diff --git a/repos/spack_repo/builtin/packages/r_go_db/package.py b/repos/spack_repo/builtin/packages/r_go_db/package.py index e0f0119cf77..d18e3d2c38d 100644 --- a/repos/spack_repo/builtin/packages/r_go_db/package.py +++ b/repos/spack_repo/builtin/packages/r_go_db/package.py @@ -16,6 +16,26 @@ class RGoDb(RPackage): bioc = "GO.db" url = "https://www.bioconductor.org/packages/release/data/annotation/src/contrib/GO.db_3.4.1.tar.gz" + version( + "3.21.0", + url="https://bioconductor.org/packages/3.21/data/annotation/src/contrib/GO.db_3.21.0.tar.gz", + sha256="77e9e35350924fee8a096de94833c4cd25b2b997c3062c5b5f9c1070f1d7a054", + ) + version( + "3.20.0", + url="https://bioconductor.org/packages/3.20/data/annotation/src/contrib/GO.db_3.20.0.tar.gz", + sha256="ff968e338624697f33cc318de6af34d684c88ed019107aeebb071f6564e110dc", + ) + version( + "3.19.1", + url="https://bioconductor.org/packages/3.19/data/annotation/src/contrib/GO.db_3.19.1.tar.gz", + sha256="0f6e6045e5cce6c842ad2ca73a13573b6838ed38f71661dd99d127033c993ba5", + ) + version( + "3.18.0", + url="https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GO.db_3.18.0.tar.gz", + sha256="f580341e7fd19efa3e5789b993dd8ef0cf813a45c49a647a173c6f49c451d87e", + ) version( "3.17.0", url="https://bioconductor.org/packages/3.17/data/annotation/src/contrib/GO.db_3.17.0.tar.gz", @@ -48,9 +68,14 @@ 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:", type=("build", "run"), when="@3.12.1:") - 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:") - depends_on("r-annotationdbi@1.59.1:", type=("build", "run"), when="@3.16.0:") + + depends_on("r-annotationdbi@1.69.0:", type=("build", "run"), when="@3.21.0:") + depends_on("r-annotationdbi@1.67.0:", type=("build", "run"), when="@3.20.0:") + depends_on("r-annotationdbi@1.65.2:", type=("build", "run"), when="@3.19.1:") + depends_on("r-annotationdbi@1.63.2:", type=("build", "run"), when="@3.18.0:") depends_on("r-annotationdbi@1.61.0:", type=("build", "run"), when="@3.17.0:") + depends_on("r-annotationdbi@1.59.1:", type=("build", "run"), when="@3.16.0:") + depends_on("r-annotationdbi@1.57.1:", type=("build", "run"), when="@3.15.0:") + depends_on("r-annotationdbi@1.55.1:", type=("build", "run"), when="@3.14.0:") + depends_on("r-annotationdbi@1.51.3:", type=("build", "run"), when="@3.12.1:") + depends_on("r-annotationdbi@1.37.4:", type=("build", "run")) diff --git a/repos/spack_repo/builtin/packages/r_org_dr_eg_db/package.py b/repos/spack_repo/builtin/packages/r_org_dr_eg_db/package.py new file mode 100644 index 00000000000..06acb08d47e --- /dev/null +++ b/repos/spack_repo/builtin/packages/r_org_dr_eg_db/package.py @@ -0,0 +1,39 @@ +# Copyright Spack Project Developers. See COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack_repo.builtin.build_systems.r import RPackage + +from spack.package import * + + +class ROrgDrEgDb(RPackage): + """Genome wide annotation for Zebrafish. + + Genome wide annotation for Zebrafish, primarily based on mapping using Entrez + Gene identifiers.""" + + bioc = "org.Dr.eg.db" + url = "https://bioconductor.org/packages/3.21/data/annotation/src/contrib/org.Dr.eg.db_3.21.0.tar.gz" + + version( + "3.21.0", + url="https://bioconductor.org/packages/3.21/data/annotation/src/contrib/org.Dr.eg.db_3.21.0.tar.gz", + sha256="4c033d4e14a6f36ac339cb5ca2d9bdfb3c7963deeacf5327bffcf94aabb37fa3", + ) + version( + "3.20.0", + url="https://bioconductor.org/packages/3.20/data/annotation/src/contrib/org.Dr.eg.db_3.20.0.tar.gz", + sha256="3aeff5e6041437c1381d9cc75c68a69e50fe51c4fdd96d8936612b2cae51db2b", + ) + version( + "3.19.1", + url="https://bioconductor.org/packages/3.19/data/annotation/src/contrib/org.Dr.eg.db_3.19.1.tar.gz", + sha256="863ac02795bf28e07190ea9998295617ddaaf3e6b3e04fd64690c709fbb83010", + ) + + depends_on("r@2.7.0:", type=("build", "run")) + + depends_on("r-annotationdbi@1.69:", type=("build", "run"), when="@3.21:") + depends_on("r-annotationdbi@1.67:", type=("build", "run"), when="@3.20:") + depends_on("r-annotationdbi@1.65.2:", type=("build", "run")) diff --git