From 5a20c4d2032a3620339826a3d80a906c261d3c1a Mon Sep 17 00:00:00 2001 From: Wouter Deconinck Date: Sat, 28 Dec 2024 15:21:36 -0600 Subject: [PATCH] r-*: remove forward declared dependencies that fail audit --- var/spack/repos/builtin/packages/r-delayedarray/package.py | 2 +- var/spack/repos/builtin/packages/r-genomeinfodb/package.py | 5 +---- var/spack/repos/builtin/packages/r-genomicranges/package.py | 4 ---- var/spack/repos/builtin/packages/r-hdf5array/package.py | 1 - var/spack/repos/builtin/packages/r-iranges/package.py | 2 -- var/spack/repos/builtin/packages/r-matrixstats/package.py | 1 + var/spack/repos/builtin/packages/r-s4vectors/package.py | 1 - 7 files changed, 3 insertions(+), 13 deletions(-) diff --git a/var/spack/repos/builtin/packages/r-delayedarray/package.py b/var/spack/repos/builtin/packages/r-delayedarray/package.py index 9437320e0c1..031f1e9b164 100644 --- a/var/spack/repos/builtin/packages/r-delayedarray/package.py +++ b/var/spack/repos/builtin/packages/r-delayedarray/package.py @@ -44,7 +44,7 @@ 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-biocgenerics@0.51.3:", type=("build", "run"), when="@0.31.13:") 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:") diff --git a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py index fcf21d3b445..a3fe383397a 100644 --- a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py +++ b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py @@ -32,17 +32,14 @@ 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@4.0.0:", type=("build", "run"), when="@1.27.3:") 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-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:") diff --git a/var/spack/repos/builtin/packages/r-genomicranges/package.py b/var/spack/repos/builtin/packages/r-genomicranges/package.py index 7faefb69f2d..b8abb793b4b 100644 --- a/var/spack/repos/builtin/packages/r-genomicranges/package.py +++ b/var/spack/repos/builtin/packages/r-genomicranges/package.py @@ -42,12 +42,10 @@ 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:") @@ -55,11 +53,9 @@ 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-hdf5array/package.py b/var/spack/repos/builtin/packages/r-hdf5array/package.py index 1a0f6770014..f2c849d2cad 100644 --- a/var/spack/repos/builtin/packages/r-hdf5array/package.py +++ b/var/spack/repos/builtin/packages/r-hdf5array/package.py @@ -44,7 +44,6 @@ class RHdf5array(RPackage): 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:") diff --git a/var/spack/repos/builtin/packages/r-iranges/package.py b/var/spack/repos/builtin/packages/r-iranges/package.py index a918ee59783..5a73ff75568 100644 --- a/var/spack/repos/builtin/packages/r-iranges/package.py +++ b/var/spack/repos/builtin/packages/r-iranges/package.py @@ -42,7 +42,6 @@ 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:") @@ -52,4 +51,3 @@ 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-matrixstats/package.py b/var/spack/repos/builtin/packages/r-matrixstats/package.py index e4a3fea3f25..a3c5b99c483 100644 --- a/var/spack/repos/builtin/packages/r-matrixstats/package.py +++ b/var/spack/repos/builtin/packages/r-matrixstats/package.py @@ -16,6 +16,7 @@ class RMatrixstats(RPackage): cran = "matrixStats" + version("1.4.1", sha256="ac6d65cab6ca30926f35bc3bc59b869946ae92e4738ceca90fad6620fc6ecd10") version("1.3.0", sha256="413ee607d95b243c514b4a7c4944c2caea1fb264d27c96ff547c3939f893245a") version("0.63.0", sha256="c000b60421742eb035ff4ceedd3e588a79e4b28985484f0c81361e5a6c351f5f") version("0.62.0", sha256="85e2016b6dd20cbfe32d38a2ef2578ae80e688d9a3590aefd1d2f4bf4bd44eca") diff --git a/var/spack/repos/builtin/packages/r-s4vectors/package.py b/var/spack/repos/builtin/packages/r-s4vectors/package.py index 8f77b1f46fa..9e09240627a 100644 --- a/var/spack/repos/builtin/packages/r-s4vectors/package.py +++ b/var/spack/repos/builtin/packages/r-s4vectors/package.py @@ -43,4 +43,3 @@ 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:")