update Bioconductor R packages (#33224)

* Add bioc attribute to r-do-db
* add version 1.38.1 to bioconductor package r-annotationforge
* add version 1.30.4 to bioconductor package r-biocparallel
* add version 2.64.1 to bioconductor package r-biostrings
* add version 4.4.4 to bioconductor package r-clusterprofiler
* add version 2.12.1 to bioconductor package r-complexheatmap
* add version 1.18.1 to bioconductor package r-delayedmatrixstats
* add version 3.22.1 to bioconductor package r-dose
* add version 3.38.4 to bioconductor package r-edger
* add version 1.16.2 to bioconductor package r-enrichplot
* add version 2.20.2 to bioconductor package r-ensembldb
* add version 1.32.4 to bioconductor package r-genomeinfodb
* add version 1.32.1 to bioconductor package r-genomicalignments
* add version 1.48.4 to bioconductor package r-genomicfeatures
* add version 1.44.1 to bioconductor package r-ggbio
* add version 3.4.4 to bioconductor package r-ggtree
* add version 1.24.2 to bioconductor package r-hdf5array
* add version 2.30.1 to bioconductor package r-iranges
* add version 1.36.3 to bioconductor package r-keggrest
* add version 3.52.4 to bioconductor package r-limma
* add version 1.8.1 to bioconductor package r-matrixgenerics
* update r-org-hs-eg-db
* add version 1.38.1 to bioconductor package r-organismdbi
* add version 1.36.1 to bioconductor package r-pathview
* add version 1.56.1 to bioconductor package r-rtracklayer
* add version 1.4.1 to bioconductor package r-scaledmatrix
* add version 1.24.1 to bioconductor package r-scran
* add version 1.6.3 to bioconductor package r-scuttle
* add version 1.18.1 to bioconductor package r-singlecellexperiment
* add version 1.20.2 to bioconductor package r-treeio
* Revert "Add bioc attribute to r-do-db"
This reverts commit 36be5c6072c98ec70bb16f9d613a6fe24407fee1.
* Fix quotes on versions

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>

29 files changed, 38 insertions, 1 deletions

diff --git a/var/spack/repos/builtin/packages/r-annotationforge/package.py b/var/spack/repos/builtin/packages/r-annotationforge/package.py
index ab4b8d0db6..cab4169145 100644
--- a/var/spack/repos/builtin/packages/r-annotationforge/package.py
+++ b/var/spack/repos/builtin/packages/r-annotationforge/package.py
@@ -14,6 +14,7 @@ class RAnnotationforge(RPackage):
 
     bioc = "AnnotationForge"
 
+    version("1.38.1", commit="2dcedf353bc57bf80818e6adb1f7129c21886f6b")
     version("1.38.0", commit="1f77750562ea3a01f0f1a46c299184fc31196ffd")
     version("1.36.0", commit="523b5f0c3ffb77e59e1568e5f36a5a470bfeeae5")
     version("1.32.0", commit="3d17c2a945951c02fe152e5a8a8e9c6cb41e30f7")
diff --git a/var/spack/repos/builtin/packages/r-biocparallel/package.py b/var/spack/repos/builtin/packages/r-biocparallel/package.py
index f1a13d964f..0a315307a9 100644
--- a/var/spack/repos/builtin/packages/r-biocparallel/package.py
+++ b/var/spack/repos/builtin/packages/r-biocparallel/package.py
@@ -15,6 +15,7 @@ class RBiocparallel(RPackage):
 
     bioc = "BiocParallel"
 
