcppziggurat/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRcppziggurat(RPackage):
+    """'Rcpp' Integration of Different "Ziggurat" Normal RNG Implementations.
+
+    The Ziggurat generator for normally distributed random numbers, originally
+    proposed by Marsaglia and Tsang (2000, <doi:10.18637/jss.v005.i08>) has
+    been improved upon a few times starting with Leong et al (2005,
+    <doi:10.18637/jss.v012.i07>). This package provides an aggregation in order
+    to compare different implementations in order to provide an 'faster but
+    good enough' alternative for use with R and C++ code."""
+
+    cran = "RcppZiggurat"
+
+    version('0.1.6', sha256='9c78255ca476c945c05a564d1e4da363de714d890e0e27f3b252fd73c50eed71')
+
+    depends_on('r-rcpp', type=('build', 'run'))
+    depends_on('r-rcppgsl', type=('build', 'run'))
+
+    # not listed as a dependency but needed
+    depends_on('gsl')
diff --git a/var/spack/repos/builtin/packages/r-reportingtools/package.py b/var/spack/repos/builtin/packages/r-reportingtools/package.py
index 76fd34b2ca..850ac4dd7f 100644
--- a/var/spack/repos/builtin/packages/r-reportingtools/package.py
+++ b/var/spack/repos/builtin/packages/r-reportingtools/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RReportingtools(RPackage):
-    """Tools for making reports in various formats
+    """Tools for making reports in various formats.
 
        The ReportingTools software package enables users to easily display
        reports of analysis results generated from sources such as microarray
@@ -21,9 +21,9 @@ class RReportingtools(RPackage):
        be viewed in a web browser. For more examples, please visit our site:
        http:// research-pub.gene.com/ReportingTools."""
 
-    homepage = "https://bioconductor.org/packages/ReportingTools"
-    git      = "https://git.bioconductor.org/packages/ReportingTools.git"
+    bioc = "ReportingTools"
 
+    version('2.34.0', commit='fb5aef0b6e1c6166d0f025d9e6ca60e54c68dbaf')
     version('2.30.0', commit='fb9aee416f38cfd308d6d7264ccbcda0467642a7')
     version('2.24.0', commit='d114c658affba9b682a37b4e2caf4341cf8da6cf')
     version('2.22.1', commit='dce6af6c6a1cddff077fe61368f2c13e5a0e7bab')
diff --git a/var/spack/repos/builtin/packages/r-restfulr/package.py b/var/spack/repos/builtin/packages/r-restfulr/package.py
new file mode 100644
index 0000000000..015588fd0d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-restfulr/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRestfulr(RPackage):
+    """R Interface to RESTful Web Services.
+
+    Models a RESTful service as if it were a nested R list."""
+
+    cran = "restfulr"
+
+    version('0.0.13', sha256='7b59f5887aaf02f46a80617f4d1e0ffd4e11e4840e9e2fbd486a9a9c7f2d64b6')
+
+    depends_on('r@3.4.0:', type=('build', 'run'))
+    depends_on('r-xml', type=('build', 'run'))
+    depends_on('r-rcurl', type=('build', 'run'))
+    depends_on('r-rjson', type=('build', 'run'))
+    depends_on('r-s4vectors@0.13.15:', type=('build', 'run'))
+    depends_on('r-yaml', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rfast/package.py b/var/spack/repos/builtin/packages/r-rfast/package.py
new file mode 100644
index 0000000000..195d45db1d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rfast/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRfast(RPackage):
+    """A Collection of Efficient and Extremely Fast R Functions.
+
+    A collection of fast (utility) functions for data analysis. Column- and
+    row- wise means, medians, variances, minimums, maximums, many t, F and
+    G-square tests, many regressions (normal, logistic, Poisson), are some of
+    the many fast functions. References: a) Tsagris M., Papadakis M. (2018).
+    Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1
+    <doi:10.7287/peerj.preprints.26605v1>. b) Tsagris M. and Papadakis M.
+    (2018). Forward regression in R: from the extreme slow to the extreme fast.
+    Journal of Data Science, 16(4): 771-780.
+    <doi:10.6339/JDS.201810_16(4).00006>."""
+
+    cran = "Rfast"
+
+    version('2.0.4', sha256='959907e36e24620c07ec282b203b40214f4914f4928c07ee6491043c27af31d9')
+
+    depends_on('r@3.5.0:', type=('build', 'run'))
+    depends_on('r-rcpp@0.12.3:', type=('build', 'run'))
+    depends_on('r-rcppziggurat', type=('build', 'run'))
+    depends_on('r-rcpparmadillo', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rgraphviz/package.py b/var/spack/repos/builtin/packages/r-rgraphviz/package.py
index 1250ca0f82..0ba51737d7 100644
--- a/var/spack/repos/builtin/packages/r-rgraphviz/package.py
+++ b/var/spack/repos/builtin/packages/r-rgraphviz/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RRgraphviz(RPackage):
-    """Provides plotting capabilities for R graph objects
+    """Provides plotting capabilities for R graph objects.
 
        Interfaces R with the AT and T graphviz library for plotting R graph
        objects from the graph package."""
 
-    homepage = "https://bioconductor.org/packages/Rgraphviz"
-    git      = "https://git.bioconductor.org/packages/Rgraphviz.git"
+    bioc = "Rgraphviz"
 
+    version('2.38.0', commit='004de09a5b171211aff6cbaa1969ab8e3a5d6c61')
     version('2.34.0', commit='9746623211be794226258631992dfcccccfd7487')
     version('2.28.0', commit='c1f57c11f037c977f1d17f227f12a09a999e8c0b')
     version('2.26.0', commit='e9b08c77121a45c65129d94a12b5c0b31c65617f')
diff --git a/var/spack/repos/builtin/packages/r-rhdf5/package.py b/var/spack/repos/builtin/packages/r-rhdf5/package.py
index 058bbdf106..84dcbb1758 100644
--- a/var/spack/repos/builtin/packages/r-rhdf5/package.py
+++ b/var/spack/repos/builtin/packages/r-rhdf5/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RRhdf5(RPackage):
-    """R Interface to HDF5
+    """R Interface to HDF5.
 
        This package provides an interface between HDF5 and R. HDF5's main
        features are the ability to store and access very large and/or complex
@@ -17,9 +17,9 @@ class RRhdf5(RPackage):
        software package, and for letting R applications work on datasets that
        are larger than the available RAM."""
 
-    homepage = "https://bioconductor.org/packages/rhdf5"
-    git      = "https://git.bioconductor.org/packages/rhdf5.git"
+    bioc = "rhdf5"
 
+    version('2.38.0', commit='f6fdfa807f5cd5a4d11d4aa6ebfaa81c118b4c3f')
     version('2.34.0', commit='ec861b81fc6962e844bf56b7549ba565a7e4c69c')
     version('2.28.1', commit='e230fa34d6f3e97dd4e6065115675baf5e8213bb')
     version('2.26.2', commit='81e11258db493661a19cf83e142b690ecac4e6cf')
@@ -27,10 +27,13 @@ class RRhdf5(RPackage):
     version('2.22.0', commit='4431bdc0a2bcbb8086ee08a0f2300129b808d1be')
     version('2.20.0', commit='37b5165325062728bbec9167f89f5f4b794f30bc')
 
-    depends_on('r@3.5.0:', when='@2.26.2:', type=('build', 'run'))
-    depends_on('r-rhdf5lib', when='@2.24.0:', type=('build', 'run'))
-    depends_on('r-rhdf5lib@1.3.2:', when='@2.26.2:', type=('build', 'run'))
-    depends_on('r-rhdf5lib@1.11.0:', when='@2.34.0:', type=('build', 'run'))
-    depends_on('r-rhdf5filters', when='@2.34.0:', type=('build', 'run'))
-    depends_on('r-zlibbioc', when='@:2.28.1', type=('build', 'run'))
+    depends_on('r@3.5.0:', type=('build', 'run'), when='@2.26.2:')
+    depends_on('r@4.0.0:', type=('build', 'run'), when='@2.38.0:')
+    depends_on('r-rhdf5lib', type=('build', 'run'), when='@2.24.0:')
+    depends_on('r-rhdf5lib@1.3.2:', type=('build', 'run'), when='@2.26.2:')
+    depends_on('r-rhdf5lib@1.11.0:', type=('build', 'run'), when='@2.34.0:')
+    depends_on('r-rhdf5lib@1.13.4:', type=('build', 'run'), when='@2.38.0:')
+    depends_on('r-rhdf5filters', type=('build', 'run'), when='@2.34.0:')
     depends_on('gmake', type='build')
+
+    depends_on('r-zlibbioc', type=('build', 'run'), when='@:2.28.1')
diff --git a/var/spack/repos/builtin/packages/r-rhdf5filters/package.py b/var/spack/repos/builtin/packages/r-rhdf5filters/package.py
index c8a8c8894b..2ed7ccaab6 100644
--- a/var/spack/repos/builtin/packages/r-rhdf5filters/package.py
+++ b/var/spack/repos/builtin/packages/r-rhdf5filters/package.py
@@ -7,13 +7,13 @@ from spack import *
 
 
 class RRhdf5filters(RPackage):
-    """HDF5 Compression Filters
+    """HDF5 Compression Filters.
 
     Provides a collection of compression filters for use with HDF5 datasets."""
 
-    homepage = "https://github.com/grimbough/rhdf5filters"
-    git      = "https://git.bioconductor.org/packages/rhdf5filters"
+    bioc = "rhdf5filters"
 
+    version('1.6.0', commit='5f7f3a5b7dabd6e7d0c50cda70290e2472ff4f53')
     version('1.2.0', commit='25af0180f926b4b3ea11b30ec9277d26ad3d56b3')
 
     depends_on('r-rhdf5lib', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rhdf5lib/package.py b/var/spack/repos/builtin/packages/r-rhdf5lib/package.py
index 8b3bd015a8..d47e579ec3 100644
--- a/var/spack/repos/builtin/packages/r-rhdf5lib/package.py
+++ b/var/spack/repos/builtin/packages/r-rhdf5lib/package.py
@@ -7,18 +7,19 @@ from spack import *
 
 
 class RRhdf5lib(RPackage):
-    """hdf5 library as an R package
+    """hdf5 library as an R package.
 
        Provides C and C++ hdf5 libraries."""
 
-    homepage = "https://bioconductor.org/packages/Rhdf5lib"
-    git      = "https://git.bioconductor.org/packages/Rhdf5lib.git"
+    bioc = "Rhdf5lib"
 
+    version('1.16.0', commit='534c49705dbdb27ae0c564acff2c72df2b27b3f1')
     version('1.12.1', commit='cf464f40fd95274d0d351cf28b586c49307c4f0b')
     version('1.6.3', commit='11ac3069f28b0068002db9c645817401f6c5b3c4')
     version('1.4.3', commit='f6be8c2659b2daa17541506058917b7981490d65')
     version('1.2.1', commit='dbf85dbedb736d5a696794d52875729c8514494e')
     version('1.0.0', commit='79608038c2016a518ba747fe6a2bf02ce53a75f9')
 
-    depends_on('r@3.3.0:', when='@1.12.1:', type='build')
+    depends_on('r@3.3.0:', type='build', when='@1.12.1:')
+    depends_on('r@4.0.0:', type='build', when='@1.16.0:')
     depends_on('gmake', type='build')
diff --git a/var/spack/repos/builtin/packages/r-rhtslib/package.py b/var/spack/repos/builtin/packages/r-rhtslib/package.py
index c052b311f0..6f86945770 100644
--- a/var/spack/repos/builtin/packages/r-rhtslib/package.py
+++ b/var/spack/repos/builtin/packages/r-rhtslib/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RRhtslib(RPackage):
-    """HTSlib high-throughput sequencing library as an R package
+    """HTSlib high-throughput sequencing library as an R package.
 
        This package provides version 1.7 of the 'HTSlib' C library for high-
        throughput sequence analysis. The package is primarily useful to
@@ -15,9 +15,9 @@ class RRhtslib(RPackage):
        Motivation and instructions for use of this package are in the vignette,
        vignette(package="Rhtslib", "Rhtslib")."""
 
