diff --git a/var/spack/repos/builtin/packages/r-affy/package.py b/var/spack/repos/builtin/packages/r-affy/package.py
index 536072c20b9..c6697241b1f 100644
--- a/var/spack/repos/builtin/packages/r-affy/package.py
+++ b/var/spack/repos/builtin/packages/r-affy/package.py
@@ -28,6 +28,7 @@ class RAffy(RPackage):
depends_on("c", type="build") # generated
+ depends_on("r@2.8.0:", type=("build", "run"))
depends_on("r@2.8.0:4.0", 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"))
diff --git a/var/spack/repos/builtin/packages/r-affyio/package.py b/var/spack/repos/builtin/packages/r-affyio/package.py
index 68127809cd6..58638d4efab 100644
--- a/var/spack/repos/builtin/packages/r-affyio/package.py
+++ b/var/spack/repos/builtin/packages/r-affyio/package.py
@@ -29,5 +29,6 @@ class RAffyio(RPackage):
depends_on("c", type="build") # generated
depends_on("r@2.6.0:", type=("build", "run"))
- depends_on("r-zlibbioc", type=("build", "run"))
depends_on("zlib-api")
+
+ depends_on("r-zlibbioc", type=("build", "run"), when="@:1.77.0")
diff --git a/var/spack/repos/builtin/packages/r-assorthead/package.py b/var/spack/repos/builtin/packages/r-assorthead/package.py
new file mode 100644
index 00000000000..5e74fc72491
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-assorthead/package.py
@@ -0,0 +1,14 @@
+# Copyright 2013-2024 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.package import *
+
+
+class RAssorthead(RPackage):
+ """Assorted header-only C++ libraries for Bioconductor."""
+
+ bioc = "assorthead"
+
+ version("1.1.9", commit="b9de4f460dcac95360ae124cfe6c551863213dc6")
diff --git a/var/spack/repos/builtin/packages/r-basilisk/package.py b/var/spack/repos/builtin/packages/r-basilisk/package.py
index f3212fcbe42..99154061d56 100644
--- a/var/spack/repos/builtin/packages/r-basilisk/package.py
+++ b/var/spack/repos/builtin/packages/r-basilisk/package.py
@@ -25,3 +25,4 @@ class RBasilisk(RPackage):
depends_on("r-reticulate", type=("build", "run"))
depends_on("r-dir-expiry", type=("build", "run"))
depends_on("r-basilisk-utils", type=("build", "run"))
+ depends_on("r-basilisk-utils@1.15.1:", type=("build", "run"), when="@1.15.1:")
diff --git a/var/spack/repos/builtin/packages/r-beachmat/package.py b/var/spack/repos/builtin/packages/r-beachmat/package.py
index b9ddbb1f643..0924d190bdf 100644
--- a/var/spack/repos/builtin/packages/r-beachmat/package.py
+++ b/var/spack/repos/builtin/packages/r-beachmat/package.py
@@ -35,10 +35,13 @@ class RBeachmat(RPackage):
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-delayedarray@0.27.2:", type=("build", "run"), when="@2.17.1:")
+ depends_on("r-sparsearray", type=("build", "run"), when="@2.17.8:")
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:")
depends_on("r-rcpp", type=("build", "run"), when="@2.10.0:")
+ depends_on("r-assorthead", type=("build", "run"), when="@2.21.6:")
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")
diff --git a/var/spack/repos/builtin/packages/r-biocgenerics/package.py b/var/spack/repos/builtin/packages/r-biocgenerics/package.py
index 51d9c67d042..904a651ed54 100644
--- a/var/spack/repos/builtin/packages/r-biocgenerics/package.py
+++ b/var/spack/repos/builtin/packages/r-biocgenerics/package.py
@@ -27,3 +27,5 @@ class RBiocgenerics(RPackage):
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:")
+
+ depends_on("r-generics", type=("build", "run"), when="@0.53.1:")
diff --git a/var/spack/repos/builtin/packages/r-biocneighbors/package.py b/var/spack/repos/builtin/packages/r-biocneighbors/package.py
index 9c350c91316..5cf7474c98a 100644
--- a/var/spack/repos/builtin/packages/r-biocneighbors/package.py
+++ b/var/spack/repos/builtin/packages/r-biocneighbors/package.py
@@ -33,10 +33,11 @@ class RBiocneighbors(RPackage):
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", type=("build", "run"), when="@1.8.2:")
- depends_on("r-rcpphnsw", type=("build", "run"), when="@1.2.0:")
+ depends_on("r-assorthead", type=("build", "run"), when="@1.99.0:")
+ depends_on("r-s4vectors", type=("build", "run"), when="@:1.21")
+ depends_on("r-biocparallel", type=("build", "run"), when="@:1.21")