+    version("1.30.4", commit="1229ebe9f6d8305f9f61e562464f83f9ba86e699")
     version("1.30.2", commit="e7e109f7a94dbfbc50f926be030c7ad8c1a053db")
     version("1.28.3", commit="2f9d88ad83659939e7911d49c2d24d2cd599c7cc")
     version("1.24.1", commit="f713caa4314ec0ddeba7fe0eb599ad417efb413f")
@@ -27,4 +28,5 @@ class RBiocparallel(RPackage):
     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-codetools", type=("build", "run"), when="@1.30.4:")
     depends_on("r-bh", type=("build", "run"), when="@1.12.0:")
diff --git a/var/spack/repos/builtin/packages/r-biostrings/package.py b/var/spack/repos/builtin/packages/r-biostrings/package.py
index b2279c62bc..b4fa9866a0 100644
--- a/var/spack/repos/builtin/packages/r-biostrings/package.py
+++ b/var/spack/repos/builtin/packages/r-biostrings/package.py
@@ -15,6 +15,7 @@ class RBiostrings(RPackage):
 
     bioc = "Biostrings"
 
+    version("2.64.1", commit="ffe263e958463bd1edb5d5d9316cfd89905be53c")
     version("2.64.0", commit="c7ad3c7af607bc8fe4a5e1c37f09e6c9bf70b4f6")
     version("2.62.0", commit="53ed287e03d16fa523789af3131c60375ccf587f")
     version("2.58.0", commit="0ec1a5455d5e9eebd14b26228906bb04e2abb197")
@@ -39,6 +40,7 @@ class RBiostrings(RPackage):
     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-iranges@2.30.1:", type=("build", "run"), when="@2.64.1:")
     depends_on("r-xvector@0.11.6:", 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:")
diff --git a/var/spack/repos/builtin/packages/r-clusterprofiler/package.py b/var/spack/repos/builtin/packages/r-clusterprofiler/package.py
index a39b6e8142..3f3d83bb60 100644
--- a/var/spack/repos/builtin/packages/r-clusterprofiler/package.py
+++ b/var/spack/repos/builtin/packages/r-clusterprofiler/package.py
@@ -15,6 +15,7 @@ class RClusterprofiler(RPackage):
 
     bioc = "clusterProfiler"
 
+    version("4.4.4", commit="9fca9a45ca1793884d8dcfd0f077353dbf75df29")
     version("4.4.1", commit="daad11fb80be2dd9b825e0b484815a0a2b1592a4")
     version("4.2.2", commit="4ebb9de8e03eedc971f54a57cf5bf1b250ed43d5")
     version("3.18.0", commit="064a6e612ce27e260e33af78b907bee4065ff821")
diff --git a/var/spack/repos/builtin/packages/r-complexheatmap/package.py b/var/spack/repos/builtin/packages/r-complexheatmap/package.py
index 2efd9ab007..6cf4964280 100644
--- a/var/spack/repos/builtin/packages/r-complexheatmap/package.py
+++ b/var/spack/repos/builtin/packages/r-complexheatmap/package.py
@@ -16,6 +16,7 @@ class RComplexheatmap(RPackage):
 
     bioc = "ComplexHeatmap"
 
+    version("2.12.1", commit="2c5fe70724219008174d4e6f83189cddbd895ec6")
     version("2.12.0", commit="8a5f060b06646f9d6a5032832ea72e3f183ca5d7")
     version("2.10.0", commit="170df82a1568e879e4019e0ff6feb0047851684f")
     version("2.6.2", commit="0383bada2c76dc3dde71cf6a625016b619aec4d3")
diff --git a/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py b/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py
index 15f852038d..df0e57aa98 100644
--- a/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py
+++ b/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py
@@ -18,6 +18,7 @@ class RDelayedmatrixstats(RPackage):
 
     bioc = "DelayedMatrixStats"
 