-    homepage = "https://bioconductor.org/packages/Rhtslib"
-    git      = "https://git.bioconductor.org/packages/Rhtslib.git"
+    bioc = "Rhtslib"
 
+    version('1.26.0', commit='f5b20e97b283942877529f750b28398782552655')
     version('1.22.0', commit='899b79faa54d42c7c9b9a2bc49972109637d367f')
     version('1.18.1', commit='751a2ebaed43b7991204b27bd6c7870645001d82')
     version('1.16.3', commit='3ed0b5db2ee3cf0df1c6096fde8855c8485eebd4')
@@ -35,7 +35,7 @@ class RRhtslib(RPackage):
     # Some versions of this package will leave the temporary installation
     # directory in the htslib shared object. R will fix this if patchelf is
     # available
-    depends_on('patchelf', when='@1.12:1.14', type='build')
+    depends_on('patchelf', type='build', when='@1.12:1.14')
 
     patch('use_spack_Makeconf.patch', when='@1.12:')
     patch('find_deps-1.12.patch', when='@1.12:1.14')
diff --git a/var/spack/repos/builtin/packages/r-rnaseqmap/package.py b/var/spack/repos/builtin/packages/r-rnaseqmap/package.py
index e1fa7b1309..0378e1f653 100644
--- a/var/spack/repos/builtin/packages/r-rnaseqmap/package.py
+++ b/var/spack/repos/builtin/packages/r-rnaseqmap/package.py
@@ -7,14 +7,13 @@ from spack import *
 
 
 class RRnaseqmap(RPackage):
-    """rnaSeq secondary analyses
+    """rnaSeq secondary analyses.
 
        The rnaSeqMap library provides classes and functions to analyze the RNA-
        sequencing data using the coverage profiles in multiple samples at a
        time"""
 
-    homepage = "https://bioconductor.org/packages/rnaSeqMap"
-    git      = "https://git.bioconductor.org/packages/rnaSeqMap.git"
+    bioc = "rnaSeqMap"
 
     version('2.48.0', commit='a8c515e518cebf571d1524c3a8a986ba7d1557db')
     version('2.42.0', commit='3a3a1030cc38d79d04536e0ab16114e4fa6721cf')
diff --git a/var/spack/repos/builtin/packages/r-roc/package.py b/var/spack/repos/builtin/packages/r-roc/package.py
index cae16c3b2d..6da81d310b 100644
--- a/var/spack/repos/builtin/packages/r-roc/package.py
+++ b/var/spack/repos/builtin/packages/r-roc/package.py
@@ -7,13 +7,13 @@ from spack import *
 
 
 class RRoc(RPackage):
-    """utilities for ROC, with microarray focus
+    """utilities for ROC, with microarray focus.
 
     Provide utilities for ROC, with microarray focus."""
 
-    homepage = "https://bioconductor.org/packages/release/bioc/html/ROC.html"
-    git      = "https://git.bioconductor.org/packages/ROC"
+    bioc = "ROC"
 
+    version('1.70.0', commit='44fd639958b9b1be4f8f731dc2be9dd91b2fa632')
     version('1.66.0', commit='62701ee41f48f99d15344127384fa032db69486f')
     version('1.62.0', commit='60250fdb091f6a938709b8a2cffe6442ee22a9a2')
 
diff --git a/var/spack/repos/builtin/packages/r-rots/package.py b/var/spack/repos/builtin/packages/r-rots/package.py
index 202344810a..329aa6f138 100644
--- a/var/spack/repos/builtin/packages/r-rots/package.py
+++ b/var/spack/repos/builtin/packages/r-rots/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RRots(RPackage):
-    """Reproducibility-Optimized Test Statistic
+    """Reproducibility-Optimized Test Statistic.
 
        Calculates the Reproducibility-Optimized Test Statistic (ROTS) for
        differential testing in omics data."""
 
-    homepage = "https://bioconductor.org/packages/ROTS"
-    git      = "https://git.bioconductor.org/packages/ROTS.git"
+    bioc = "ROTS"
 
+    version('1.22.0', commit='a53ec77c40ed3b3c84e91d794c1602dd509cad83')
     version('1.18.0', commit='1d4e206a8ce68d5a1417ff51c26174ed9d0ba7d2')
     version('1.12.0', commit='7e2c96fd8fd36710321498745f24cc6b59ac02f0')
     version('1.10.1', commit='1733d3f868cef4d81af6edfc102221d80793937b')
diff --git a/var/spack/repos/builtin/packages/r-rsamtools/package.py b/var/spack/repos/builtin/packages/r-rsamtools/package.py
index b96f7c1b6e..bfaa8e2c4d 100644
--- a/var/spack/repos/builtin/packages/r-rsamtools/package.py
+++ b/var/spack/repos/builtin/packages/r-rsamtools/package.py
@@ -8,16 +8,16 @@ from spack import *
 
 class RRsamtools(RPackage):
     """Binary alignment (BAM), FASTA, variant call (BCF), and tabix file
-       import
+       import.
 
        This package provides an interface to the 'samtools', 'bcftools', and
        'tabix' utilities for manipulating SAM (Sequence Alignment / Map),
        FASTA, binary variant call (BCF) and compressed indexed tab-delimited
        (tabix) files."""
 
-    homepage = "https://bioconductor.org/packages/Rsamtools"
-    git      = "https://git.bioconductor.org/packages/Rsamtools.git"
+    bioc = "Rsamtools"
 
+    version('2.10.0', commit='b19738e85a467f9032fc7903be3ba10e655e7061')
     version('2.6.0', commit='f2aea061517c5a55e314c039251ece9831c7fad2')
     version('2.2.1', commit='f10084658b4c9744961fcacd79c0ae9a7a40cd30')
     version('2.0.3', commit='17d254cc026574d20db67474260944bf60befd70')
@@ -26,24 +26,25 @@ class RRsamtools(RPackage):
     version('1.30.0', commit='61b365fe3762e796b3808cec7238944b7f68d7a6')
     version('1.28.0', commit='dfa5b6abef68175586f21add7927174786412472')
 
+    depends_on('r@3.5.0:', type=('build', 'run'), when='@2.10.0:')
     depends_on('r-genomeinfodb@1.1.3:', type=('build', 'run'))
     depends_on('r-genomicranges@1.21.6:', type=('build', 'run'))
-    depends_on('r-genomicranges@1.31.8:', when='@1.32.3:', type=('build', 'run'))
+    depends_on('r-genomicranges@1.31.8:', type=('build', 'run'), when='@1.32.3:')
     depends_on('r-biostrings@2.37.1:', type=('build', 'run'))
-    depends_on('r-biostrings@2.47.6:', when='@1.32.3:', type=('build', 'run'))
+    depends_on('r-biostrings@2.47.6:', type=('build', 'run'), when='@1.32.3:')
     depends_on('r-biocgenerics@0.1.3:', type=('build', 'run'))
-    depends_on('r-biocgenerics@0.25.1:', when='@1.32.3:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.25.1:', type=('build', 'run'), when='@1.32.3:')
     depends_on('r-s4vectors@0.13.8:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.17.25:', when='@1.32.3:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.25:', type=('build', 'run'), when='@1.32.3:')
     depends_on('r-iranges@2.3.7:', type=('build', 'run'))
-    depends_on('r-iranges@2.13.12:', when='@1.32.3:', type=('build', 'run'))
+    depends_on('r-iranges@2.13.12:', type=('build', 'run'), when='@1.32.3:')
     depends_on('r-xvector@0.15.1:', type=('build', 'run'))
-    depends_on('r-xvector@0.19.7:', when='@1.32.3:', type=('build', 'run'))
+    depends_on('r-xvector@0.19.7:', type=('build', 'run'), when='@1.32.3:')
     depends_on('r-zlibbioc', type=('build', 'run'))
     depends_on('r-bitops', type=('build', 'run'))
     depends_on('r-biocparallel', type=('build', 'run'))
-    depends_on('r-rhtslib@1.16.3', when='@2.0.3', type=('build', 'run'))
-    depends_on('r-rhtslib@1.17.7:', when='@2.2.1:', type=('build', 'run'))
+    depends_on('r-rhtslib@1.16.3', type=('build', 'run'), when='@2.0.3')
+    depends_on('r-rhtslib@1.17.7:', type=('build', 'run'), when='@2.2.1:')
     depends_on('gmake', type='build')
 
     # this is not a listed dependency but is needed
diff --git a/var/spack/repos/builtin/packages/r-rtracklayer/package.py b/var/spack/repos/builtin/packages/r-rtracklayer/package.py
index b2b1db51cb..56280ffc87 100644
--- a/var/spack/repos/builtin/packages/r-rtracklayer/package.py
+++ b/var/spack/repos/builtin/packages/r-rtracklayer/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RRtracklayer(RPackage):
-    """R interface to genome annotation files and the UCSC genome browser
+    """R interface to genome annotation files and the UCSC genome browser.
 
        Extensible framework for interacting with multiple genome browsers
        (currently UCSC built-in) and manipulating annotation tracks in various
@@ -16,9 +16,9 @@ class RRtracklayer(RPackage):
        browsers, as well as query and modify the browser state, such as the
        current viewport."""
 
-    homepage = "https://bioconductor.org/packages/rtracklayer"
-    git      = "https://git.bioconductor.org/packages/rtracklayer.git"
+    bioc = "rtracklayer"
 
+    version('1.54.0', commit='04cdd75521a8364e67a49d7352500dd4a3e83c55')
     version('1.50.0', commit='d2e61f72ff5d5a94c2c487ba108a37f23bfcc1e6')
     version('1.44.4', commit='aec96e85daf53b5c5eb2e89250d2755352be4de3')
     version('1.42.2', commit='76702f671faea736807d54aeecfbadcd152d94c5')
@@ -28,27 +28,29 @@ class RRtracklayer(RPackage):
 
     depends_on('r@3.3:', type=('build', 'run'))
     depends_on('r-genomicranges@1.21.20:', type=('build', 'run'))
-    depends_on('r-genomicranges@1.37.2:', when='@1.50.0:', type=('build', 'run'))
+    depends_on('r-genomicranges@1.37.2:', type=('build', 'run'), when='@1.50.0:')
     depends_on('r-xml@1.98-0:', type=('build', 'run'))
     depends_on('r-biocgenerics@0.13.8:', type=('build', 'run'))
-    depends_on('r-biocgenerics@0.25.1:', when='@1.40.6:', type=('build', 'run'))
-    depends_on('r-biocgenerics@0.35.3:', when='@1.50.0:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.25.1:', type=('build', 'run'), when='@1.40.6:')
+    depends_on('r-biocgenerics@0.35.3:', type=('build', 'run'), when='@1.50.0:')
     depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.17.25:', when='@1.40.6:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.19.22:', when='@1.42.2:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.23.18:', when='@1.50.0:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.25:', type=('build', 'run'), when='@1.40.6:')
+    depends_on('r-s4vectors@0.19.22:', type=('build', 'run'), when='@1.42.2:')
+    depends_on('r-s4vectors@0.23.18:', type=('build', 'run'), when='@1.50.0:')
     depends_on('r-iranges@2.3.7:', type=('build', 'run'))
-    depends_on('r-iranges@2.11.12:', when='@1.38.3:', type=('build', 'run'))
-    depends_on('r-iranges@2.13.13:', when='@1.40.6:', type=('build', 'run'))
+    depends_on('r-iranges@2.11.12:', type=('build', 'run'), when='@1.38.3:')
+    depends_on('r-iranges@2.13.13:', type=('build', 'run'), when='@1.40.6:')
     depends_on('r-xvector@0.9.4:', type=('build', 'run'))
-    depends_on('r-xvector@0.19.7:', when='@1.40.6:', type=('build', 'run'))
+    depends_on('r-xvector@0.19.7:', type=('build', 'run'), when='@1.40.6:')
     depends_on('r-genomeinfodb@1.3.14:', type=('build', 'run'))
-    depends_on('r-genomeinfodb@1.15.2:', when='@1.40.6:', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.15.2:', type=('build', 'run'), when='@1.40.6:')
     depends_on('r-biostrings@2.43.7:', type=('build', 'run'))
-    depends_on('r-biostrings@2.47.6:', when='@1.40.6:', type=('build', 'run'))
+    depends_on('r-biostrings@2.47.6:', type=('build', 'run'), when='@1.40.6:')
     depends_on('r-zlibbioc', type=('build', 'run'))
     depends_on('r-rcurl@1.4-2:', type=('build', 'run'))
     depends_on('r-rsamtools@1.17.8:', type=('build', 'run'))
-    depends_on('r-rsamtools@1.31.2:', when='@1.40.6:', type=('build', 'run'))
+    depends_on('r-rsamtools@1.31.2:', type=('build', 'run'), when='@1.40.6:')
     depends_on('r-genomicalignments@1.5.4:', type=('build', 'run'))
-    depends_on('r-genomicalignments@1.15.6:', when='@1.40.6:', type=('build', 'run'))
+    depends_on('r-genomicalignments@1.15.6:', type=('build', 'run'), when='@1.40.6:')
+    depends_on('r-biocio', type=('build', 'run'), when='@1.54.0:')
+    depends_on('r-restfulr@0.0.13:', type=('build', 'run'), when='@1.54.0:')
diff --git a/var/spack/repos/builtin/packages/r-s4vectors/package.py b/var/spack/repos/builtin/packages/r-s4vectors/package.py
index 58053088a5..ca6cec34ee 100644
--- a/var/spack/repos/builtin/packages/r-s4vectors/package.py
+++ b/var/spack/repos/builtin/packages/r-s4vectors/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RS4vectors(RPackage):
-    """Foundation of vector-like and list-like containers in Bioconductor
+    """Foundation of vector-like and list-like containers in Bioconductor.
 