+ depends_on("r-matrix", type=("build", "run"), when="@1.8.2:1.21")
+ depends_on("r-rcpphnsw", type=("build", "run"), when="@1.2.0:1.21")
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-biocversion/package.py b/var/spack/repos/builtin/packages/r-biocversion/package.py
index 55e5b72a63d..0922c1771e5 100644
--- a/var/spack/repos/builtin/packages/r-biocversion/package.py
+++ b/var/spack/repos/builtin/packages/r-biocversion/package.py
@@ -24,3 +24,4 @@ class RBiocversion(RPackage):
depends_on("r@4.1.0:", type=("build", "run"), when="@3.14.0:")
depends_on("r@4.2.0:", type=("build", "run"), when="@3.15.2:")
depends_on("r@4.3.0:", type=("build", "run"), when="@3.17.1:")
+ depends_on("r@4.5.0:", type=("build", "run"), when="@3.21.1:")
diff --git a/var/spack/repos/builtin/packages/r-bluster/package.py b/var/spack/repos/builtin/packages/r-bluster/package.py
index 629331d9a5e..795ca42fc73 100644
--- a/var/spack/repos/builtin/packages/r-bluster/package.py
+++ b/var/spack/repos/builtin/packages/r-bluster/package.py
@@ -29,3 +29,4 @@ class RBluster(RPackage):
depends_on("r-s4vectors", type=("build", "run"))
depends_on("r-biocparallel", type=("build", "run"))
depends_on("r-biocneighbors", type=("build", "run"))
+ depends_on("r-assorthead", type=("build", "run"), when="@1.15.1:")
diff --git a/var/spack/repos/builtin/packages/r-cairo/package.py b/var/spack/repos/builtin/packages/r-cairo/package.py
index 5256dd5a24b..a7cf0d71c0b 100644
--- a/var/spack/repos/builtin/packages/r-cairo/package.py
+++ b/var/spack/repos/builtin/packages/r-cairo/package.py
@@ -44,4 +44,5 @@ class RCairo(RPackage):
conflicts(
"^cairo ~fc", when="^cairo +ft", msg="For cairo freetype support, also need fontconfig."
)
+ depends_on("pkgconfig", type="build")
depends_on("libxt")
diff --git a/var/spack/repos/builtin/packages/r-delayedarray/package.py b/var/spack/repos/builtin/packages/r-delayedarray/package.py
index 7924b60e687..c301825bb64 100644
--- a/var/spack/repos/builtin/packages/r-delayedarray/package.py
+++ b/var/spack/repos/builtin/packages/r-delayedarray/package.py
@@ -42,6 +42,7 @@ class RDelayedarray(RPackage):
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-biocgenerics@0.43.4:", type=("build", "run"), when="@0.24.0:")
+ depends_on("r-biocgenerics@0.53.3:", type=("build", "run"), when="@0.33.2:")
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:", type=("build", "run"), when="@0.4.1:")
@@ -52,6 +53,8 @@ class RDelayedarray(RPackage):
depends_on("r-iranges", 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-s4arrays@1.5.4:", type=("build", "run"), when="@0.31.14:")
+ depends_on("r-sparsearray@1.5.42:", type=("build", "run"), when="@0.31.14:")
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 73957548c3c..e61540e490d 100644
--- a/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py
+++ b/var/spack/repos/builtin/packages/r-delayedmatrixstats/package.py
@@ -31,24 +31,28 @@ class RDelayedmatrixstats(RPackage):
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-matrixgenerics@1.15.1:", type=("build", "run"), when="@1.25.3:")
depends_on("r-delayedarray", 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:", 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-delayedarray@0.31.7:", type=("build", "run"), when="@1.27.2:")
depends_on("r-sparsematrixstats", type=("build", "run"), when="@1.12.2:")
+ depends_on("r-sparsematrixstats@1.13.2:", type=("build", "run"), when="@1.23.1:")
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"))
depends_on("r-iranges@2.25.10:", type=("build", "run"), when="@1.16.0:")
+ depends_on("r-sparsearray@1.5.19:", type=("build", "run"), when="@1.27.2:")
+ depends_on("r-matrixstats@0.53.1:", type=("build", "run"), when="@:1.23.7")
+ depends_on("r-matrixstats@0.55.0:", type=("build", "run"), when="@1.6.1:1.23.7")
+ depends_on("r-matrixstats@0.56.0:", type=("build", "run"), when="@1.12.2:1.23.7")
+ depends_on("r-matrixstats@0.60.0:", type=("build", "run"), when="@1.16.0:1.23.7")
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-densvis/package.py b/var/spack/repos/builtin/packages/r-densvis/package.py
index 6cc7094028f..5390d65d1f1 100644
--- a/var/spack/repos/builtin/packages/r-densvis/package.py
