diff options
22 files changed, 71 insertions, 47 deletions
diff --git a/var/spack/repos/builtin/packages/r-a4/package.py b/var/spack/repos/builtin/packages/r-a4/package.py index 0c6a1e588a..25a8bf1a41 100644 --- a/var/spack/repos/builtin/packages/r-a4/package.py +++ b/var/spack/repos/builtin/packages/r-a4/package.py @@ -29,10 +29,11 @@ class RA4(RPackage): """Automated Affymetrix Array Analysis Umbrella Package.""" homepage = "https://www.bioconductor.org/packages/a4/" - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/a4_1.24.0.tar.gz" + url = "https://git.bioconductor.org/packages/a4" list_url = homepage - version('1.24.0', 'dfa17ec5b1914300360ff11f43955fdd') + version('1.24.0', git='https://git.bioconductor.org/packages/a4', commit='79b5143652176787c85a0d587b3bbfad6b4a19f4') + depends_on('r@3.4.0:3.4.9', when='@1.24.0') depends_on('r-a4base', type=('build', 'run')) depends_on('r-a4preproc', type=('build', 'run')) depends_on('r-a4classif', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-a4base/package.py b/var/spack/repos/builtin/packages/r-a4base/package.py index 8e02f52214..c04cb33de7 100644 --- a/var/spack/repos/builtin/packages/r-a4base/package.py +++ b/var/spack/repos/builtin/packages/r-a4base/package.py @@ -29,10 +29,11 @@ class RA4base(RPackage): """Automated Affymetrix Array Analysis.""" homepage = "https://www.bioconductor.org/packages/a4Base/" - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/a4Base_1.24.0.tar.gz" + url = "'https://git.bioconductor.org/packages/a4Base'" list_url = homepage - version('1.24.0', '98f53cb437f1b8bb7ba8c2628c0f44c6') + version('1.24.0', git='https://git.bioconductor.org/packages/a4Base', commit='f674afe424a508df2c8ee6c87a06fbd4aa410ef6') + depends_on('r@3.4.0:3.4.9', when='@1.24.0') depends_on('r-biobase', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) depends_on('r-annaffy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-a4classif/package.py b/var/spack/repos/builtin/packages/r-a4classif/package.py index 3fd06599e0..51efdf5c4c 100644 --- a/var/spack/repos/builtin/packages/r-a4classif/package.py +++ b/var/spack/repos/builtin/packages/r-a4classif/package.py @@ -28,12 +28,13 @@ from spack import * class RA4classif(RPackage): """Automated Affymetrix Array Analysis Classification Package.""" - homepage = "https://www.bioconductor.org" - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/a4Classif_1.24.0.tar.gz" + homepage = "https://www.bioconductor.org/packages/a4Classif/" + url = "https://git.bioconductor.org/packages/a4Classif" list_url = homepage - version('1.24.0', 'b3367ba63a5d5a38d94e671d027098ff') + version('1.24.0', git='https://git.bioconductor.org/packages/a4Classif', commit='ca06bf274c87a73fc12c29a6eea4b90289fe30b1') + depends_on('r@3.4.0:3.4.9', when='@1.24.0') depends_on('r-a4core', type=('build', 'run')) depends_on('r-a4preproc', type=('build', 'run')) depends_on('r-mlinterfaces', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-a4core/package.py b/var/spack/repos/builtin/packages/r-a4core/package.py index 6fb70248df..a72fe7e272 100644 --- a/var/spack/repos/builtin/packages/r-a4core/package.py +++ b/var/spack/repos/builtin/packages/r-a4core/package.py @@ -28,10 +28,11 @@ from spack import * class RA4core(RPackage): """Automated Affymetrix Array Analysis Core Package.""" - homepage = "https://www.bioconductor.org" - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/a4Core_1.24.0.tar.gz" + homepage = "https://www.bioconductor.org/packages/a4Core/" + url = "https://git.bioconductor.org/packages/a4Core" - version('1.24.0', 'd7f79c350ae0a6175f2ecc9a337ca61f') + version('1.24.0', git='https://git.bioconductor.org/packages/a4Core', commit='c871faa3e1ab6be38a9ea3018816cf31b58b0ed3') + depends_on('r@3.4.0:3.4.9', when='@1.24.0') depends_on('r-biobase', type=('build', 'run')) depends_on('r-glmnet', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-a4preproc/package.py b/var/spack/repos/builtin/packages/r-a4preproc/package.py index