        The S4Vectors package defines the Vector and List virtual classes and a
        set of generic functions that extend the semantic of ordinary vectors
@@ -18,9 +18,9 @@ class RS4vectors(RPackage):
        more are implemented in the IRanges package and in other Bioconductor
        infrastructure packages)."""
 
-    homepage = "https://bioconductor.org/packages/S4Vectors"
-    git      = "https://git.bioconductor.org/packages/S4Vectors.git"
+    bioc = "S4Vectors"
 
+    version('0.32.3', commit='ad90e78fd3a4059cfcf2846498fb0748b4394e1a')
     version('0.28.1', commit='994cb7ef830e76f8b43169cc72b553869fafb2ed')
     version('0.26.1', commit='935769c')
     version('0.22.1', commit='d25e517b48ca4184a4c2ee1f8223c148a55a8b8a')
@@ -30,8 +30,9 @@ class RS4vectors(RPackage):
     version('0.14.7', commit='40af17fe0b8e93b6a72fc787540d2961773b8e23')
 
     depends_on('r@3.3.0:', type=('build', 'run'))
-    depends_on('r@4.0.0:', when='@0.28.1:', type=('build', 'run'))
+    depends_on('r@4.0.0:', type=('build', 'run'), when='@0.28.1:')
     depends_on('r-biocgenerics@0.21.1:', type=('build', 'run'))
-    depends_on('r-biocgenerics@0.23.3:', when='@0.16.0:0.22.1', type=('build', 'run'))
-    depends_on('r-biocgenerics@0.31.1:', when='@0.26.1:', type=('build', 'run'))
-    depends_on('r-biocgenerics@0.36.0:', when='@0.28.1:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.23.3:', type=('build', 'run'), when='@0.16.0:0.22.1')
+    depends_on('r-biocgenerics@0.31.1:', type=('build', 'run'), when='@0.26.1:')
+    depends_on('r-biocgenerics@0.36.0:', type=('build', 'run'), when='@0.28.1:')
+    depends_on('r-biocgenerics@0.37.0:', type=('build', 'run'), when='@0.32.3:')
diff --git a/var/spack/repos/builtin/packages/r-scaledmatrix/package.py b/var/spack/repos/builtin/packages/r-scaledmatrix/package.py
new file mode 100644
index 0000000000..0d92fadf2d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-scaledmatrix/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RScaledmatrix(RPackage):
+    """Creating a DelayedMatrix of Scaled and Centered Values.
+
+    Provides delayed computation of a matrix of scaled and centered values.
+    The result is equivalent to using the scale() function but avoids explicit
+    realization of a dense matrix during block processing. This permits greater
+    efficiency in common operations, most notably matrix multiplication."""
+
+    bioc = "ScaledMatrix"
+
+    version('1.2.0', commit='d0573e14ca537b40ade7dd1c9cf0cadae60d4349')
+
+    depends_on('r-matrix', type=('build', 'run'))
+    depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-delayedarray', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-scater/package.py b/var/spack/repos/builtin/packages/r-scater/package.py
index cd1d966935..ac914eee67 100644
--- a/var/spack/repos/builtin/packages/r-scater/package.py
+++ b/var/spack/repos/builtin/packages/r-scater/package.py
@@ -7,15 +7,15 @@ from spack import *
 
 
 class RScater(RPackage):
-    """Single-Cell Analysis Toolkit for Gene Expression Data in R
+    """Single-Cell Analysis Toolkit for Gene Expression Data in R.
 
        A collection of tools for doing various analyses of single-cell RNA-seq
        gene expression data, with a focus on quality control and
        visualization."""
 
-    homepage = "https://bioconductor.org/packages/scater"
-    git      = "https://git.bioconductor.org/packages/scater.git"
+    bioc = "scater"
 
+    version('1.22.0', commit='ea2c95c53adb8c6fab558c1cb869e2eab36aa9f8')
     version('1.18.3', commit='a94e7f413bf0f5f527b41b0b34e7a8e5c947ae37')
     version('1.12.2', commit='1518dc27a87c79181c34107d639e95fe55e55092')
     version('1.10.1', commit='2e6694af2929092f263c2b0830d48b3f9632e70c')
@@ -23,41 +23,45 @@ class RScater(RPackage):
     version('1.6.3', commit='964effb4e883102d7c8cae627dbac4ba5d216a75')
     version('1.4.0', commit='90a2eab66ff82ba6dd7fbb33e41cd0ded20fa218')
 
-    depends_on('r@3.3:', when='@1.4.0', type=('build', 'run'))
-    depends_on('r@3.4:', when='@1.6.3', type=('build', 'run'))
-    depends_on('r@3.5:', when='@1.8.4', type=('build', 'run'))
-    depends_on('r@3.6:', when='@1.12.2', type=('build', 'run'))
-    depends_on('r-singlecellexperiment', when='@1.6.3:', type=('build', 'run'))
+    depends_on('r@3.3:', type=('build', 'run'), when='@1.4.0')
+    depends_on('r@3.4:', type=('build', 'run'), when='@1.6.3')
+    depends_on('r@3.5:', type=('build', 'run'), when='@1.8.4')
+    depends_on('r@3.6:', type=('build', 'run'), when='@1.12.2')
+    depends_on('r-singlecellexperiment', type=('build', 'run'), when='@1.6.3:')
+    depends_on('r-scuttle', type=('build', 'run'), when='@1.18.3:')
     depends_on('r-ggplot2', type=('build', 'run'))
-    depends_on('r-gridextra', when='@1.18.3:', type=('build', 'run'))
+    depends_on('r-gridextra', type=('build', 'run'), when='@1.18.3:')
     depends_on('r-matrix', type=('build', 'run'))
     depends_on('r-biocgenerics', type=('build', 'run'))
-    depends_on('r-s4vectors', when='@1.6.3:', type=('build', 'run'))
-    depends_on('r-summarizedexperiment', when='@1.6.3:', type=('build', 'run'))
-    depends_on('r-delayedarray', when='@1.8.4:', type=('build', 'run'))
-    depends_on('r-delayedmatrixstats', when='@1.8.4:', type=('build', 'run'))
-    depends_on('r-biocneighbors', when='@1.12.2:', type=('build', 'run'))
-    depends_on('r-biocsingular', when='@1.12.2:', type=('build', 'run'))
-    depends_on('r-biocparallel', when='@1.10.1:', type=('build', 'run'))
-    depends_on('r-scuttle', when='@1.18.3:', type=('build', 'run'))
-    depends_on('r-rlang', when='@1.18.3:', type=('build', 'run'))
+    depends_on('r-s4vectors', type=('build', 'run'), when='@1.6.3:')
+    depends_on('r-summarizedexperiment', type=('build', 'run'), when='@1.6.3:')
+    depends_on('r-delayedarray', type=('build', 'run'), when='@1.8.4:')
+    depends_on('r-delayedmatrixstats', type=('build', 'run'), when='@1.8.4:')
+    depends_on('r-beachmat', type=('build', 'run'), when='@1.6.3:1.12.2,1.22.0:')
+    depends_on('r-biocneighbors', type=('build', 'run'), when='@1.12.2:')
+    depends_on('r-biocsingular', type=('build', 'run'), when='@1.12.2:')
+    depends_on('r-biocparallel', type=('build', 'run'), when='@1.10.1:')
+    depends_on('r-rlang', type=('build', 'run'), when='@1.18.3:')
     depends_on('r-ggbeeswarm', type=('build', 'run'))
     depends_on('r-viridis', type=('build', 'run'))
-    depends_on('r-biobase', when='@1.4.0:1.8.4', type=('build', 'run'))
-    depends_on('r-biomart', when='@1.4.0:1.6.3', type=('build', 'run'))
-    depends_on('r-data-table', when='@1.4.0:1.6.3', type=('build', 'run'))
-    depends_on('r-dplyr', when='@1.4.0:1.12.2', type=('build', 'run'))
-    depends_on('r-edger', when='@1.4.0:1.8.4', type=('build', 'run'))
-    depends_on('r-limma', when='@1.4.0:1.8.4', type=('build', 'run'))
-    depends_on('r-matrixstats', when='@1.4.0:1.6.3', type=('build', 'run'))
-    depends_on('r-plyr', when='@1.4.0:1.8.4', type=('build', 'run'))
-    depends_on('r-reshape2', when='@1.4.0:1.10.1', type=('build', 'run'))
-    depends_on('r-rhdf5', when='@1.4.0:1.8.4', type=('build', 'run'))
-    depends_on('r-rjson', when='@1.4.0:1.8.4', type=('build', 'run'))
-    depends_on('r-shiny', when='@1.4.0:1.8.4', type=('build', 'run'))
-    depends_on('r-shinydashboard', when='@1.4.0:1.8.4', type=('build', 'run'))
-    depends_on('r-tximport', when='@1.4.0:1.8.4', type=('build', 'run'))
-    depends_on('r-rcpp', when='@1.6.3:1.12.2', type=('build', 'run'))
-    depends_on('r-rcpp@0.12.14:', when='@1.8.4:1.12.2', type=('build', 'run'))
-    depends_on('r-rhdf5lib', when='@1.6.3:1.10.1', type=('build', 'run'))
-    depends_on('r-beachmat', when='@1.6.3:1.12.2', type=('build', 'run'))
+    depends_on('r-rtsne', type=('build', 'run'), when='@1.22.0:')
+    depends_on('r-rcolorbrewer', type=('build', 'run'), when='@1.22.0:')
+    depends_on('r-ggrepel', type=('build', 'run'), when='@1.22.0:')
+
+    depends_on('r-biobase', type=('build', 'run'), when='@1.4.0:1.8.4')
+    depends_on('r-biomart', type=('build', 'run'), when='@1.4.0:1.6.3')
+    depends_on('r-data-table', type=('build', 'run'), when='@1.4.0:1.6.3')
+    depends_on('r-dplyr', type=('build', 'run'), when='@1.4.0:1.12.2')
+    depends_on('r-edger', type=('build', 'run'), when='@1.4.0:1.8.4')
+    depends_on('r-limma', type=('build', 'run'), when='@1.4.0:1.8.4')
+    depends_on('r-matrixstats', type=('build', 'run'), when='@1.4.0:1.6.3')
+    depends_on('r-plyr', type=('build', 'run'), when='@1.4.0:1.8.4')
+    depends_on('r-reshape2', type=('build', 'run'), when='@1.4.0:1.10.1')
+    depends_on('r-rhdf5', type=('build', 'run'), when='@1.4.0:1.8.4')
+    depends_on('r-rjson', type=('build', 'run'), when='@1.4.0:1.8.4')
+    depends_on('r-shiny', type=('build', 'run'), when='@1.4.0:1.8.4')
+    depends_on('r-shinydashboard', type=('build', 'run'), when='@1.4.0:1.8.4')
+    depends_on('r-tximport', type=('build', 'run'), when='@1.4.0:1.8.4')
+    depends_on('r-rcpp', type=('build', 'run'), when='@1.6.3:1.12.2')
+    depends_on('r-rcpp@0.12.14:', type=('build', 'run'), when='@1.8.4:1.12.2')
+    depends_on('r-rhdf5lib', type=('build', 'run'), when='@1.6.3:1.10.1')
diff --git a/var/spack/repos/builtin/packages/r-scuttle/package.py b/var/spack/repos/builtin/packages/r-scuttle/package.py
index 602b92d402..9cf8a47490 100644
--- a/var/spack/repos/builtin/packages/r-scuttle/package.py
+++ b/var/spack/repos/builtin/packages/r-scuttle/package.py
@@ -7,16 +7,16 @@ from spack import *
 
 
 class RScuttle(RPackage):
-    """Single-Cell RNA-Seq Analysis Utilities
+    """Single-Cell RNA-Seq Analysis Utilities.
 