+    version("1.18.1", commit="9c4658d11fc20b7d88e05b9c52140c2ca8a65768")
     version("1.18.0", commit="50c9aab259b6e8f68abf44b78122662a41c8bf47")
     version("1.16.0", commit="d44a3d765769cb022193428a77af25bf19916be7")
     version("1.12.3", commit="2b3091dfa9b3bab914e3a4157182063714ba86ae")
@@ -40,6 +41,7 @@ class RDelayedmatrixstats(RPackage):
     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-matrix@1.5.0:", type=("build", "run"), when="@1.18.1:")
     depends_on("r-s4vectors", type=("build", "run"))
     depends_on("r-s4vectors@0.17.5:", type=("build", "run"), when="@1.2.0:")
     depends_on("r-iranges", 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 3b1716da58..99c36609ab 100644
--- a/var/spack/repos/builtin/packages/r-dose/package.py
+++ b/var/spack/repos/builtin/packages/r-dose/package.py
@@ -18,6 +18,7 @@ class RDose(RPackage):
 
     bioc = "DOSE"
 
+    version("3.22.1", commit="6b711a0f076a9fefcb00ddef66e8f198039e6dfa")
     version("3.22.0", commit="242ac1b746c44fbbf281fbe6e5e4424a8dc74375")
     version("3.20.1", commit="bf434f24d035217822cb1b0ab08a486b9a53edb4")
     version("3.16.0", commit="a534a4f2ef1e54e8b92079cf1bbedb5042fd90cd")
diff --git a/var/spack/repos/builtin/packages/r-edger/package.py b/var/spack/repos/builtin/packages/r-edger/package.py
index ab3610f473..2dc5026083 100644
--- a/var/spack/repos/builtin/packages/r-edger/package.py
+++ b/var/spack/repos/builtin/packages/r-edger/package.py
@@ -19,6 +19,7 @@ class REdger(RPackage):
 
     bioc = "edgeR"
 
+    version("3.38.4", commit="f5a3bb568a23b34146ac66329a95ee4785093536")
     version("3.38.1", commit="e58bf52f34ec451096f593126922ad7e5d517f7e")
     version("3.36.0", commit="c7db03addfc42138a1901834409c02da9d873026")
     version("3.32.1", commit="b881d801d60e5b38413d27f149384c218621c55a")
diff --git a/var/spack/repos/builtin/packages/r-enrichplot/package.py b/var/spack/repos/builtin/packages/r-enrichplot/package.py
index dc7597b6ea..24f204a5ea 100644
--- a/var/spack/repos/builtin/packages/r-enrichplot/package.py
+++ b/var/spack/repos/builtin/packages/r-enrichplot/package.py
@@ -16,6 +16,7 @@ class REnrichplot(RPackage):
 
     bioc = "enrichplot"
 
+    version("1.16.2", commit="eeb21345288d96c116ac308649fa772d03760259")
     version("1.16.1", commit="cff77b622b2312be546714ec437aa4bc585bac87")
     version("1.14.1", commit="ccf3a6d9b7cd9cffd8de6d6263efdffe59d2ec36")
     version("1.10.2", commit="77ee04f60a07cc31151f8f47f8ee64f3a43c9760")
@@ -49,5 +50,5 @@ class REnrichplot(RPackage):
     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"))
+    depends_on("r-cowplot", when="@:1.16.1")
diff --git a/var/spack/repos/builtin/packages/r-ensembldb/package.py b/var/spack/repos/builtin/packages/r-ensembldb/package.py
index 8e2403c6bf..da2dc2dfe2 100644
--- a/var/spack/repos/builtin/packages/r-ensembldb/package.py
+++ b/var/spack/repos/builtin/packages/r-ensembldb/package.py
@@ -24,6 +24,7 @@ class REnsembldb(RPackage):
 
     bioc = "ensembldb"
 
+    version("2.20.2", commit="ac1fb8389efd88099600af298d6bb3384206f9ed")
     version("2.20.1", commit="e547d184730cfe5e65f59e4f3512395fb1cdba1a")
     version("2.18.3", commit="e2fcfc0c7700110df070a171d2d542b37ec098f3")
     version("2.14.0", commit="c7150519ed4ef38e5eac1043209863dbc7be43a1")
diff --git a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py
index de08108955..e9218f10e0 100644
--- a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py
+++ b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py
@@ -17,6 +17,7 @@ class RGenomeinfodb(RPackage):
 
     bioc = "GenomeInfoDb"
 