+++ b/var/spack/repos/builtin/packages/r-densvis/package.py
@@ -44,3 +44,4 @@ class RDensvis(RPackage):
depends_on("r-assertthat", type=("build", "run"))
depends_on("r-reticulate", type=("build", "run"))
depends_on("r-irlba", type=("build", "run"))
+ depends_on("r-rtsne", type=("build", "run"), when="@1.12.0:")
diff --git a/var/spack/repos/builtin/packages/r-dupradar/package.py b/var/spack/repos/builtin/packages/r-dupradar/package.py
index 484d30f98e0..fb2a61a2a76 100644
--- a/var/spack/repos/builtin/packages/r-dupradar/package.py
+++ b/var/spack/repos/builtin/packages/r-dupradar/package.py
@@ -19,7 +19,7 @@ class RDupradar(RPackage):
version("1.30.3", commit="19e3b13a148c47e69686cd1e872182c564fd4dcd")
version("1.30.0", commit="3d53d2d2e0c404a25845d78b8df8fee3f6b34eb5")
- depends_on("r@3.2:", type=("build", "run"))
+ depends_on("r@3.2.0:", type=("build", "run"))
depends_on("r-kernsmooth", type=("build", "run"))
- depends_on("r-rsubread", type=("build", "run"))
+ depends_on("r-rsubread@1.14.1:", type=("build", "run"))
depends_on("subread", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/r-edger/package.py b/var/spack/repos/builtin/packages/r-edger/package.py
index ba6d3030c0e..f686139492b 100644
--- a/var/spack/repos/builtin/packages/r-edger/package.py
+++ b/var/spack/repos/builtin/packages/r-edger/package.py
@@ -39,5 +39,7 @@ class REdger(RPackage):
depends_on("r-limma", 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-limma@3.61.9:", type=("build", "run"), when="@4.3.8:")
depends_on("r-locfit", type=("build", "run"))
- depends_on("r-rcpp", type=("build", "run"), when="@3.20.9:")
+
+ depends_on("r-rcpp", type=("build", "run"), when="@3.20.9:4.3.10")
diff --git a/var/spack/repos/builtin/packages/r-fgsea/package.py b/var/spack/repos/builtin/packages/r-fgsea/package.py
index 044104788b8..bd6caffaeee 100644
--- a/var/spack/repos/builtin/packages/r-fgsea/package.py
+++ b/var/spack/repos/builtin/packages/r-fgsea/package.py
@@ -32,6 +32,7 @@ class RFgsea(RPackage):
depends_on("cxx", type="build") # generated
depends_on("r@3.3:", type=("build", "run"))
+ depends_on("r@4.1:", type=("build", "run"), when="@1.27.1:")
depends_on("r-rcpp", type=("build", "run"))
depends_on("r-data-table", type=("build", "run"))
depends_on("r-biocparallel", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py
index c07cdaec7e4..ed5730558ec 100644
--- a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py
+++ b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py
@@ -33,10 +33,15 @@ class RGenomeinfodb(RPackage):
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-biocgenerics@0.53.2:", type=("build", "run"), when="@1.43.1:")
depends_on("r-s4vectors@0.9.25:", 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-s4vectors@0.45.2:", type=("build", "run"), when="@1.43.1:")
depends_on("r-iranges@1.99.26:", 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-iranges@2.41.1:", type=("build", "run"), when="@1.43.1:")
depends_on("r-genomeinfodbdata", type=("build", "run"))
+ depends_on("r-ucsc-utils", type=("build", "run"), when="@1.39.12:")
+
+ depends_on("r-rcurl", type=("build", "run"), when="@:1.39.7")
diff --git a/var/spack/repos/builtin/packages/r-genomicranges/package.py b/var/spack/repos/builtin/packages/r-genomicranges/package.py
index f7befdbe684..66fe2b5946a 100644
--- a/var/spack/repos/builtin/packages/r-genomicranges/package.py
+++ b/var/spack/repos/builtin/packages/r-genomicranges/package.py
@@ -40,10 +40,12 @@ class RGenomicranges(RPackage):
depends_on("r-biocgenerics@0.21.2:", 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-biocgenerics@0.53.2:", type=("build", "run"), when="@1.59.1:")
depends_on("r-s4vectors@0.9.47:", 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-s4vectors@0.45.2:", type=("build", "run"), when="@1.59.1:")
depends_on("r-iranges@2.9.11:", 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:")
@@ -51,9 +53,11 @@ class RGenomicranges(RPackage):
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-iranges@2.31.2:", type=("build", "run"), when="@1.50.1:")
+ depends_on("r-iranges@2.41.1:", type=("build", "run"), when="@1.59.1:")