     Provides basic utility functions for performing single-cell analyses,
     focusing on simple normalization, quality control and data transformations.
     Also provides some helper functions to assist development of other
     packages."""
 
-    homepage = "https://bioconductor.org/packages/scuttle/"
-    git      = "https://git.bioconductor.org/packages/scuttle"
+    bioc = "scuttle"
 
+    version('1.4.0', commit='b335263dd56bb859b5dd3ea27ee00dffa0215313')
     version('1.0.4', commit='a827e2759d80e6c3510e2f8fd4bd680274206d9f')
 
     depends_on('r-singlecellexperiment', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-seqlogo/package.py b/var/spack/repos/builtin/packages/r-seqlogo/package.py
index b092d9e958..4b6e04664f 100644
--- a/var/spack/repos/builtin/packages/r-seqlogo/package.py
+++ b/var/spack/repos/builtin/packages/r-seqlogo/package.py
@@ -7,15 +7,15 @@ from spack import *
 
 
 class RSeqlogo(RPackage):
-    """Sequence logos for DNA sequence alignments
+    """Sequence logos for DNA sequence alignments.
 
        seqLogo takes the position weight matrix of a DNA sequence motif and
        plots the corresponding sequence logo as introduced by Schneider and
        Stephens (1990)."""
 
-    homepage = "https://bioconductor.org/packages/seqLogo"
-    git      = "https://git.bioconductor.org/packages/seqLogo.git"
+    bioc = "seqLogo"
 
+    version('1.60.0', commit='4115c8e1d01accb8c8cc1cf96f23359466827e16')
     version('1.56.0', commit='169260c43fc58dc75becb3b7842cac3d0038a8d5')
     version('1.50.0', commit='57986221c90c3920f9829756c4b3ee566dc1e14d')
     version('1.48.0', commit='dde85582e7fd0c08c5b8bc73f9aed8f23b727d9d')
diff --git a/var/spack/repos/builtin/packages/r-shortread/package.py b/var/spack/repos/builtin/packages/r-shortread/package.py
index 664de313c2..4e53af95b8 100644
--- a/var/spack/repos/builtin/packages/r-shortread/package.py
+++ b/var/spack/repos/builtin/packages/r-shortread/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RShortread(RPackage):
-    """FASTQ input and manipulation
+    """FASTQ input and manipulation.
 
        This package implements sampling, iteration, and input of FASTQ files.
        The package includes functions for filtering and trimming reads, and for
@@ -16,9 +16,9 @@ class RShortread(RPackage):
        purposes. The package also contains legacy support for early single-end,
        ungapped alignment formats."""
 
-    homepage = "https://bioconductor.org/packages/ShortRead"
-    git      = "https://git.bioconductor.org/packages/ShortRead.git"
+    bioc = "ShortRead"
 
+    version('1.52.0', commit='4d7304d7b5a0ca5c904c0b919d6c95599db72a39')
     version('1.48.0', commit='ba44cd2517bc0e6f46d2cfcfce393f86eec814d0')
     version('1.42.0', commit='daa2576a48278460caf87f42c022c796652f4908')
     version('1.40.0', commit='0cbe4b62b0be4c5f2e2670da17493423446e008f')
@@ -27,26 +27,26 @@ class RShortread(RPackage):
     version('1.34.2', commit='25daac63b301df66a8ef6e98cc2977522c6786cd')
 
     depends_on('r-biocgenerics@0.22.1:', type=('build', 'run'))
-    depends_on('r-biocgenerics@0.23.3:', when='@1.36.1:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.23.3:', type=('build', 'run'), when='@1.36.1:')
     depends_on('r-biocparallel', type=('build', 'run'))
     depends_on('r-biostrings@2.37.1:', type=('build', 'run'))
-    depends_on('r-biostrings@2.47.6:', when='@1.38.0:', type=('build', 'run'))
+    depends_on('r-biostrings@2.47.6:', type=('build', 'run'), when='@1.38.0:')
     depends_on('r-rsamtools@1.21.4:', type=('build', 'run'))
-    depends_on('r-rsamtools@1.31.2:', when='@1.38.0:', type=('build', 'run'))
+    depends_on('r-rsamtools@1.31.2:', type=('build', 'run'), when='@1.38.0:')
     depends_on('r-genomicalignments@1.5.4:', type=('build', 'run'))
-    depends_on('r-genomicalignments@1.15.6:', when='@1.38.0:', type=('build', 'run'))
+    depends_on('r-genomicalignments@1.15.6:', type=('build', 'run'), when='@1.38.0:')
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-s4vectors@0.13.8:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.17.25:', when='@1.38.0:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.25:', type=('build', 'run'), when='@1.38.0:')
     depends_on('r-iranges@2.3.7:', type=('build', 'run'))
-    depends_on('r-iranges@2.13.12:', when='@1.38.0:', type=('build', 'run'))
+    depends_on('r-iranges@2.13.12:', type=('build', 'run'), when='@1.38.0:')
     depends_on('r-genomeinfodb@1.1.19:', type=('build', 'run'))
-    depends_on('r-genomeinfodb@1.15.2:', when='@1.38.0:', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.15.2:', type=('build', 'run'), when='@1.38.0:')
     depends_on('r-genomicranges@1.21.6:', type=('build', 'run'))
-    depends_on('r-genomicranges@1.31.8:', when='@1.38.0:', type=('build', 'run'))
+    depends_on('r-genomicranges@1.31.8:', type=('build', 'run'), when='@1.38.0:')
     depends_on('r-hwriter', type=('build', 'run'))
     depends_on('r-zlibbioc', type=('build', 'run'))
     depends_on('r-lattice', type=('build', 'run'))
     depends_on('r-latticeextra', type=('build', 'run'))
     depends_on('r-xvector', type=('build', 'run'))
-    depends_on('r-rhtslib', when='@1.48.0:', type=('build', 'run'))
+    depends_on('r-rhtslib', type=('build', 'run'), when='@1.48.0:')
diff --git a/var/spack/repos/builtin/packages/r-siggenes/package.py b/var/spack/repos/builtin/packages/r-siggenes/package.py
index 7d3e136ac9..838cb4cc5f 100644
--- a/var/spack/repos/builtin/packages/r-siggenes/package.py
+++ b/var/spack/repos/builtin/packages/r-siggenes/package.py
@@ -7,16 +7,16 @@ from spack import *
 
 
 class RSiggenes(RPackage):
-    """Multiple Testing using SAM and Efron's Empirical Bayes Approaches
+    """Multiple Testing using SAM and Efron's Empirical Bayes Approaches.
 
        Identification of differentially expressed genes and estimation of the
        False Discovery Rate (FDR) using both the Significance Analysis of
        Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays
        (EBAM)."""
 
-    homepage = "https://bioconductor.org/packages/siggenes"
-    git      = "https://git.bioconductor.org/packages/siggenes.git"
+    bioc = "siggenes"
 
+    version('1.68.0', commit='a29bf02b19cc9003c8401608831232b7c2af26e7')
     version('1.64.0', commit='3b528d37c16fc41bbc5c98165f606394313aa050')
     version('1.58.0', commit='69500158d69942cf7c62f583830933cf8baf89a1')
     version('1.56.0', commit='3e929feaa76311be07ff51ad807e657b0b521f6f')
@@ -26,4 +26,4 @@ class RSiggenes(RPackage):
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-multtest', type=('build', 'run'))
-    depends_on('r-scrime@1.2.5:', when='@1.58.0:', type=('build', 'run'))
+    depends_on('r-scrime@1.2.5:', type=('build', 'run'), when='@1.58.0:')
diff --git a/var/spack/repos/builtin/packages/r-simpleaffy/package.py b/var/spack/repos/builtin/packages/r-simpleaffy/package.py
index 2484360eeb..1b1282345b 100644
--- a/var/spack/repos/builtin/packages/r-simpleaffy/package.py
+++ b/var/spack/repos/builtin/packages/r-simpleaffy/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RSimpleaffy(RPackage):
-    """Very simple high level analysis of Affymetrix data
+    """Very simple high level analysis of Affymetrix data.
 
        Provides high level functions for reading Affy .CEL files, phenotypic
        data, and then computing simple things with it, such as t-tests, fold
@@ -15,8 +15,7 @@ class RSimpleaffy(RPackage):
        basic scatter plot functions and mechanisms for generating high
        resolution journal figures..."""
 
-    homepage = "https://bioconductor.org/packages/simpleaffy"
-    git      = "https://git.bioconductor.org/packages/simpleaffy.git"
+    bioc = "simpleaffy"
 
     version('2.66.0', commit='902db69e4ea4b6d306f0c744d3be600f1418ebc9')
     version('2.60.0', commit='b32b5e7d5c65e43c10f98ab8684a1086a06d04f9')
diff --git a/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py b/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py
index 5fc11ec6b6..24374acbec 100644
--- a/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py
+++ b/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py
@@ -7,16 +7,16 @@ from spack import *
 
 
 class RSinglecellexperiment(RPackage):
-    """S4 Classes for Single Cell Data
+    """S4 Classes for Single Cell Data.
 
        Defines a S4 class for storing data from single-cell experiments. This
        includes specialized methods to store and retrieve spike-in information,
        dimensionality reduction coordinates and size factors for each cell,
        along with the usual metadata for genes and libraries."""
 
-    homepage = "https://bioconductor.org/packages/SingleCellExperiment"
-    git      = "https://git.bioconductor.org/packages/SingleCellExperiment.git"
+    bioc = "SingleCellExperiment"
 
+    version('1.16.0', commit='bb27609ba08052607fc08529ffbbbcf1eab265cb')
     version('1.12.0', commit='66063b74c8b0bd0fd1277c7ad425ad11823ab356')
     version('1.6.0', commit='baa51d77a8dacd2a22e7293095a8cffaaa3293b4')
     version('1.4.1', commit='b1efcb338e9176ae6829bb897957aa37e74d4870')
@@ -24,7 +24,9 @@ class RSinglecellexperiment(RPackage):
     version('1.0.0', commit='545e974aa7ca7855e039bf9e3030290cd71d9031')
 
     depends_on('r@3.4:', type=('build', 'run'))
-    depends_on('r@3.5:', when='@1.2.0:1.6.0', type=('build', 'run'))
+    depends_on('r@3.5:', type=('build', 'run'), when='@1.2.0:1.6.0')
     depends_on('r-summarizedexperiment', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
     depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r-genomicranges', type=('build', 'run'), when='@1.16.0:')
+    depends_on('r-delayedarray', type=('build', 'run'), when='@1.16.0:')
diff --git a/var/spack/repos/builtin/packages/r-snprelate/package.py b/var/spack/repos/builtin/packages/r-snprelate/package.py
index a755119caf..8d8ef691b6 100644
--- a/var/spack/repos/builtin/packages/r-snprelate/package.py
+++ b/var/spack/repos/builtin/packages/r-snprelate/package.py
@@ -8,7 +8,7 @@ from spack import *
 
 class RSnprelate(RPackage):
     """Parallel Computing Toolset for Relatedness and Principal Component
-       Analysis of SNP Data
+       Analysis of SNP Data.
 
        Genome-wide association studies (GWAS) are widely used to investigate
        the genetic basis of diseases and traits, but they pose many
@@ -27,9 +27,9 @@ class RSnprelate(RPackage):
        variations (SNVs), insertion/deletion polymorphism (indel) and
        structural variation calls."""
 