+    version("1.32.4", commit="69df6a5a10027fecf6a6d1c8298f3f686b990d8f")
     version("1.32.2", commit="2e40af38f00ee86d2c83d140e234c1349baa27de")
     version("1.30.1", commit="bf8b385a2ffcecf9b41e581794056f267895863d")
     version("1.26.2", commit="96dd27a7e3ef476790b1475aab50dbbed7df67a2")
diff --git a/var/spack/repos/builtin/packages/r-genomicalignments/package.py b/var/spack/repos/builtin/packages/r-genomicalignments/package.py
index 3a2cb8c2de..20f659508c 100644
--- a/var/spack/repos/builtin/packages/r-genomicalignments/package.py
+++ b/var/spack/repos/builtin/packages/r-genomicalignments/package.py
@@ -16,6 +16,7 @@ class RGenomicalignments(RPackage):
 
     bioc = "GenomicAlignments"
 
+    version("1.32.1", commit="2553580d0b8a8a5fd7835c1446616b39f707b8a9")
     version("1.32.0", commit="7a660a914a04e2eb0758082b6f64c4124a887ef3")
     version("1.30.0", commit="2d2c5fce3529c2962fdcefd736d8b7f7c0ec2d54")
     version("1.26.0", commit="6c74c74ee53efcd880171126366fee4bd72357bc")
diff --git a/var/spack/repos/builtin/packages/r-genomicfeatures/package.py b/var/spack/repos/builtin/packages/r-genomicfeatures/package.py
index 491b8632bc..2da0705694 100644
--- a/var/spack/repos/builtin/packages/r-genomicfeatures/package.py
+++ b/var/spack/repos/builtin/packages/r-genomicfeatures/package.py
@@ -20,6 +20,7 @@ class RGenomicfeatures(RPackage):
 
     bioc = "GenomicFeatures"
 
+    version("1.48.4", commit="06e37dc1847d49d91391264caec877ed33abf359")
     version("1.48.3", commit="b0ddea0e101e3861928f3ad353348df047d90382")
     version("1.46.4", commit="d3ab6fd069624904ce7fcdf75dad884473f97975")
     version("1.42.1", commit="2e82891974138b0e976799d64a8938f0be61284d")
diff --git a/var/spack/repos/builtin/packages/r-ggbio/package.py b/var/spack/repos/builtin/packages/r-ggbio/package.py
index b310a41ee4..1ea9655c07 100644
--- a/var/spack/repos/builtin/packages/r-ggbio/package.py
+++ b/var/spack/repos/builtin/packages/r-ggbio/package.py
@@ -21,6 +21,7 @@ class RGgbio(RPackage):
 
     bioc = "ggbio"
 
+    version("1.44.1", commit="0301d9464e304a8113ea4479185cd358855ca365")
     version("1.44.0", commit="cb21284a9803917fa76e116adfc456525c95f660")
     version("1.42.0", commit="3540047ef018957d59fba8af7d3c58e4659f8e26")
     version("1.38.0", commit="c39c51993f419cfc2f094e664477f25f5212a242")
diff --git a/var/spack/repos/builtin/packages/r-ggtree/package.py b/var/spack/repos/builtin/packages/r-ggtree/package.py
index bc3e5eddfd..9128cffcf8 100644
--- a/var/spack/repos/builtin/packages/r-ggtree/package.py
+++ b/var/spack/repos/builtin/packages/r-ggtree/package.py
@@ -16,6 +16,7 @@ class RGgtree(RPackage):
 
     bioc = "ggtree"
 