e8ddf1b748..7b28ca94a1 100644 --- a/var/spack/repos/builtin/packages/r-a4preproc/package.py +++ b/var/spack/repos/builtin/packages/r-a4preproc/package.py @@ -29,8 +29,9 @@ class RA4preproc(RPackage): """Automated Affymetrix Array Analysis Preprocessing Package.""" homepage = "https://www.bioconductor.org/packages/a4Preproc/" - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/a4Preproc_1.24.0.tar.gz" + url = "https://git.bioconductor.org/packages/a4Preproc" - version('1.24.0', '8de73ad20a28155f34a4636c3f7c6539') + version('1.24.0', git='https://git.bioconductor.org/packages/a4Preproc', commit='651014b8102807aea4f1274e34e083e70b5e7ee7') + depends_on('r@3.4.0:3.4.9', when='@1.24.0') depends_on('r-annotationdbi', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-a4reporting/package.py b/var/spack/repos/builtin/packages/r-a4reporting/package.py index cb59a4e161..4a445c8cb3 100644 --- a/var/spack/repos/builtin/packages/r-a4reporting/package.py +++ b/var/spack/repos/builtin/packages/r-a4reporting/package.py @@ -28,10 +28,11 @@ from spack import * class RA4reporting(RPackage): """Automated Affymetrix Array Analysis Reporting Package.""" - homepage = "https://www.bioconductor.org" - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/a4Reporting_1.24.0.tar.gz" + homepage = "https://www.bioconductor.org/packages/a4Reporting" + url = "https://git.bioconductor.org/packages/a4Reporting" list_url = homepage - version('1.24.0', '0d69505cae81da94e77b69184ae30abd') + version('1.24.0', git='https://git.bioconductor.org/packages/a4Reporting', commit='bf22c4d50daf40fc9eaf8c476385bf4a24a5b5ce') + depends_on('r@3.4.0:3.4.9', when='@1.24.0') depends_on('r-annaffy', type=('build', 'run')) depends_on('r-xtable', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-abaenrichment/package.py b/var/spack/repos/builtin/packages/r-abaenrichment/package.py index 6029c185d8..dc32fd7316 100644 --- a/var/spack/repos/builtin/packages/r-abaenrichment/package.py +++ b/var/spack/repos/builtin/packages/r-abaenrichment/package.py @@ -42,10 +42,11 @@ class RAbaenrichment(RPackage): user-defined brain regions.""" homepage = "https://bioconductor.org/packages/ABAEnrichment/" - url = "https://bioconductor.org/packages/release/bioc/src/contrib/ABAEnrichment_1.6.0.tar.gz" + url = "https://git.bioconductor.org/packages/ABAEnrichment" - version('1.6.0', '810eb4ee9ce2a5049babbb174dc8d588') + version('1.6.0', git='https://git.bioconductor.org/packages/ABAEnrichment', commit='d2a0467dcb7aa6e103e3b83dccd6510b0e142ac1') + depends_on('r@3.4.0:3.4.9', when='@1.6.0') depends_on('r-rcpp', type=('build', 'run')) depends_on('r-gplots', type=('build', 'run')) depends_on('r-gtools', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-absseq/package.py b/var/spack/repos/builtin/packages/r-absseq/package.py index 951aa09b1e..5d0e2a9b60 100644 --- a/var/spack/repos/builtin/packages/r-absseq/package.py +++ b/var/spack/repos/builtin/packages/r-absseq/package.py @@ -32,9 +32,10 @@ class RAbsseq(RPackage): of dispersion across expression level.""" homepage = "https://www.bioconductor.org/packages/ABSSeq/" - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/ABSSeq_1.22.8.tar.gz" + url = "https://git.bioconductor.org/packages/ABSSeq" - version('1.22.8', 'bfdb1800f2e7c60dfa7f6b43026ec8f9') + version('1.22.8', git='https://git.bioconductor.org/packages/ABSSeq', commit='a67ba49bc156a4522092519644f3ec83d58ebd6a') + depends_on('r@3.4.0:3.4.9', when='@1.22.8') depends_on('r-locfit', type=('build', 'run')) depends_on('r-limma', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-acgh/package.py b/var/spack/repos/builtin/packages/r-acgh/package.py index a683334e2f..00a20af76f 100644 --- a/var/spack/repos/builtin/packages/r-acgh/package.py +++ b/var/spack/repos/builtin/packages/r-acgh/package.py @@ -32,10 +32,11 @@ class RAcgh(RPackage): printing and plotting aCGH objects.""" homepage = "https://www.bioconductor.org/packages/aCGH/" - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/aCGH_1.54.0.tar.gz" + url = "https://git.bioconductor.org/packages/aCGH" - version('1.54.0', '8e5bd1800b2760e46fcab4179c2e920c') + version('1.54.0', git='https://git.bioconductor.org/packages/aCGH', commit='be2ed339449f55c8d218e10c435e4ad356683693') + depends_on('r@3.4.0:3.4.9', when='@1.54.0') depends_on('r-cluster', type=('build', 'run')) depends_on('r-survival', type=('build', 'run')) depends_on('r-multtest', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-acme/package.py b/var/spack/repos/builtin/packages/r-acme/package.py index 5e8ae24e85..a922121c30 100644 --- a/var/spack/repos/builtin/packages/r-acme/package.py +++ b/var/spack/repos/builtin/packages/r-acme/package.py @@ -37,9 +37,10 @@ class RAcme(RPackage): experiments quite easily with enough memory.""" homepage = "https://www.bioconductor.org/packages/ACME/" - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/ACME_2.32.0.tar.gz" + url = "https://git.bioconductor.org/packages/ACME" - version('2.32.0', 'f99ea6b94399fd7a10f55ac7e7ec04fa') + version('2.32.0', git='https://git.bioconductor.org/packages/ACME', commit='76372255d7714a0c8128a11c028bf70214dac407') + depends_on('r@3.4.0:3.4.9', when='@2.32.0') depends_on('r-biobase', type=('build', 'run')) depends_on('r-biocgenerics', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-adsplit/package.py b/var/spack/repos/builtin/packages/r-adsplit/package.py index 9419c69bae..35eb36f45a 100644 --- a/var/spack/repos/builtin/packages/r-adsplit/package.py +++ b/var/spack/repos/builtin/packages/r-adsplit/package.py @@ -32,10 +32,11 @@ class RAdsplit(RPackage): significance of the supporting gene set is determined.""" homepage = "https://www.bioconductor.org/packages/adSplit/" - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/adSplit_1.46.0.tar.gz" + url = "https://git.bioconductor.org/packages/adSplit" - version('1.46.0', '7638432c734c1fe458acbb9b29384f57') + version('1.46.0', git='https://git.bioconductor.org/packages/adSplit', commit='7e81a83f34d371447f491b3a146bf6851e260c7c') + depends_on('r@3.4.0:3.4.9', when='@1.46.0') depends_on('r-annotationdbi', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-cluster', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affxparser/package.py b/var/spack/repos/builtin/packages/r-affxparser/package.py index 7b001b4ace..541aecef7c 100644 --- a/var/spack/repos/builtin/packages/r-affxparser/package.py +++ b/var/spack/repos/builtin/packages/r-affxparser/package.py @@ -36,7 +36,9 @@ class RAffxparser(RPackage): from a set of CEL files into a convenient list structure.""" homepage = "https://www.bioconductor.org/packages/affxparser/" - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/affxparser_1.48.0.tar.gz" + url = "https://git.bioconductor.org/packages/affxparser" list_url = homepage - version('1.48.0', '20ae3f61e3ea25c3baeabf949b1f1165') + version('1.48.0', git='https://git.bioconductor.org/packages/affxparser', commit='2461ea88f310b59c4a9a997a4b3dadedbd65a4aa') + + depends_on('r@3.4.0:3.4.9', when='@1.48.0') diff --git a/var/spack/repos/builtin/packages/r-affycomp/package.py b/var/spack/repos/builtin/packages/r-affycomp/package.py index 490e9bec09..5a27638154 100644 --- a/var/spack/repos/builtin/packages/r-affycomp/package.py +++ b/var/spack/repos/builtin/packages/r-affycomp/package.py @@ -30,8 +30,9 @@ class RAffycomp(RPackage): expression measures for Affymetrix Oligonucleotide Arrays.""" homepage = "https://www.bioconductor.org/packages/affycomp/" - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/affycomp_1.52.0.tar.gz" + url = "https://git.bioconductor.org/packages/affycomp" - version('1.52.0', 'efa67e67701f2083fadbed99bf7d60b9') + version('1.52.0', git='https://git.bioconductor.org/packages/affycomp', commit='1b97a1cb21ec93bf1e5c88d5d55b988059612790') + depends_on('r@3.4.0:3.4.9', when='@1.52.0') depends_on('r-biobase', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affycompatible/package.py b/var/spack/repos/builtin/packages/r-affycompatible/package.py