depends_on("r-genomeinfodb@1.11.5:", 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-genomeinfodb@1.43.1:", type=("build", "run"), when="@1.59.1:")
depends_on("r-xvector", 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 432c3881aae..21ebf886e9b 100644
--- a/var/spack/repos/builtin/packages/r-geoquery/package.py
+++ b/var/spack/repos/builtin/packages/r-geoquery/package.py
@@ -39,7 +39,13 @@ class RGeoquery(RPackage):
depends_on("r-magrittr", type=("build", "run"), when="@2.46.15:")
depends_on("r-limma", type=("build", "run"), when="@2.46.15:")
depends_on("r-curl", type=("build", "run"), when="@2.64.2:")
+ depends_on("r-rentrez", type=("build", "run"), when="@2.65.3:")
depends_on("r-r-utils", type=("build", "run"), when="@2.62.2:")
+ depends_on("r-stringr", type=("build", "run"), when="@2.73.2:")
+ depends_on("r-summarizedexperiment", type=("build", "run"), when="@2.73.2:")
+ depends_on("r-s4vectors", type=("build", "run"), when="@2.73.2:")
+ depends_on("r-rvest", type=("build", "run"), when="@2.73.2:")
+ depends_on("r-httr2", type=("build", "run"), when="@2.73.2:")
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-hdf5array/package.py b/var/spack/repos/builtin/packages/r-hdf5array/package.py
index 68a2e2a5436..f665f2b911f 100644
--- a/var/spack/repos/builtin/packages/r-hdf5array/package.py
+++ b/var/spack/repos/builtin/packages/r-hdf5array/package.py
@@ -35,12 +35,14 @@ class RHdf5array(RPackage):
depends_on("c", type="build") # generated
depends_on("r@3.4:", type=("build", "run"))
+ depends_on("r-sparsearray@1.5.42:", type=("build", "run"), when="@1.33.8:")
depends_on("r-delayedarray@0.2.4:", 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-delayedarray@0.33.1:", type=("build", "run"), when="@1.35.1:")
depends_on("r-rhdf5", 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:")
@@ -49,10 +51,12 @@ class RHdf5array(RPackage):
depends_on("r-biocgenerics", 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-biocgenerics@0.51.2:", type=("build", "run"), when="@1.33.7:")
depends_on("r-s4vectors", 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-s4arrays@1.1.1:", type=("build", "run"), when="@1.29.1:")
depends_on("r-rhdf5lib", type=("build", "run"), when="@1.12.3:")
depends_on("gmake", type="build")
depends_on("zlib-api")
diff --git a/var/spack/repos/builtin/packages/r-iranges/package.py b/var/spack/repos/builtin/packages/r-iranges/package.py
index e82e8f65b3e..6511f9578aa 100644
--- a/var/spack/repos/builtin/packages/r-iranges/package.py
+++ b/var/spack/repos/builtin/packages/r-iranges/package.py
@@ -40,6 +40,7 @@ class RIranges(RPackage):
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-biocgenerics@0.53.2:", type=("build", "run"), when="@2.41.2:")
depends_on("r-s4vectors@0.13.17:", 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:")
@@ -49,3 +50,4 @@ class RIranges(RPackage):
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:")
depends_on("r-s4vectors@0.33.3:", type=("build", "run"), when="@2.30.0:")
+ depends_on("r-s4vectors@0.45.2:", type=("build", "run"), when="@2.41.1:")
diff --git a/var/spack/repos/builtin/packages/r-limma/package.py b/var/spack/repos/builtin/packages/r-limma/package.py
index 3778054fa37..84e5f868833 100644
--- a/var/spack/repos/builtin/packages/r-limma/package.py
+++ b/var/spack/repos/builtin/packages/r-limma/package.py
@@ -30,3 +30,5 @@ class RLimma(RPackage):
depends_on("r@2.3.0:", type=("build", "run"))
depends_on("r@3.6.0:", type=("build", "run"), when="@3.40.6:")
+
+ depends_on("r-statmod", type=("build", "run"), when="@3.57.7:")
diff --git a/var/spack/repos/builtin/packages/r-matrixgenerics/package.py b/var/spack/repos/builtin/packages/r-matrixgenerics/package.py
index d90713c3e9e..86a6ac569c7 100644
--- a/var/spack/repos/builtin/packages/r-matrixgenerics/package.py
+++ b/var/spack/repos/builtin/packages/r-matrixgenerics/package.py
@@ -28,3 +28,4 @@ class RMatrixgenerics(RPackage):
depends_on("r-matrixstats@0.57.1:", type=("build", "run"))
depends_on("r-matrixstats@0.60.1:", type=("build", "run"), when="@1.6.0:")
+ depends_on("r-matrixstats@1.4.1:", type=("build", "run"), when="@1.17.1:")