-    homepage = "https://bioconductor.org/packages/SNPRelate"
-    git      = "https://git.bioconductor.org/packages/SNPRelate.git"
+    bioc = "SNPRelate"
 
+    version('1.28.0', commit='8fcd837f4627a3bb77cb8d992b2baedd0589d123')
     version('1.24.0', commit='419b13b761ea39a8b1b9bc73097fb0359c59f1c2')
     version('1.18.1', commit='81c581bf76392efdc8ba237ca2e42ca1dba788ca')
     version('1.16.0', commit='0e38e8df4af87dff6c27a23af2867661998c0d85')
diff --git a/var/spack/repos/builtin/packages/r-snpstats/package.py b/var/spack/repos/builtin/packages/r-snpstats/package.py
index 3088540131..78d5a47daf 100644
--- a/var/spack/repos/builtin/packages/r-snpstats/package.py
+++ b/var/spack/repos/builtin/packages/r-snpstats/package.py
@@ -7,15 +7,15 @@ from spack import *
 
 
 class RSnpstats(RPackage):
-    """SnpMatrix and XSnpMatrix classes and methods
+    """SnpMatrix and XSnpMatrix classes and methods.
 
        Classes and statistical methods for large SNP association studies. This
        extends the earlier snpMatrix package, allowing for uncertainty in
        genotypes."""
 
-    homepage = "https://bioconductor.org/packages/snpStats"
-    git      = "https://git.bioconductor.org/packages/snpStats.git"
+    bioc = "snpStats"
 
+    version('1.44.0', commit='72392dab4e75de2da459b1e95f1d48947811597b')
     version('1.40.0', commit='5fcac6f3b4bb6f45c19dff8f3089b693b74a56ce')
     version('1.34.0', commit='e31cdfb18a9e12d70d6a3e8e6fbf7cf8faa3ea5b')
     version('1.32.0', commit='7c31158183b4e39da6dc30c7da275acc36b2e32f')
diff --git a/var/spack/repos/builtin/packages/r-somaticsignatures/package.py b/var/spack/repos/builtin/packages/r-somaticsignatures/package.py
index d83e517bd9..d4f2f781a3 100644
--- a/var/spack/repos/builtin/packages/r-somaticsignatures/package.py
+++ b/var/spack/repos/builtin/packages/r-somaticsignatures/package.py
@@ -7,16 +7,16 @@ from spack import *
 
 
 class RSomaticsignatures(RPackage):
-    """Somatic Signatures
+    """Somatic Signatures.
 
        The SomaticSignatures package identifies mutational signatures of single
        nucleotide variants (SNVs). It provides a infrastructure related to the
        methodology described in Nik-Zainal (2012, Cell), with flexibility in
        the matrix decomposition algorithms."""
 
-    homepage = "https://bioconductor.org/packages/SomaticSignatures"
-    git      = "https://git.bioconductor.org/packages/SomaticSignatures.git"
+    bioc = "SomaticSignatures"
 
+    version('2.30.0', commit='03f7ad707f6530fa7f62093f808884b6e83b0526')
     version('2.26.0', commit='9d4bed6e118ac76755ffb7abd058b09bac58a9d7')
     version('2.20.0', commit='dbedc30d92b600b3a17de596ebe38d15982c70c6')
     version('2.18.0', commit='facccd67eee5202fcbe6ad32e667546546e7ccff')
@@ -35,7 +35,7 @@ class RSomaticsignatures(RPackage):
     depends_on('r-ggplot2', type=('build', 'run'))
     depends_on('r-ggbio', type=('build', 'run'))
     depends_on('r-reshape2', type=('build', 'run'))
-    depends_on('r-nmf', when='@2.26.0:', type=('build', 'run'))
+    depends_on('r-nmf', type=('build', 'run'), when='@2.26.0:')
     depends_on('r-pcamethods', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-proxy', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-sparsematrixstats/package.py b/var/spack/repos/builtin/packages/r-sparsematrixstats/package.py
index 04562ed37c..ab20069edb 100644
--- a/var/spack/repos/builtin/packages/r-sparsematrixstats/package.py
+++ b/var/spack/repos/builtin/packages/r-sparsematrixstats/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RSparsematrixstats(RPackage):
-    """Summary Statistics for Rows and Columns of Sparse Matrices
+    """Summary Statistics for Rows and Columns of Sparse Matrices.
 
     High performance functions for row and column operations on sparse
     matrices.  For example: col / rowMeans2, col / rowMedians, col / rowVars
@@ -15,12 +15,14 @@ class RSparsematrixstats(RPackage):
     format.  This package is inspired by the matrixStats package by Henrik
     Bengtsson."""
 
-    homepage = "https://bioconductor.org/packages/sparseMatrixStats/"
-    git      = "https://git.bioconductor.org/packages/sparseMatrixStats"
+    bioc = "sparseMatrixStats"
 
+    version('1.6.0', commit='78627a842790af42b6634893087b2bb1f4ac0392')
     version('1.2.1', commit='9726f3d5e0f03b50c332d85d5e4c339c18b0494c')
 
     depends_on('r-matrixgenerics', type=('build', 'run'))
+    depends_on('r-matrixgenerics@1.5.3:', type=('build', 'run'), when='@1.6.0:')
     depends_on('r-rcpp', type=('build', 'run'))
     depends_on('r-matrix', type=('build', 'run'))
     depends_on('r-matrixstats', type=('build', 'run'))
+    depends_on('r-matrixstats@0.60.0:', type=('build', 'run'), when='@1.6.0:')
diff --git a/var/spack/repos/builtin/packages/r-spem/package.py b/var/spack/repos/builtin/packages/r-spem/package.py
index 4f79da2b43..f9b490e9f0 100644
--- a/var/spack/repos/builtin/packages/r-spem/package.py
+++ b/var/spack/repos/builtin/packages/r-spem/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RSpem(RPackage):
-    """S-system parameter estimation method
+    """S-system parameter estimation method.
 
        This package can optimize the parameter in S-system models given time
        series data"""
 
-    homepage = "https://bioconductor.org/packages/SPEM"
-    git      = "https://git.bioconductor.org/packages/SPEM.git"
+    bioc = "SPEM"
 
+    version('1.34.0', commit='53fd404638a04ec8e2e826e55c3f2d91d8b28e3d')
     version('1.30.0', commit='6b2eb64bfe6287846b1408297dd46dc772431031')
     version('1.24.0', commit='537ed19e466008f2972a246479b327c95177a99e')
     version('1.22.0', commit='fddb7cd1f81e47eae603724ea149c2adca5b3eb4')
diff --git a/var/spack/repos/builtin/packages/r-sseq/package.py b/var/spack/repos/builtin/packages/r-sseq/package.py
index 72f98ba17d..d6e42020b3 100644
--- a/var/spack/repos/builtin/packages/r-sseq/package.py
+++ b/var/spack/repos/builtin/packages/r-sseq/package.py
@@ -8,7 +8,7 @@ from spack import *
 
 class RSseq(RPackage):
     """Shrinkage estimation of dispersion in Negative Binomial models for RNA-
-       seq experiments with small sample size
+       seq experiments with small sample size.
 
        The purpose of this package is to discover the genes that are
        differentially expressed between two conditions in RNA-seq experiments.
@@ -21,9 +21,9 @@ class RSseq(RPackage):
        calculated, and used to test the hypothesis that the expected expression
        of a gene in two conditions identically follow a NB distribution."""
 
-    homepage = "https://bioconductor.org/packages/sSeq"
-    git      = "https://git.bioconductor.org/packages/sSeq.git"
+    bioc = "sSeq"
 
+    version('1.32.0', commit='c0d3c305755d888f64d334a4ab5fa54c623054cf')
     version('1.28.0', commit='401f6805628bdf6579cc0e643b7ed54319f024be')
     version('1.22.0', commit='fa3895c9578edddca17b5d13a2678ee5830b85cc')
     version('1.20.1', commit='91f31440323612cb04beb44404ab0a1bcb3ad87d')
diff --git a/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py b/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py
index 815a57a611..9477845f76 100644
--- a/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py
+++ b/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py
@@ -7,16 +7,16 @@ from spack import *
 
 
 class RSummarizedexperiment(RPackage):
-    """SummarizedExperiment container
+    """SummarizedExperiment container.
 
        The SummarizedExperiment container contains one or more assays, each
        represented by a matrix-like object of numeric or other mode. The rows
        typically represent genomic ranges of interest and the columns represent
        samples."""
 
-    homepage = "https://bioconductor.org/packages/SummarizedExperiment"
-    git      = "https://git.bioconductor.org/packages/SummarizedExperiment.git"
+    bioc = "SummarizedExperiment"
 
+    version('1.24.0', commit='d37f19383d03c107a8a41c0df2326e28efe46b28')
     version('1.20.0', commit='874aa87a481e4076a0ec3369f55c9c0a1ab8025e')
     version('1.18.2', commit='e22fafe')
     version('1.14.1', commit='2c68d99e11c7345e5ed388370822ea48395c64a4')
@@ -26,24 +26,26 @@ class RSummarizedexperiment(RPackage):
     version('1.6.5', commit='ec69cd5cfbccaef148a9f6abdfb3e22e888695d0')
 
     depends_on('r@3.2:', type=('build', 'run'))
+    depends_on('r@4.0.0:', type=('build', 'run'), when='@1.24.0:')
     depends_on('r-matrixgenerics@1.1.3:', type=('build', 'run'))
     depends_on('r-genomicranges@1.27.22:', type=('build', 'run'))
-    depends_on('r-genomicranges@1.29.14:', when='@1.8.1:', type=('build', 'run'))
-    depends_on('r-genomicranges@1.31.17:', when='@1.10.1:', type=('build', 'run'))
-    depends_on('r-genomicranges@1.33.6:', when='@1.12.0:', type=('build', 'run'))
-    depends_on('r-genomicranges@1.41.5:', when='@1.20.0:', type=('build', 'run'))
+    depends_on('r-genomicranges@1.29.14:', type=('build', 'run'), when='@1.8.1:')
+    depends_on('r-genomicranges@1.31.17:', type=('build', 'run'), when='@1.10.1:')
+    depends_on('r-genomicranges@1.33.6:', type=('build', 'run'), when='@1.12.0:')
+    depends_on('r-genomicranges@1.41.5:', type=('build', 'run'), when='@1.20.0:')
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-matrix', type=('build', 'run'))
     depends_on('r-biocgenerics@0.15.3:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.37.0:', type=('build', 'run'), when='@1.24.0:')
     depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.17.25:', when='@1.10.1:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.27.12:', when='@1.20.0:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.25:', type=('build', 'run'), when='@1.10.1:')
+    depends_on('r-s4vectors@0.27.12:', type=('build', 'run'), when='@1.20.0:')
     depends_on('r-iranges@2.7.2:', type=('build', 'run'))
-    depends_on('r-iranges@2.11.17:', when='@1.8.1:', type=('build', 'run'))
-    depends_on('r-iranges@2.13.16:', when='@1.10.1:', type=('build', 'run'))
-    depends_on('r-iranges@2.23.9:', when='@1.20.0:', type=('build', 'run'))
+    depends_on('r-iranges@2.11.17:', type=('build', 'run'), when='@1.8.1:')
+    depends_on('r-iranges@2.13.16:', type=('build', 'run'), when='@1.10.1:')
+    depends_on('r-iranges@2.23.9:', type=('build', 'run'), when='@1.20.0:')
     depends_on('r-genomeinfodb@1.11.4:', type=('build', 'run'))
-    depends_on('r-genomeinfodb@1.13.1:', when='@1.8.1:', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.13.1:', type=('build', 'run'), when='@1.8.1:')
     depends_on('r-delayedarray@0.1.9:', type=('build', 'run'))
-    depends_on('r-delayedarray@0.3.20:', when='@1.8.1:', type=('build', 'run'))
-    depends_on('r-delayedarray@0.15.10:', when='@1.20.0:', type=('build', 'run'))
+    depends_on('r-delayedarray@0.3.20:', type=('build', 'run'), when='@1.8.1:')
+    depends_on('r-delayedarray@0.15.10:', type=('build', 'run'), when='@1.20.0:')
diff --git a/var/spack/repos/builtin/packages/r-sva/package.py b/var/spack/repos/builtin/packages/r-sva/package.py
index 472f9bdd18..59ad4aeac5 100644
--- a/var/spack/repos/builtin/packages/r-sva/package.py
+++ b/var/spack/repos/builtin/packages/r-sva/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RSva(RPackage):
-    """Surrogate Variable Analysis
+    """Surrogate Variable Analysis.
 
        The sva package contains functions for removing batch effects and other
        unwanted variation in high-throughput experiment. Specifically, the sva
@@ -28,9 +28,9 @@ class RSva(RPackage):
        2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat. Reviews
        Genetics)."""
 