index 3f78340e0b..80dd6ff45c 100644 --- a/var/spack/repos/builtin/packages/r-affycompatible/package.py +++ b/var/spack/repos/builtin/packages/r-affycompatible/package.py @@ -34,9 +34,9 @@ class RAffycompatible(RPackage): (AGCC)-compatible sample annotation files.""" homepage = "https://www.bioconductor.org/packages/AffyCompatible/" - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/AffyCompatible_1.36.0.tar.gz" + url = "https://git.bioconductor.org/packages/AffyCompatible" - version('1.36.0', '0e30d7f20308d7c48beb4a03b5ea20c6') + version('1.36.0', 'https://git.bioconductor.org/packages/AffyCompatible', commit='dbbfd43a54ae1de6173336683a9461084ebf38c3') depends_on('r@3.4.0:3.4.9', when=('@1.36.0')) depends_on('r-xml', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-affycontam/package.py b/var/spack/repos/builtin/packages/r-affycontam/package.py index df5975ff0b..198018129d 100644 --- a/var/spack/repos/builtin/packages/r-affycontam/package.py +++ b/var/spack/repos/builtin/packages/r-affycontam/package.py @@ -30,9 +30,9 @@ class RAffycontam(RPackage): effectiveness.""" homepage = "https://www.bioconductor.org/packages/affyContam/" - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/affyContam_1.34.0.tar.gz" + url = "https://git.bioconductor.org/packages/affyContam" - version('1.34.0', '19e4452b65701482e8ee65aa8ce54fb9') + version('1.34.0', git='https://git.bioconductor.org/packages/affyContam', commit='03529f26d059c19e069cdda358dbf7789b6d4c40') depends_on('r@3.4.0:3.4.9', when=('@1.34.0')) depends_on('r-biobase', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-annaffy/package.py b/var/spack/repos/builtin/packages/r-annaffy/package.py index 7abebba8a8..e3a88a609e 100644 --- a/var/spack/repos/builtin/packages/r-annaffy/package.py +++ b/var/spack/repos/builtin/packages/r-annaffy/package.py @@ -35,10 +35,11 @@ class RAnnaffy(RPackage): using various criteria.""" homepage = "https://www.bioconductor.org/packages/annaffy/" - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/annaffy_1.48.0.tar.gz" + url = "https://git.bioconductor.org/packages/annaffy" - version('1.48.0', 'c51219a222b377403fe4bc08a6c57e7f') + version('1.48.0', git='https://git.bioconductor.org/packages/annaffy', commit='89a03c64ac9df5d963ed60b87893a3fffa6798a0') + depends_on('r@3.4.0:3.4.9', when='@1.48.0') depends_on('r-biobase', type=('build', 'run')) depends_on('r-go-db', type=('build', 'run')) depends_on('r-kegg-db', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-annotate/package.py b/var/spack/repos/builtin/packages/r-annotate/package.py index fd6b28cfbc..e0b4d0d4ce 100644 --- a/var/spack/repos/builtin/packages/r-annotate/package.py +++ b/var/spack/repos/builtin/packages/r-annotate/package.py @@ -29,10 +29,11 @@ class RAnnotate(RPackage): """Using R enviroments for annotation.""" homepage = "https://www.bioconductor.org/packages/annotate/" - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/annotate_1.54.0.tar.gz" + url = "https://git.bioconductor.org/packages/annotate" list_url = homepage - version('1.54.0', '01a4961ef28fc88943e168f946592d44') + version('1.54.0', git='https://git.bioconductor.org/packages/annotate', commit='860cc5b696795a31b18beaf4869f9c418d74549e') + depends_on('r@3.4.0:3.4.9', when='@1.54.0') depends_on('r-annotationdbi', type=('build', 'run')) depends_on('r-xml', type=('build', 'run')) depends_on('r-rcurl', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-annotationdbi/package.py b/var/spack/repos/builtin/packages/r-annotationdbi/package.py index aaac979029..f09cdc29cd 100644 --- a/var/spack/repos/builtin/packages/r-annotationdbi/package.py +++ b/var/spack/repos/builtin/packages/r-annotationdbi/package.py @@ -32,10 +32,11 @@ class RAnnotationdbi(RPackage): annotation data packages using SQLite data storage.""" homepage = "https://www.bioconductor.org/packages/AnnotationDbi/" - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/AnnotationDbi_1.38.2.tar.gz" + url = "https://git.bioconductor.org/packages/AnnotationDbi" list_url = homepage - version('1.38.2', 'aea4a5cd1f752b59cb9f4a8dcca05734') + version('1.38.2', git='https://git.bioconductor.org/packages/AnnotationDbi', commit='67d46facba8c15fa5f0eb47c4e39b53dbdc67c36') + depends_on('r@3.4.0:3.4.9', when='@1.38.2') depends_on('r-biocgenerics', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-iranges', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-genefilter/package.py b/var/spack/repos/builtin/packages/r-genefilter/package.py index 1d2e4fa4b2..609ccecd35 100644 --- a/var/spack/repos/builtin/packages/r-genefilter/package.py +++ b/var/spack/repos/builtin/packages/r-genefilter/package.py @@ -29,9 +29,11 @@ class RGenefilter(RPackage): """Some basic functions for filtering genes""" homepage = "https://bioconductor.org/packages/genefilter/" - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/genefilter_1.58.1.tar.gz" + url = "https://git.bioconductor.org/packages/genefilter" list_url = homepage - version('1.58.1', 'bc1a90bdf93d8db994220545cd80f438') + version('1.58.1', git='https://git.bioconductor.org/packages/genefilter', commit='ace2556049677f60882adfe91f8cc96791556fc2') + + depends_on('r@3.4.0:3.4.9', when='@1.58.1') depends_on('r-s4vectors', type=('build', 'run')) depends_on('r-annotationdbi', type=('build', 'run')) depends_on('r-annotate', 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 e17a4b83a8..a16ce16a09 100644 --- a/var/spack/repos/builtin/packages/r-limma/package.py +++ b/var/spack/repos/builtin/packages/r-limma/package.py @@ -30,8 +30,10 @@ class RLimma(RPackage): for microarray data.""" homepage = "https://www.bioconductor.org/packages/limma/" - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/limma_3.32.6.tar.gz" + url = "https://git.bioconductor.org/packages/limma" list_url = homepage - version('3.32.7', '9fb616ba50b4758307b0e89dbe3143d9') + version('3.32.10', git='https://git.bioconductor.org/packages/limma', commit='593edf28e21fe054d64137ae271b8a52ab05bc60') version('3.32.6', 'df5dc2b85189a24e939efa3a8e6abc41') + + depends_on('r@3.4.0:3.4.9', when='@3.32.10') diff --git a/var/spack/repos/builtin/packages/r-mlinterfaces/package.py b/var/spack/repos/builtin/packages/r-mlinterfaces/package.py index 295e9104fb..4aebba0931 100644 --- a/var/spack/repos/builtin/packages/r-mlinterfaces/package.py +++ b/var/spack/repos/builtin/packages/r-mlinterfaces/package.py @@ -30,10 +30,11 @@ class RMlinterfaces(RPackage): code for data in R and Bioconductor containers.""" homepage = "https://www.bioconductor.org/packages/MLInterfaces/" - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/MLInterfaces_1.56.0.tar.gz" + url = "https://git.bioconductor.org/packages/MLInterfaces" - version('1.56.0', '14245ac510304af211734079a81e3b4a') + version('1.56.0', git='https://git.bioconductor.org/packages/MLInterfaces', commit='31fe6fb20d859fcb01d5552f42bca6bab16cc67f') + depends_on('r@3.4.0:3.4.9', when='@1.56.0') depends_on('r-biocgenerics', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) depends_on('r-gdata', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-multtest/package.py b/var/spack/repos/builtin/packages/r-multtest/package.py index 3e6428b44c..5ffa84711f 100644 --- a/var/spack/repos/builtin/packages/r-multtest/package.py +++ b/var/spack/repos/builtin/packages/r-multtest/package.py @@ -29,8 +29,10 @@ class RMulttest(RPackage): """Resampling-based multiple hypothesis testing""" homepage = "https://www.bioconductor.org/packages/multtest/" - url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/multtest_2.32.0.tar.gz" - version('2.32.0', 'edfa82ac11e4f86c438609e9d2128e5c') + url = "https://git.bioconductor.org/packages/multtest" + version('2.32.0', git='https://git.bioconductor.org/packages/multtest', commit='c5e890dfbffcc3a3f107303a24b6085614312f4a') + + depends_on('r@3.4.0:3.4.9', when='@2.32.0') depends_on('r-biocgenerics', type=('build', 'run')) depends_on('r-biobase', type=('build', 'run')) |