+    version("3.4.4", commit="8e48d3e2ea445b6c2213f0471462108a7a72b333")
     version("3.4.0", commit="23f08a3da1829d1bbb6827ed1c4cf878daa4b539")
     version("3.2.1", commit="d3747e636fe1a6a9e09b56a3a3899208ebd05547")
 
diff --git a/var/spack/repos/builtin/packages/r-hdf5array/package.py b/var/spack/repos/builtin/packages/r-hdf5array/package.py
index 024eee78fe..ca60baa1e1 100644
--- a/var/spack/repos/builtin/packages/r-hdf5array/package.py
+++ b/var/spack/repos/builtin/packages/r-hdf5array/package.py
@@ -20,6 +20,7 @@ class RHdf5array(RPackage):
 
     bioc = "HDF5Array"
 
+    version("1.24.2", commit="fb213ba36631b04dfe754705f701f3a015c4fc82")
     version("1.24.1", commit="d002fe70c84baaadb62058ce467d6c1ea032d8f5")
     version("1.22.1", commit="b3f091fbc159609e8e0792d2bf9fbef52c6ceede")
     version("1.18.0", commit="d5bd55d170cb384fdebdf60751e1e28483782caa")
diff --git a/var/spack/repos/builtin/packages/r-iranges/package.py b/var/spack/repos/builtin/packages/r-iranges/package.py
index 80e44d5d7e..4cf880670a 100644
--- a/var/spack/repos/builtin/packages/r-iranges/package.py
+++ b/var/spack/repos/builtin/packages/r-iranges/package.py
@@ -18,6 +18,7 @@ class RIranges(RPackage):
 
     bioc = "IRanges"
 
+    version("2.30.1", commit="ead506a14d6cc89ac2f14b55a4b04496755e4e50")
     version("2.30.0", commit="9b5f3ca12812fb76c23b1550aa3a794384384d9b")
     version("2.28.0", commit="d85ee908a379e12d1e32599e999c71ab37c25e57")
     version("2.24.1", commit="6c61fddf4c5830f69a0f7f108888c67cd0a12b19")
diff --git a/var/spack/repos/builtin/packages/r-keggrest/package.py b/var/spack/repos/builtin/packages/r-keggrest/package.py
index 4a081d7132..20bf8b0e31 100644
--- a/var/spack/repos/builtin/packages/r-keggrest/package.py
+++ b/var/spack/repos/builtin/packages/r-keggrest/package.py
@@ -15,6 +15,7 @@ class RKeggrest(RPackage):
 
     bioc = "KEGGREST"
 
+    version("1.36.3", commit="1827cde76863aa80c83264a0dd95514654358df3")
     version("1.36.0", commit="591818bbc9195bfd0657cf4f5c7c771ea7f86830")
     version("1.34.0", commit="2056750dc202fa04a34b84c6c712e884c7cad2bd")
     version("1.30.1", commit="fd9970ea9df117d625257b8c6351cf85098cfbc1")
diff --git a/var/spack/repos/builtin/packages/r-limma/package.py b/var/spack/repos/builtin/packages/r-limma/package.py
index 6bc580bb2f..8d92ec5505 100644
--- a/var/spack/repos/builtin/packages/r-limma/package.py
+++ b/var/spack/repos/builtin/packages/r-limma/package.py
@@ -14,6 +14,7 @@ class RLimma(RPackage):
 
     bioc = "limma"
 
+    version("3.52.4", commit="3226c29ad8c18aa7e6722f4a2c95ff8ac900437e")
     version("3.52.1", commit="c81c539a217ac1cf46e850f8a20266cecfafed50")
     version("3.50.0", commit="657b19bbc33c5c941af79aeb68967bf42ea40e23")
     version("3.46.0", commit="ff03542231827f39ebde6464cdbba0110e24364e")
diff --git a/var/spack/repos/builtin/packages/r-matrixgenerics/package.py b/var/spack/repos/builtin/packages/r-matrixgenerics/package.py
index bfada6c30d..289f23d36a 100644
--- a/var/spack/repos/builtin/packages/r-matrixgenerics/package.py
+++ b/var/spack/repos/builtin/packages/r-matrixgenerics/package.py
@@ -19,6 +19,7 @@ class RMatrixgenerics(RPackage):
 
     bioc = "MatrixGenerics"
 