diff --git a/var/spack/repos/builtin/packages/r-rentrez/package.py b/var/spack/repos/builtin/packages/r-rentrez/package.py
new file mode 100644
index 00000000000..a92c9d9f49b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rentrez/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2024 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.package import *
+
+
+class RRentrez(RPackage):
+ """'Entrez' in R.
+
+ Provides an R interface to the NCBI's 'EUtils' API,
+ allowing users to search databases like 'GenBank'
+ and 'PubMed'
+ , process the
+ results of those searches and pull data into their R sessions."""
+
+ cran = "rrentrez"
+
+ version("1.2.3", sha256="")
+
+ depends_on("c", type="build") # generated
+
+ depends_on("r@2.6.0:", type=("build", "run"))
+ depends_on("r-xml", type=("build", "run"))
+ depends_on("r-httr@0.5:", type=("build", "run"))
+ depends_on("r-jsonlite@0.9:", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/r-rhdf5/package.py b/var/spack/repos/builtin/packages/r-rhdf5/package.py
index b6f068009c8..c019de63e4d 100644
--- a/var/spack/repos/builtin/packages/r-rhdf5/package.py
+++ b/var/spack/repos/builtin/packages/r-rhdf5/package.py
@@ -40,6 +40,7 @@ class RRhdf5(RPackage):
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("r-rhdf5filters@1.15.5:", type=("build", "run"), when="@2.48.0:")
depends_on("gmake", type="build")
depends_on("zlib-api")
diff --git a/var/spack/repos/builtin/packages/r-rhtslib/package.py b/var/spack/repos/builtin/packages/r-rhtslib/package.py
index 01fa80dcaf3..62f8d3b19a6 100644
--- a/var/spack/repos/builtin/packages/r-rhtslib/package.py
+++ b/var/spack/repos/builtin/packages/r-rhtslib/package.py
@@ -40,12 +40,13 @@ class RRhtslib(RPackage):
depends_on("c", type="build") # generated
- depends_on("r-zlibbioc", type=("build", "run"))
depends_on("bzip2", type=("build", "link", "run"))
depends_on("xz", type=("build", "link", "run"))
depends_on("curl", type=("build", "link", "run"))
depends_on("gmake", type="build")
+ depends_on("r-zlibbioc", type=("build", "run"), when="@:3.3.0")
+
# Some versions of this package will leave the temporary installation
# directory in the htslib shared object. R will fix this if patchelf is
# available
diff --git a/var/spack/repos/builtin/packages/r-rsubread/package.py b/var/spack/repos/builtin/packages/r-rsubread/package.py
index 1829dd98d7f..57d70be38be 100644
--- a/var/spack/repos/builtin/packages/r-rsubread/package.py
+++ b/var/spack/repos/builtin/packages/r-rsubread/package.py
@@ -18,5 +18,4 @@ class RRsubread(RPackage):
depends_on("r", type=("build", "run"))
depends_on("r-matrix", type=("build", "run"))
- depends_on("r-r-utils", type=("build", "run"))
depends_on("zlib-api", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/r-rtracklayer/package.py b/var/spack/repos/builtin/packages/r-rtracklayer/package.py
index 93e560d484d..57dde1246c2 100644
--- a/var/spack/repos/builtin/packages/r-rtracklayer/package.py
+++ b/var/spack/repos/builtin/packages/r-rtracklayer/package.py
@@ -52,8 +52,9 @@ class RRtracklayer(RPackage):
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:", type=("build", "run"), when="@1.40.6:")
+ depends_on("r-curl", type=("build", "run"), when="@1.63.2:")
+ depends_on("r-httr", type=("build", "run"), when="@1.63.1:")
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:", type=("build", "run"), when="@1.40.6:")
depends_on("r-genomicalignments@1.5.4:", type=("build", "run"))
@@ -62,3 +63,5 @@ class RRtracklayer(RPackage):
depends_on("r-restfulr@0.0.13:", type=("build", "run"), when="@1.54.0:")
depends_on("zlib-api")
depends_on("openssl")
+
+ depends_on("r-rcurl@1.4-2:", type=("build", "run"), when="@:1.63.0")
diff --git a/var/spack/repos/builtin/packages/r-s4arrays/package.py b/var/spack/repos/builtin/packages/r-s4arrays/package.py
new file mode 100644
index 00000000000..4d1608387c9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-s4arrays/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2024 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.package import *
+
+
+class RS4arrays(RPackage):
+ """Foundation of array-like containers in Bioconductor."""