-    homepage = "https://bioconductor.org/packages/sva"
-    git      = "https://git.bioconductor.org/packages/sva.git"
+    bioc = "sva"
 
+    version('3.42.0', commit='54c843cc46437be233ecb43b6aa868e968d71138')
     version('3.38.0', commit='5ded8ba649200ec4829051f86a59e1a2548a7ab8')
     version('3.32.1', commit='1b8286734d00533b49d9f1456b6523cc778bb744')
     version('3.30.1', commit='fdb98bc2299dc5213c62d83cb7c0b1c1b4912f0c')
@@ -44,4 +44,4 @@ class RSva(RPackage):
     depends_on('r-biocparallel', type=('build', 'run'))
     depends_on('r-matrixstats', type=('build', 'run'))
     depends_on('r-limma', type=('build', 'run'))
-    depends_on('r-edger', when='@3.38.0:', type=('build', 'run'))
+    depends_on('r-edger', type=('build', 'run'), when='@3.38.0:')
diff --git a/var/spack/repos/builtin/packages/r-tfbstools/package.py b/var/spack/repos/builtin/packages/r-tfbstools/package.py
index 1912180b7f..2a59c6cbb8 100644
--- a/var/spack/repos/builtin/packages/r-tfbstools/package.py
+++ b/var/spack/repos/builtin/packages/r-tfbstools/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RTfbstools(RPackage):
-    """Software Package for Transcription Factor Binding Site (TFBS) Analysis
+    """Software Package for Transcription Factor Binding Site (TFBS) Analysis.
 
        TFBSTools is a package for the analysis and manipulation of
        transcription factor binding sites. It includes matrices conversion
@@ -16,9 +16,9 @@ class RTfbstools(RPackage):
        from sequence/alignment, query JASPAR database and provides a wrapper of
        de novo motif discovery software."""
 
-    homepage = "https://bioconductor.org/packages/TFBSTools"
-    git      = "https://git.bioconductor.org/packages/TFBSTools.git"
+    bioc = "TFBSTools"
 
+    version('1.32.0', commit='235505626b910de29156a07e1f990daa3b5d57d9')
     version('1.28.0', commit='15e7cf76f39ee3280a27284d58f7adef1c33f193')
     version('1.22.0', commit='613d3567fd662b65269bd200c5aa5f87ac6a4612')
     version('1.20.0', commit='74035fc6beb1af82f171c11ef2b0a8817714c5bc')
diff --git a/var/spack/repos/builtin/packages/r-tidytree/package.py b/var/spack/repos/builtin/packages/r-tidytree/package.py
new file mode 100644
index 0000000000..b714615544
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-tidytree/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RTidytree(RPackage):
+    """A Tidy Tool for Phylogenetic Tree Data Manipulation.
+
+    Phylogenetic tree generally contains multiple components including node,
+    edge, branch and associated data. 'tidytree' provides an approach to
+    convert tree object to tidy data frame as well as provides tidy interfaces
+    to manipulate tree data."""
+
+    cran = "tidytree"
+
+    version('0.3.7', sha256='7816f2d48ec94ca0c1bef15ec3d536adf44a969ea3c3cfc203ceebe16808e4f2')
+
+    depends_on('r@3.4.0:', type=('build', 'run'))
+    depends_on('r-ape', type=('build', 'run'))
+    depends_on('r-dplyr', type=('build', 'run'))
+    depends_on('r-lazyeval', type=('build', 'run'))
+    depends_on('r-magrittr', type=('build', 'run'))
+    depends_on('r-rlang', type=('build', 'run'))
+    depends_on('r-tibble', type=('build', 'run'))
+    depends_on('r-tidyr', type=('build', 'run'))
+    depends_on('r-tidyselect', type=('build', 'run'))
+    depends_on('r-yulab-utils@0.0.4:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-tmixclust/package.py b/var/spack/repos/builtin/packages/r-tmixclust/package.py
index a48e1432a3..865b5cd14b 100644
--- a/var/spack/repos/builtin/packages/r-tmixclust/package.py
+++ b/var/spack/repos/builtin/packages/r-tmixclust/package.py
@@ -8,7 +8,7 @@ from spack import *
 
 class RTmixclust(RPackage):
     """Time Series Clustering of Gene Expression with Gaussian Mixed-Effects
-       Models and Smoothing Splines
+       Models and Smoothing Splines.
 
        Implementation of a clustering method for time series gene expression
        data based on mixed-effects models with Gaussian variables and non-
@@ -16,9 +16,9 @@ class RTmixclust(RPackage):
        the high levels of noise present in typical gene expression time series
        datasets."""
 
-    homepage = "https://bioconductor.org/packages/TMixClust"
-    git      = "https://git.bioconductor.org/packages/TMixClust.git"
+    bioc = "TMixClust"
 
+    version('1.16.0', commit='e525cfd9c729a73a1964c243e5c34c37343f7bfa')
     version('1.12.0', commit='982b31bd7e22a3dc638bbda0336546220444f0c2')
     version('1.6.0', commit='9f5f78e52538d15f402c8f6e4c60f7212c7bc548')
     version('1.4.0', commit='a52fcae6e7a5dd41e7afbe128f35397e8bc8cb12')
diff --git a/var/spack/repos/builtin/packages/r-topgo/package.py b/var/spack/repos/builtin/packages/r-topgo/package.py
index f927372ecc..3f9a8cc89a 100644
--- a/var/spack/repos/builtin/packages/r-topgo/package.py
+++ b/var/spack/repos/builtin/packages/r-topgo/package.py
@@ -7,16 +7,16 @@ from spack import *
 
 
 class RTopgo(RPackage):
-    """Enrichment Analysis for Gene Ontology
+    """Enrichment Analysis for Gene Ontology.
 
        topGO package provides tools for testing GO terms while accounting for
        the topology of the GO graph. Different test statistics and different
        methods for eliminating local similarities and dependencies between GO
        terms can be implemented and applied."""
 
-    homepage = "https://bioconductor.org/packages/topGO"
-    git      = "https://git.bioconductor.org/packages/topGO.git"
+    bioc = "topGO"
 
+    version('2.46.0', commit='2bfa9dff41fff261aa6188f8368aebd6e8250b18')
     version('2.42.0', commit='3a33cf53883de45bda506953303e1809ab982adc')
     version('2.36.0', commit='c2f6c187b41c4aa44cc92ac781fdd878491a4019')
     version('2.34.0', commit='44cb5eaba515b365b7b2a8c22df0a45883db6b4d')
diff --git a/var/spack/repos/builtin/packages/r-treeio/package.py b/var/spack/repos/builtin/packages/r-treeio/package.py
new file mode 100644
index 0000000000..9e792f3cf9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-treeio/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RTreeio(RPackage):
+    """Base Classes and Functions for Phylogenetic Tree Input and Output.
+
+    'treeio' is an R package to make it easier to import and store phylogenetic
+    tree with associated data; and to link external data from different sources
+    to phylogeny. It also supports exporting phylogenetic tree with
+    heterogeneous associated data to a single tree file and can be served as a
+    platform for merging tree with associated data and converting file
+    formats."""
+
+    bioc = "treeio"
+
+    version('1.18.1', commit='a06b6b3d2a64f1b22c6c8c5f97c08f5863349c83')
+
+    depends_on('r@3.6.0:', type=('build', 'run'))
+    depends_on('r-ape', type=('build', 'run'))
+    depends_on('r-dplyr', type=('build', 'run'))
+    depends_on('r-jsonlite', type=('build', 'run'))
+    depends_on('r-magrittr', type=('build', 'run'))
+    depends_on('r-rlang', type=('build', 'run'))
+    depends_on('r-tibble', type=('build', 'run'))
+    depends_on('r-tidytree@0.3.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg18-knowngene/package.py b/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg18-knowngene/package.py
index d0aa846bb0..dab13e7888 100644
--- a/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg18-knowngene/package.py
+++ b/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg18-knowngene/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RTxdbHsapiensUcscHg18Knowngene(RPackage):
-    """Annotation package for TxDb object(s)
+    """Annotation package for TxDb object(s).
 
     Exposes an annotation databases generated from UCSC by exposing these as
     TxDb objects"""
 
     # This is a bioconductor package but ther is no available git repo
-    homepage = "https://bioconductor.org/packages/release/data/annotation/html/TxDb.Hsapiens.UCSC.hg18.knownGene.html"
-    url      = "https://bioconductor.org/packages/release/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2.tar.gz"
+    bioc = "TxDb.Hsapiens.UCSC.hg18.knownGene"
+    url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2.tar.gz"
 
     version('3.2.2', sha256='bc9ca40b4eab87f5ca64a4b876d42502b9b8e9f5983d745bfe0ee349d97b69fa')
 
diff --git a/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg19-knowngene/package.py b/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg19-knowngene/package.py
index e1a0dddbcc..0e47f7a35a 100644
--- a/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg19-knowngene/package.py
+++ b/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg19-knowngene/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RTxdbHsapiensUcscHg19Knowngene(RPackage):
-    """Annotation package for TxDb object(s)
+    """Annotation package for TxDb object(s).
 
     Exposes an annotation databases generated from UCSC by exposing these as
     TxDb objects."""
 
     # This is a bioconductor package but there is no available git repo.
-    homepage = "https://bioconductor.org/packages/release/data/annotation/html/TxDb.Hsapiens.UCSC.hg19.knownGene.html"
-    url      = "https://bioconductor.org/packages/release/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz"
+    bioc = "TxDb.Hsapiens.UCSC.hg19.knownGene"
+    url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz"
 
     version('3.2.2', sha256='063de2b1174782a0b2b8ab7f04a0bdf3c43252cb67c685a9f8ef2b8e318352e9')
 
diff --git a/var/spack/repos/builtin/packages/r-tximport/package.py b/var/spack/repos/builtin/packages/r-tximport/package.py
index 1ac89a6969..b3cf968d7a 100644
--- a/var/spack/repos/builtin/packages/r-tximport/package.py
+++ b/var/spack/repos/builtin/packages/r-tximport/package.py
@@ -8,7 +8,7 @@ from spack import *
 
 class RTximport(RPackage):
     """Import and summarize transcript-level estimates for transcript- and
-       gene-level analysis
+       gene-level analysis.
 
        Imports transcript-level abundance, estimated counts and transcript
        lengths, and summarizes into matrices for use with downstream gene-level
@@ -17,9 +17,9 @@ class RTximport(RPackage):
        can be used as an offset for different expression of gene-level
        counts."""
 
-    homepage = "https://bioconductor.org/packages/tximport"
-    git      = "https://git.bioconductor.org/packages/tximport.git"
+    bioc = "tximport"
 
+    version('1.22.0', commit='335213baee3492fbf6baaa8b4e067ac0ef384684')
     version('1.18.0', commit='58b20cbc566648586b6990b30ebc70bef308cb05')
     version('1.12.3', commit='acbdead961471c3b910d720f73bd0af1b7a07c57')
     version('1.10.1', commit='cd8f81cf7140f61d4a4f25f89451fb49e2cd4bd3')
diff --git a/var/spack/repos/builtin/packages/r-tximportdata/package.py b/var/spack/repos/builtin/packages/r-tximportdata/package.py
index 18a419f734..34e92e2b30 100644
--- a/var/spack/repos/builtin/packages/r-tximportdata/package.py
+++ b/var/spack/repos/builtin/packages/r-tximportdata/package.py
@@ -8,7 +8,7 @@ from spack import *
 
 class RTximportdata(RPackage):
     """Import and summarize transcript-level estimates for transcript- and
-    gene-level analysis
+    gene-level analysis.
 
     Imports transcript-level abundance, estimated counts and transcript
     lengths, and summarizes into matrices for use with downstream gene-level
@@ -16,7 +16,7 @@ class RTximportdata(RPackage):
     transcript abundance estimates, is provided as a matrix which can be used
     as an offset for different expression of gene-level counts."""
 
-    homepage = "https://github.com/mikelove/tximport"
-    git      = "https://git.bioconductor.org/packages/tximportData"
+    bioc = "tximportData"
 
+    version('1.22.0', commit='c576b18e43985baf8beab327cbc54afe8324659c')
     version('1.18.0', commit='24945f8dd1e4e441ad5145fb7a37a1630912f929')
diff --git a/var/spack/repos/builtin/packages/r-variantannotation/package.py b/var/spack/repos/builtin/packages/r-variantannotation/package.py
index c4d61c5a85..6dec776a64 100644
--- a/var/spack/repos/builtin/packages/r-variantannotation/package.py
+++ b/var/spack/repos/builtin/packages/r-variantannotation/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RVariantannotation(RPackage):
-    """Annotation of Genetic Variants
+    """Annotation of Genetic Variants.
 