+    version("1.8.1", commit="a4a21089e9f78275dd4a6f0df0c4b6b45c4650c7")
     version("1.8.0", commit="e4cc34d53bcfb9a5914afd79fda31ecd5037a47a")
     version("1.6.0", commit="4588a60e5cc691424c17faa281bdd7d99d83ec34")
     version("1.2.1", commit="abcc9ca0504e0b915cd7933a3169a8e9e5bd2fe9")
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 d8edda67ff..2892bc3480 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
@@ -16,6 +16,11 @@ class ROrgHsEgDb(RPackage):
     url = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/org.Hs.eg.db_3.4.1.tar.gz"
 
     version(
+        "3.15.0",
+        sha256="1dc9bb6019e0f0a222b9ec84a1c5870cdbca480f45d9ad08e35f77278baa3c5f",
+        url="https://www.bioconductor.org/packages/3.15/data/annotation/src/contrib/org.Hs.eg.db_3.15.0.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",
@@ -41,3 +46,4 @@ class ROrgHsEgDb(RPackage):
     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:")
+    depends_on("r-annotationdbi@1.57.1:", type=("build", "run"), when="@3.15.0:")
diff --git a/var/spack/repos/builtin/packages/r-organismdbi/package.py b/var/spack/repos/builtin/packages/r-organismdbi/package.py
index bd28958586..5ae90de629 100644
--- a/var/spack/repos/builtin/packages/r-organismdbi/package.py
+++ b/var/spack/repos/builtin/packages/r-organismdbi/package.py
@@ -16,6 +16,7 @@ class ROrganismdbi(RPackage):
 
     bioc = "OrganismDbi"
 
+    version("1.38.1", commit="fa8da4dd42ab15e1d21fd9f8286440596d50b1ec")
     version("1.38.0", commit="2ca01830a6ffcd0c0018d2bdbd3de8b4df716771")
     version("1.36.0", commit="3e7a90d248ff09f05ccd381ff921e12373a4b330")
     version("1.32.0", commit="c8100c4fea17bf1b10d4efacc73a7e2866d649e3")
diff --git a/var/spack/repos/builtin/packages/r-pathview/package.py b/var/spack/repos/builtin/packages/r-pathview/package.py
index 01a8f0f870..92b017f158 100644
--- a/var/spack/repos/builtin/packages/r-pathview/package.py
+++ b/var/spack/repos/builtin/packages/r-pathview/package.py
@@ -20,6 +20,7 @@ class RPathview(RPackage):
 
     bioc = "pathview"
 
+    version("1.36.1", commit="f2e86b106c1cd91aac703337f968b7593a61c68d")
     version("1.36.0", commit="4f6be090a4089b5259d8e796d62f9830e2d63943")
     version("1.34.0", commit="a8788902a3bb047f8ee785966e57f84596076bbd")
     version("1.30.1", commit="a6a32395db408798cb076894678e90148bae6bf4")
diff --git a/var/spack/repos/builtin/packages/r-rtracklayer/package.py b/var/spack/repos/builtin/packages/r-rtracklayer/package.py
index e095dd3251..a52013b329 100644
--- a/var/spack/repos/builtin/packages/r-rtracklayer/package.py
+++ b/var/spack/repos/builtin/packages/r-rtracklayer/package.py
@@ -18,6 +18,7 @@ class RRtracklayer(RPackage):
 
     bioc = "rtracklayer"
 