+
+ bioc = "S4Arrays"
+
+ version("1.7.1", commit="7081384e789c081b337a3867040d052d93adfb11")
+
+ depends_on("r@4.3.0:", type=("build", "run"))
+ depends_on("r-abind", type=("build", "run"))
+ depends_on("r-biocgenerics@0.45.2:", type=("build", "run"))
+ depends_on("r-crayon", type=("build", "run"))
+ depends_on("r-iranges", type=("build", "run"))
+ depends_on("r-matrix", type=("build", "run"))
+ depends_on("r-s4vectors", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/r-s4vectors/package.py b/var/spack/repos/builtin/packages/r-s4vectors/package.py
index a7277722765..57b4703edf4 100644
--- a/var/spack/repos/builtin/packages/r-s4vectors/package.py
+++ b/var/spack/repos/builtin/packages/r-s4vectors/package.py
@@ -41,3 +41,4 @@ class RS4vectors(RPackage):
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:")
+ depends_on("r-biocgenerics@0.53.2:", type=("build", "run"), when="@0.45.2:")
diff --git a/var/spack/repos/builtin/packages/r-sparsearray/package.py b/var/spack/repos/builtin/packages/r-sparsearray/package.py
new file mode 100644
index 00000000000..f8398108a93
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-sparsearray/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2024 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.package import *
+
+
+class RSparsearray(RPackage):
+ """High-performance sparse data representation and manipulation in R."""
+
+ bioc = "SparseArray"
+
+ version("1.7.2", commit="49e375d8e6d7d7a95aa3c7009d9f0fb199fd824f")
+
+ depends_on("r@4.3.0:", type=("build", "run"))
+ depends_on("r-biocgenerics@0.43.1:", type=("build", "run"))
+ depends_on("r-iranges", type=("build", "run"))
+ depends_on("r-matrix", type=("build", "run"))
+ depends_on("r-matrixgenerics@1.11.1:", type=("build", "run"))
+ depends_on("r-matrixstats", type=("build", "run"))
+ depends_on("r-s4arrays@1.5.11:", type=("build", "run"))
+ depends_on("r-s4vectors@0.43.2:", type=("build", "run"))
+ depends_on("r-xvector", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/r-ucsc-utils/package.py b/var/spack/repos/builtin/packages/r-ucsc-utils/package.py
new file mode 100644
index 00000000000..1c50064dcdf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ucsc-utils/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2024 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.package import *
+
+
+class RUcscUtils(RPackage):
+ """Low-level utilities to retrieve data from the UCSC Genome Browser."""
+
+ bioc = "UCSC.utils"
+
+ version("1.3.0", commit="1fe2970955d486197d62791b34d0984656c5edf5")
+
+ depends_on("r-httr", type=("build", "run"))
+ depends_on("r-jsonlite", type=("build", "run"))
+ depends_on("r-s4vectors", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/r-xvector/package.py b/var/spack/repos/builtin/packages/r-xvector/package.py
index 5f5832ff618..6db4f320c39 100644
--- a/var/spack/repos/builtin/packages/r-xvector/package.py
+++ b/var/spack/repos/builtin/packages/r-xvector/package.py
@@ -42,5 +42,6 @@ class RXvector(RPackage):
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-api")
+
+ depends_on("r-zlibbioc", type=("build", "run"), when="@:0.47.0")