        Annotate variants, compute amino acid coding changes, predict coding
        outcomes."""
 
-    homepage = "https://bioconductor.org/packages/VariantAnnotation"
-    git      = "https://git.bioconductor.org/packages/VariantAnnotation.git"
+    bioc = "VariantAnnotation"
 
+    version('1.40.0', commit='50ead7cb60cedf3c053853fab92d9f104f9f85bd')
     version('1.36.0', commit='9918bd19a2e6f89e5edc5fe03c8812f500bb3e19')
     version('1.30.1', commit='fb1ab00872570afb280522c4663e347dafc07a9e')
     version('1.28.13', commit='0393347b8ce2d5edf1a61589be93e6a93eda3419')
@@ -23,42 +23,44 @@ class RVariantannotation(RPackage):
     version('1.22.3', commit='3a91b6d4297aa416d5f056dec6f8925eb1a8eaee')
 
     depends_on('r@2.8.0:', type=('build', 'run'))
+    depends_on('r@4.0.0:', type=('build', 'run'), when='@1.40.0:')
     depends_on('r-biocgenerics@0.15.3:', type=('build', 'run'))
-    depends_on('r-matrixgenerics', when='@1.36.0:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.37.0:', type=('build', 'run'), when='@1.40.0:')
+    depends_on('r-matrixgenerics', type=('build', 'run'), when='@1.36.0:')
     depends_on('r-genomeinfodb@1.11.4:', type=('build', 'run'))
-    depends_on('r-genomeinfodb@1.15.2:', when='@1.26.1:', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.15.2:', type=('build', 'run'), when='@1.26.1:')
     depends_on('r-genomicranges@1.27.6:', type=('build', 'run'))
-    depends_on('r-genomicranges@1.31.8:', when='@1.26.1:', type=('build', 'run'))
-    depends_on('r-genomicranges@1.41.5:', when='@1.36.0:', type=('build', 'run'))
+    depends_on('r-genomicranges@1.31.8:', type=('build', 'run'), when='@1.26.1:')
+    depends_on('r-genomicranges@1.41.5:', type=('build', 'run'), when='@1.36.0:')
     depends_on('r-summarizedexperiment@1.5.3:', type=('build', 'run'))
-    depends_on('r-summarizedexperiment@1.19.5:', when='@1.36.0:', type=('build', 'run'))
+    depends_on('r-summarizedexperiment@1.19.5:', type=('build', 'run'), when='@1.36.0:')
     depends_on('r-rsamtools@1.23.10:', type=('build', 'run'))
-    depends_on('r-rsamtools@1.31.2:', when='@1.26.1:', type=('build', 'run'))
-    depends_on('r-rsamtools@1.33.6:', when='@1.28.13:', type=('build', 'run'))
-    depends_on('r-rsamtools@1.99.0:', when='@1.30.1:', type=('build', 'run'))
+    depends_on('r-rsamtools@1.31.2:', type=('build', 'run'), when='@1.26.1:')
+    depends_on('r-rsamtools@1.33.6:', type=('build', 'run'), when='@1.28.13:')
+    depends_on('r-rsamtools@1.99.0:', type=('build', 'run'), when='@1.30.1:')
     depends_on('r-dbi', type=('build', 'run'))
     depends_on('r-zlibbioc', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.17.24:', when='@1.26.1:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.27.12:', when='@1.36.0:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.24:', type=('build', 'run'), when='@1.26.1:')
+    depends_on('r-s4vectors@0.27.12:', type=('build', 'run'), when='@1.36.0:')
     depends_on('r-iranges@2.3.25:', type=('build', 'run'))
-    depends_on('r-iranges@2.13.13:', when='@1.26.1:', type=('build', 'run'))
-    depends_on('r-iranges@2.23.9:', when='@1.36.0:', type=('build', 'run'))
+    depends_on('r-iranges@2.13.13:', type=('build', 'run'), when='@1.26.1:')
+    depends_on('r-iranges@2.23.9:', type=('build', 'run'), when='@1.36.0:')
     depends_on('r-xvector@0.5.6:', type=('build', 'run'))
-    depends_on('r-xvector@0.19.7:', when='@1.26.1:', type=('build', 'run'))
-    depends_on('r-xvector@0.29.2:', when='@1.36.0:', type=('build', 'run'))
+    depends_on('r-xvector@0.19.7:', type=('build', 'run'), when='@1.26.1:')
+    depends_on('r-xvector@0.29.2:', type=('build', 'run'), when='@1.36.0:')
     depends_on('r-biostrings@2.33.5:', type=('build', 'run'))
-    depends_on('r-biostrings@2.47.6:', when='@1.26.1:', type=('build', 'run'))
-    depends_on('r-biostrings@2.57.2:', when='@1.36.0:', type=('build', 'run'))
+    depends_on('r-biostrings@2.47.6:', type=('build', 'run'), when='@1.26.1:')
+    depends_on('r-biostrings@2.57.2:', type=('build', 'run'), when='@1.36.0:')
     depends_on('r-annotationdbi@1.27.9:', type=('build', 'run'))
     depends_on('r-rtracklayer@1.25.16:', type=('build', 'run'))
-    depends_on('r-rtracklayer@1.39.7:', when='@1.26.1:', type=('build', 'run'))
+    depends_on('r-rtracklayer@1.39.7:', type=('build', 'run'), when='@1.26.1:')
     depends_on('r-bsgenome@1.37.6:', type=('build', 'run'))
-    depends_on('r-bsgenome@1.47.3:', when='@1.26.1:', type=('build', 'run'))
+    depends_on('r-bsgenome@1.47.3:', type=('build', 'run'), when='@1.26.1:')
     depends_on('r-genomicfeatures@1.27.4:', type=('build', 'run'))
-    depends_on('r-genomicfeatures@1.31.3:', when='@1.26.1:', type=('build', 'run'))
-    depends_on('r-rhtslib', when='@1.30.1:', type=('build', 'run'))
+    depends_on('r-genomicfeatures@1.31.3:', type=('build', 'run'), when='@1.26.1:')
+    depends_on('r-rhtslib', type=('build', 'run'), when='@1.30.1:')
     depends_on('gmake', type='build')
 
     # Not listed but needed
diff --git a/var/spack/repos/builtin/packages/r-vsn/package.py b/var/spack/repos/builtin/packages/r-vsn/package.py
index f05b46f0f9..e37198624f 100644
--- a/var/spack/repos/builtin/packages/r-vsn/package.py
+++ b/var/spack/repos/builtin/packages/r-vsn/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RVsn(RPackage):
-    """Variance stabilization and calibration for microarray data
+    """Variance stabilization and calibration for microarray data.
 
        The package implements a method for normalising microarray intensities,
        and works for single- and multiple-color arrays. It can also be used for
@@ -22,9 +22,9 @@ class RVsn(RPackage):
        they are usually more sensitive and specific in detecting differential
        transcription."""
 
-    homepage = "https://bioconductor.org/packages/vsn"
-    git      = "https://git.bioconductor.org/packages/vsn.git"
+    bioc = "vsn"
 
+    version('3.62.0', commit='6ae7f4e07ec1a5a9482cab892d98175983bfcd50')
     version('3.58.0', commit='a451e6ae989623750feacf26d99683a7955adf85')
     version('3.52.0', commit='e80642d850ae93bc141654200a8970b561a94fbe')
     version('3.50.0', commit='ad49fcc288c6065d0f04040acd688e7f0d7d927e')
@@ -33,10 +33,12 @@ class RVsn(RPackage):
     version('3.44.0', commit='e54513fcdd07ccfb8094359e93cef145450f0ee0')
 
     depends_on('r@3.0.0:', type=('build', 'run'))
-    depends_on('r@3.4.0:', when='@3.46.0:', type=('build', 'run'))
+    depends_on('r@3.4.0:', type=('build', 'run'), when='@3.46.0:')
+    depends_on('r@4.0.0:', type=('build', 'run'), when='@3.62.0:')
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-affy', type=('build', 'run'))
     depends_on('r-limma', type=('build', 'run'))
     depends_on('r-lattice', type=('build', 'run'))
     depends_on('r-ggplot2', type=('build', 'run'))
-    depends_on('r-hexbin', when='@3.44.0:3.52.0', type=('build', 'run'))
+
+    depends_on('r-hexbin', type=('build', 'run'), when='@3.44.0:3.52.0')
diff --git a/var/spack/repos/builtin/packages/r-watermelon/package.py b/var/spack/repos/builtin/packages/r-watermelon/package.py
index 4b058d4194..a4edcffb89 100644
--- a/var/spack/repos/builtin/packages/r-watermelon/package.py
+++ b/var/spack/repos/builtin/packages/r-watermelon/package.py
@@ -7,18 +7,19 @@ from spack import *
 
 
 class RWatermelon(RPackage):
-    """Illumina 450 methylation array normalization and metrics
+    """Illumina 450 methylation array normalization and metrics.
 
     15 flavours of betas and three performance metrics, with methods for
     objects produced by methylumi and minfi packages."""
 
-    homepage = "https://bioconductor.org/packages/release/bioc/html/wateRmelon.html"
-    git      = "https://git.bioconductor.org/packages/wateRmelon"
+    bioc = "wateRmelon"
 
+    version('2.0.0', commit='f6a331bdf50e0e5c94009fb67be873d996348ade')
     version('1.34.0', commit='3fa2745535c22068a438747b41b9d793196098d4')
     version('1.30.0', commit='66d7579fe49206d965832288df7937c3d43ed578')
 
     depends_on('r@2.10:', type=('build', 'run'))
+    depends_on('r@3.5.0:', type=('build', 'run'), when='@2.0.0:')
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-limma', type=('build', 'run'))
     depends_on('r-matrixstats', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-xde/package.py b/var/spack/repos/builtin/packages/r-xde/package.py
index 02e64f8eff..6e24162c00 100644
--- a/var/spack/repos/builtin/packages/r-xde/package.py
+++ b/var/spack/repos/builtin/packages/r-xde/package.py
@@ -7,15 +7,15 @@ from spack import *
 
 
 class RXde(RPackage):
-    """XDE: a Bayesian hierarchical model for cross-study analysis of
-       differential gene expression
+    """a Bayesian hierarchical model for cross-study analysis of
+       differential gene expression.
 
     Multi-level model for cross-study detection of differential gene
     expression."""
 
-    homepage = "https://bioconductor.org/packages/XDE"
-    git      = "https://git.bioconductor.org/packages/XDE.git"
+    bioc = "XDE"
 
+    version('2.40.0', commit='bfc3c54787aec97b70bef7b99a6adc75d2cf5ed2')
     version('2.36.0', commit='0277f9dffbd7d1880be77cb8581fc614501b3293')
     version('2.30.0', commit='058af6f1e431522778f970bf61f834620d3d7dd7')
     version('2.28.0', commit='b8cc7d0840ce1324644e8b4a750fbb964884498b')
@@ -29,7 +29,8 @@ class RXde(RPackage):
     depends_on('r-genefilter', type=('build', 'run'))
     depends_on('r-gtools', type=('build', 'run'))
     depends_on('r-mvtnorm', type=('build', 'run'))
-    depends_on('r-rcolorbrewer', when='@2.24.0:', type=('build', 'run'))
-    depends_on('r-genemeta', when='@2.24.0:', type=('build', 'run'))
-    depends_on('r-siggenes', when='@2.24.0:', type=('build', 'run'))
-    depends_on('r-mergemaid', when='@:2.30.0', type=('build', 'run'))
+    depends_on('r-rcolorbrewer', type=('build', 'run'), when='@2.24.0:')
+    depends_on('r-genemeta', type=('build', 'run'), when='@2.24.0:')
+    depends_on('r-siggenes', type=('build', 'run'), when='@2.24.0:')
+
+    depends_on('r-mergemaid', type=('build', 'run'), when='@:2.30.0')
diff --git a/var/spack/repos/builtin/packages/r-xmapbridge/package.py b/var/spack/repos/builtin/packages/r-xmapbridge/package.py
index cda8c6fe25..94c2117eff 100644
--- a/var/spack/repos/builtin/packages/r-xmapbridge/package.py
+++ b/var/spack/repos/builtin/packages/r-xmapbridge/package.py
@@ -7,14 +7,14 @@ from spack import *
 
 
 class RXmapbridge(RPackage):
-    """Export plotting files to the xmapBridge for visualisation in X:Map
+    """Export plotting files to the xmapBridge for visualisation in X:Map.
 
        xmapBridge can plot graphs in the X:Map genome browser. This package
        exports plotting files in a suitable format."""
 