a/repos/spack_repo/builtin/packages/r_org_hs_eg_db/package.py b/repos/spack_repo/builtin/packages/r_org_hs_eg_db/package.py index 65b42b109a6..b5ef67d1796 100644 --- a/repos/spack_repo/builtin/packages/r_org_hs_eg_db/package.py +++ b/repos/spack_repo/builtin/packages/r_org_hs_eg_db/package.py @@ -16,6 +16,26 @@ class ROrgHsEgDb(RPackage): bioc = "org.Hs.eg.db" url = "https://www.bioconductor.org/packages/release/data/annotation/src/contrib/org.Hs.eg.db_3.4.1.tar.gz" + version( + "3.21.0", + url="https://bioconductor.org/packages/3.21/data/annotation/src/contrib/org.Hs.eg.db_3.21.0.tar.gz", + sha256="3494ddec079cf57f63a7a32dc5d58825b376218631132f7c49477eab48bf31c5", + ) + version( + "3.20.0", + url="https://bioconductor.org/packages/3.20/data/annotation/src/contrib/org.Hs.eg.db_3.20.0.tar.gz", + sha256="8c36c3cde805cae99f1d391cf00aec8983f6d0b4fabd75e71aa8ef3f5d6ed3bf", + ) + version( + "3.19.0", + url="https://bioconductor.org/packages/3.19/data/annotation/src/contrib/org.Hs.eg.db_3.19.1.tar.gz", + sha256="1932eff4d5d46c1ab219565dfff6706c93cfddc6bcbc65223832cc583f702bf7", + ) + version( + "3.18.0", + url="https://bioconductor.org/packages/3.18/data/annotation/src/contrib/org.Hs.eg.db_3.18.0.tar.gz", + sha256="41dc753ed5f4d31dcf0d645ef32b6339b1b70cc48b7c4c4673767643b129c5ca", + ) version( "3.17.0", url="https://www.bioconductor.org/packages/3.17/data/annotation/src/contrib/org.Hs.eg.db_3.17.0.tar.gz", @@ -53,10 +73,15 @@ 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@1.69:", type=("build", "run"), when="@3.21:") + depends_on("r-annotationdbi@1.67:", type=("build", "run"), when="@3.20:") + depends_on("r-annotationdbi@1.65.2:", type=("build", "run"), when="@3.19.1:") + depends_on("r-annotationdbi@1.63.2:", type=("build", "run"), when="@3.18:") + depends_on("r-annotationdbi@1.61:", type=("build", "run"), when="@3.17:") + depends_on("r-annotationdbi@1.59.1:", type=("build", "run"), when="@3.16:") + depends_on("r-annotationdbi@1.57.1:", type=("build", "run"), when="@3.15:") + depends_on("r-annotationdbi@1.55.1:", type=("build", "run"), when="@3.14:") + depends_on("r-annotationdbi@1.51.3:", type=("build", "run"), when="@3.12:") 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:") - depends_on("r-annotationdbi@1.59.1:", type=("build", "run"), when="@3.16.0:") - depends_on("r-annotationdbi@1.61.0:", type=("build", "run"), when="@3.17.0:") + depends_on("r-annotationdbi@1.37.4:", type=("build", "run")) diff --git a/repos/spack_repo/builtin/packages/r_org_mm_eg_db/package.py b/repos/spack_repo/builtin/packages/r_org_mm_eg_db/package.py new file mode 100644 index 00000000000..16071832237 --- /dev/null +++ b/repos/spack_repo/builtin/packages/r_org_mm_eg_db/package.py @@ -0,0 +1,39 @@ +# Copyright Spack Project Developers. See COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack_repo.builtin.build_systems.r import RPackage + +from spack.package import * + + +class ROrgMmEgDb(RPackage): + """Genome wide annotation for Mouse. + + Genome wide annotation for Mouse, primarily based on mapping using Entrez + Gene identifiers.""" + + bioc = "org.Mm.eg.db" + url = "https://bioconductor.org/packages/3.21/data/annotation/src/contrib/org.Mm.eg.db_3.21.0.tar.gz" + + version( + "3.21.0", + url="https://bioconductor.org/packages/3.21/data/annotation/src/contrib/org.Mm.eg.db_3.21.0.tar.gz", + sha256="0b8e75105f37fb84586e4e3875c28bfe09a2889c2b711303c636073399c22e07", + ) + version( + "3.20.0", + url="https://bioconductor.org/packages/3.20/data/annotation/src/contrib/org.Mm.eg.db_3.20.0.tar.gz", + sha256="87cc0e4314771d1d09a54b67e4595cf138ff8c601204c45b7569438031198cf2", + ) + version( + "3.19.1", + url="https://bioconductor.org/packages/3.19/data/annotation/src/contrib/org.Mm.eg.db_3.19.1.tar.gz", + sha256="47cee87aff4ccb7879eb33a50839f45578ee99acb8aff6bbfb78f7655ca6a889", + ) + + depends_on("r@2.7.0:", type=("build", "run")) + + depends_on("r-annotationdbi@1.69:", type=("build", "run"), when="@3.21:") + depends_on("r-annotationdbi@1.67:", type=("build", "run"), when="@3.20:") + depends_on("r-annotationdbi@1.65.2:", type=("build", "run"))