+    version("1.56.1", commit="4c6d2201fcb102d471bd88f4f51cc34317669955")
     version("1.56.0", commit="1d70f7dc464ad87a1fde61588cd9ae0cb86b6e86")
     version("1.54.0", commit="04cdd75521a8364e67a49d7352500dd4a3e83c55")
     version("1.50.0", commit="d2e61f72ff5d5a94c2c487ba108a37f23bfcc1e6")
diff --git a/var/spack/repos/builtin/packages/r-scaledmatrix/package.py b/var/spack/repos/builtin/packages/r-scaledmatrix/package.py
index e99dc8dac2..b49f1235d5 100644
--- a/var/spack/repos/builtin/packages/r-scaledmatrix/package.py
+++ b/var/spack/repos/builtin/packages/r-scaledmatrix/package.py
@@ -16,6 +16,7 @@ class RScaledmatrix(RPackage):
 
     bioc = "ScaledMatrix"
 
+    version("1.4.1", commit="15e2efcb6b11e26c31ef2d44968355f71cc1f4fc")
     version("1.4.0", commit="32e6e918bc7bb64bbf75613d353ca268c7d04292")
     version("1.2.0", commit="d0573e14ca537b40ade7dd1c9cf0cadae60d4349")
 
diff --git a/var/spack/repos/builtin/packages/r-scran/package.py b/var/spack/repos/builtin/packages/r-scran/package.py
index fcf4f46534..cac48a6e17 100644
--- a/var/spack/repos/builtin/packages/r-scran/package.py
+++ b/var/spack/repos/builtin/packages/r-scran/package.py
@@ -17,6 +17,7 @@ class RScran(RPackage):
 
     bioc = "scran"
 
+    version("1.24.1", commit="1a83eb7c948b1dc49253080c23b26cefb3a0f3b9")
     version("1.24.0", commit="c3f9e169c4538ce827d4f14a4141571c2366cd31")
 
     depends_on("r-singlecellexperiment", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/r-scuttle/package.py b/var/spack/repos/builtin/packages/r-scuttle/package.py
index 6862bf3806..2ed9145d15 100644
--- a/var/spack/repos/builtin/packages/r-scuttle/package.py
+++ b/var/spack/repos/builtin/packages/r-scuttle/package.py
@@ -16,6 +16,7 @@ class RScuttle(RPackage):
 
     bioc = "scuttle"
 
+    version("1.6.3", commit="df23680da9fa4d685df77e4561467f491c850b50")
     version("1.6.2", commit="afdfc555151d84cc332757b4ec0b97cb7f39d2d5")
     version("1.4.0", commit="b335263dd56bb859b5dd3ea27ee00dffa0215313")
     version("1.0.4", commit="a827e2759d80e6c3510e2f8fd4bd680274206d9f")
diff --git a/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py b/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py
index d024ae131a..47719faeb7 100644
--- a/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py
+++ b/var/spack/repos/builtin/packages/r-singlecellexperiment/package.py
@@ -16,6 +16,7 @@ class RSinglecellexperiment(RPackage):
 
     bioc = "SingleCellExperiment"
 
+    version("1.18.1", commit="db7768a7cb5eca724bcf7e4cea3234992ac714a1")
     version("1.18.0", commit="3a72dcd97e628055b2d02294eaecca9a41aba604")
     version("1.16.0", commit="bb27609ba08052607fc08529ffbbbcf1eab265cb")
     version("1.12.0", commit="66063b74c8b0bd0fd1277c7ad425ad11823ab356")
diff --git a/var/spack/repos/builtin/packages/r-treeio/package.py b/var/spack/repos/builtin/packages/r-treeio/package.py
index 64b8dce420..17cf92167d 100644
--- a/var/spack/repos/builtin/packages/r-treeio/package.py
+++ b/var/spack/repos/builtin/packages/r-treeio/package.py
@@ -18,6 +18,7 @@ class RTreeio(RPackage):
 
     bioc = "treeio"
 
+    version("1.20.2", commit="ed457d6fd85a50e0993c8c9acbd9b701be01a348")
     version("1.20.0", commit="5f7c3704fc8202c52451d092148fdcfe683f026a")
     version("1.18.1", commit="a06b6b3d2a64f1b22c6c8c5f97c08f5863349c83")