-    homepage = "https://bioconductor.org/packages/xmapbridge"
-    git      = "https://git.bioconductor.org/packages/xmapbridge.git"
+    bioc = "xmapbridge"
 
+    version('1.52.0', commit='fe32fcd2a83432c721eb948cb3af73dd187065f6')
     version('1.48.0', commit='1cefe6b56c6dcb1f18028b3b7d6a67d490bc9730')
     version('1.42.0', commit='d79c80dfc1a0ed3fd6d3e7a7c3a4aff778537ca9')
     version('1.40.0', commit='00a2993863f28711e237bc937fa0ba2d05f81684')
diff --git a/var/spack/repos/builtin/packages/r-xvector/package.py b/var/spack/repos/builtin/packages/r-xvector/package.py
index e249373286..390d527b4b 100644
--- a/var/spack/repos/builtin/packages/r-xvector/package.py
+++ b/var/spack/repos/builtin/packages/r-xvector/package.py
@@ -8,14 +8,14 @@ from spack import *
 
 class RXvector(RPackage):
     """Foundation of external vector representation and manipulation in
-       Bioconductor
+       Bioconductor.
 
        Provides memory efficient S4 classes for storing sequences "externally"
        (e.g. behind an R external pointer, or on disk)."""
 
-    homepage = "https://bioconductor.org/packages/XVector"
-    git      = "https://git.bioconductor.org/packages/XVector.git"
+    bioc = "XVector"
 
+    version('0.34.0', commit='06adb25ac51c707b90fb8e0637fa06df237a863c')
     version('0.30.0', commit='985e963e0b1c3ff004dd0b07ad7c9ff7ed853ec0')
     version('0.24.0', commit='e5109cb2687724b9fddddf296c07a82bae4c551d')
     version('0.22.0', commit='b5e107a5fd719e18374eb836eb498b529afa4473')
@@ -24,16 +24,18 @@ class RXvector(RPackage):
     version('0.16.0', commit='54615888e1a559da4a81de33e934fc0f1c3ad99f')
 
     depends_on('r@2.8.0:', type=('build', 'run'))
+    depends_on('r@4.0.0:', type=('build', 'run'), when='@0.34.0:')
     depends_on('r-biocgenerics@0.19.2:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.37.0:', type=('build', 'run'), when='@0.34.0:')
     depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.15.14:', when='@0.18.0:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.17.24:', when='@0.20.0:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.19.15:', when='@0.22.0:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.21.13:', when='@0.24.0:', type=('build', 'run'))
-    depends_on('r-s4vectors@0.27.12:', when='@0.30.0:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.15.14:', type=('build', 'run'), when='@0.18.0:')
+    depends_on('r-s4vectors@0.17.24:', type=('build', 'run'), when='@0.20.0:')
+    depends_on('r-s4vectors@0.19.15:', type=('build', 'run'), when='@0.22.0:')
+    depends_on('r-s4vectors@0.21.13:', type=('build', 'run'), when='@0.24.0:')
+    depends_on('r-s4vectors@0.27.12:', type=('build', 'run'), when='@0.30.0:')
     depends_on('r-iranges@2.9.18:', type=('build', 'run'))
-    depends_on('r-iranges@2.13.16:', when='@0.20.0:', type=('build', 'run'))
-    depends_on('r-iranges@2.15.12:', when='@0.22.0:', type=('build', 'run'))
-    depends_on('r-iranges@2.23.9:', when='@0.30.0:', type=('build', 'run'))
+    depends_on('r-iranges@2.13.16:', type=('build', 'run'), when='@0.20.0:')
+    depends_on('r-iranges@2.15.12:', type=('build', 'run'), when='@0.22.0:')
+    depends_on('r-iranges@2.23.9:', type=('build', 'run'), when='@0.30.0:')
     depends_on('r-zlibbioc', type=('build', 'run'))
     depends_on('zlib')
diff --git a/var/spack/repos/builtin/packages/r-yapsa/package.py b/var/spack/repos/builtin/packages/r-yapsa/package.py
index 9982a655c6..1ee33769fd 100644
--- a/var/spack/repos/builtin/packages/r-yapsa/package.py
+++ b/var/spack/repos/builtin/packages/r-yapsa/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RYapsa(RPackage):
-    """Yet Another Package for Signature Analysis
+    """Yet Another Package for Signature Analysis.
 
        This package provides functions and routines useful in the analysis of
        somatic signatures (cf. L. Alexandrov et al., Nature 2013). In
@@ -16,9 +16,9 @@ class RYapsa(RPackage):
        analysis on stratified mutational catalogue (SMC = stratify mutational
        catalogue) are provided."""
 
-    homepage = "https://bioconductor.org/packages/YAPSA"
-    git      = "https://git.bioconductor.org/packages/YAPSA.git"
+    bioc = "YAPSA"
 
+    version('1.20.1', commit='6c3f437911859df6f6e4a9af5571c3a5aafbffb2')
     version('1.16.0', commit='f344cdb81bb886c633f9325f811912fb59d58eb1')
     version('1.10.0', commit='06af18e424868eb0f0be6c80e90cbab1eabf3d73')
     version('1.8.0', commit='402f3f7774fdf8afc7883579ad651c26df0f8fdb')
@@ -27,10 +27,10 @@ class RYapsa(RPackage):
     version('1.2.0', commit='320809b69e470e30a777a383f8341f93064ec24d')
 
     depends_on('r@3.3.0:', type=('build', 'run'))
-    depends_on('r@3.6.0:', when='@1.16.0:', type=('build', 'run'))
+    depends_on('r@3.6.0:', type=('build', 'run'), when='@1.16.0:')
     depends_on('r-genomicranges', type=('build', 'run'))
     depends_on('r-ggplot2', type=('build', 'run'))
-    depends_on('r-limsolve', when='@1.16.0:', type=('build', 'run'))
+    depends_on('r-limsolve', type=('build', 'run'), when='@1.16.0:')
     depends_on('r-somaticsignatures', type=('build', 'run'))
     depends_on('r-variantannotation', type=('build', 'run'))
     depends_on('r-genomeinfodb', type=('build', 'run'))
@@ -41,14 +41,16 @@ class RYapsa(RPackage):
     depends_on('r-getoptlong', type=('build', 'run'))
     depends_on('r-circlize', type=('build', 'run'))
     depends_on('r-gtrellis', type=('build', 'run'))
-    depends_on('r-doparallel', when='@1.16.0:', type=('build', 'run'))
-    depends_on('r-pmcmr', type=('build', 'run'))
-    depends_on('r-ggbeeswarm', when='@1.16.0:', type=('build', 'run'))
+    depends_on('r-doparallel', type=('build', 'run'), when='@1.16.0:')
+    depends_on('r-pmcmrplus', type=('build', 'run'), when='@1.20.1:')
+    depends_on('r-ggbeeswarm', type=('build', 'run'), when='@1.16.0:')
     depends_on('r-complexheatmap', type=('build', 'run'))
     depends_on('r-keggrest', type=('build', 'run'))
-    depends_on('r-biostrings', when='@1.16.0:', type=('build', 'run'))
-    depends_on('r-bsgenome-hsapiens-ucsc-hg19', when='@1.16.0:', type=('build', 'run'))
-    depends_on('r-magrittr', when='@1.16.0:', type=('build', 'run'))
-    depends_on('r-pracma', when='@1.16.0:', type=('build', 'run'))
-    depends_on('r-dplyr', when='@1.16.0:', type=('build', 'run'))
-    depends_on('r-lsei', when='@:1.10.0', type=('build', 'run'))
+    depends_on('r-biostrings', type=('build', 'run'), when='@1.16.0:')
+    depends_on('r-bsgenome-hsapiens-ucsc-hg19', type=('build', 'run'), when='@1.16.0:')
+    depends_on('r-magrittr', type=('build', 'run'), when='@1.16.0:')
+    depends_on('r-pracma', type=('build', 'run'), when='@1.16.0:')
+    depends_on('r-dplyr', type=('build', 'run'), when='@1.16.0:')
+
+    depends_on('r-lsei', type=('build', 'run'), when='@:1.10.0')
+    depends_on('r-pmcmr', type=('build', 'run'), when='@:1.16.0')
diff --git a/var/spack/repos/builtin/packages/r-yaqcaffy/package.py b/var/spack/repos/builtin/packages/r-yaqcaffy/package.py
index 61bc60d04a..cdaef69fb8 100644
--- a/var/spack/repos/builtin/packages/r-yaqcaffy/package.py
+++ b/var/spack/repos/builtin/packages/r-yaqcaffy/package.py
@@ -7,14 +7,13 @@ from spack import *
 
 
 class RYaqcaffy(RPackage):
-    """Affymetrix expression data quality control and reproducibility analysis
+    """Affymetrix expression data quality control and reproducibility analysis.
 
        Quality control of Affymetrix GeneChip expression data and
        reproducibility analysis of human whole genome chips with the MAQC
        reference datasets."""
 
-    homepage = "https://bioconductor.org/packages/yaqcaffy"
-    git      = "https://git.bioconductor.org/packages/yaqcaffy.git"
+    bioc = "yaqcaffy"
 
     version('1.50.0', commit='b32e6b947ca9c4ab7163cfddc084a1bc0a34780e')
     version('1.44.0', commit='00898f3ec9ac0beadbcf57bda3d3c1c99fb0c3c0')
diff --git a/var/spack/repos/builtin/packages/r-yarn/package.py b/var/spack/repos/builtin/packages/r-yarn/package.py
index b6753c8e27..ef790997e6 100644
--- a/var/spack/repos/builtin/packages/r-yarn/package.py
+++ b/var/spack/repos/builtin/packages/r-yarn/package.py
@@ -7,7 +7,7 @@ from spack import *
 
 
 class RYarn(RPackage):
-    """YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
+    """Robust Multi-Condition RNA-Seq Preprocessing and Normalization.
 
        Expedite large RNA-Seq analyses using a combination of previously
        developed tools. YARN is meant to make it easier for the user in
@@ -16,9 +16,9 @@ class RYarn(RPackage):
        and statistical techniques to account for the large heterogeneity and
        sparsity found in very large RNA-seq experiments."""
 
-    homepage = "https://bioconductor.org/packages/yarn"
-    git      = "https://git.bioconductor.org/packages/yarn.git"
+    bioc = "yarn"
 
+    version('1.20.0', commit='b41e4ef14f980518af2fc59f202ad8ec148e8b47')
     version('1.16.0', commit='ff5a18cb946ffec3cb773fe32af401c8a72d674a')
     version('1.10.0', commit='36ffe84148eb871e93bc8f9e697475319b5ea472')
     version('1.8.1', commit='ee0723d4dbf082b4469ca9c22cce4f1a2ac81c04')
diff --git a/var/spack/repos/builtin/packages/r-zlibbioc/package.py b/var/spack/repos/builtin/packages/r-zlibbioc/package.py
index 76fd05f1d9..9714100b5e 100644
--- a/var/spack/repos/builtin/packages/r-zlibbioc/package.py
+++ b/var/spack/repos/builtin/packages/r-zlibbioc/package.py
@@ -7,16 +7,16 @@ from spack import *
 
 
 class RZlibbioc(RPackage):
-    """An R packaged zlib-1.2.5
+    """An R packaged zlib-1.2.5.
 
        This package uses the source code of zlib-1.2.5 to create libraries for
        systems that do not have these available via other means (most Linux and
        Mac users should have system-level access to zlib, and no direct need
        for this package). See the vignette for instructions on use."""
 
-    homepage = "https://bioconductor.org/packages/zlibbioc"
-    git      = "https://git.bioconductor.org/packages/zlibbioc.git"
+    bioc = "zlibbioc"
 
+    version('1.40.0', commit='3f116b39d104c1ea8288f6b8f0ef94bb95f41f69')
     version('1.36.0', commit='62e888cd7fb482d512c6c31961b657e0b924e357')
     version('1.30.0', commit='99eae5b05968bf6abc9b54b9031afd93517381e0')
     version('1.28.0', commit='b825b042742ba45455fc284b988ff4cd2a33222c')