Skip to content

r-go-db: add @3.18:3.21; r-org-dr-eg-db: new package; r-org-hs-eg-db: add @3.18:3.21; r-org-mm-eg-db: new package #5654

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
bernhardkaindl merged 4 commits into from
Jul 20, 2026
+139 −11
Merged

r-go-db: add @3.18:3.21; r-org-dr-eg-db: new package; r-org-hs-eg-db: add @3.18:3.21; r-org-mm-eg-db: new package #5654

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
1653f03
r-go-db: add @3.18:3.21
w8jcik Jul 19, 2026
bc7a5d4
r-org-dr-eg-db: new package
w8jcik Jul 19, 2026
8316bd4
r-org-hs-eg-db: add @3.18:3.21
w8jcik Jul 19, 2026
f69dd58
r-org-mm-eg-db: new package
w8jcik Jul 19, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
35 changes: 30 additions & 5 deletions repos/spack_repo/builtin/packages/r_go_db/package.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -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"))
39 changes: 39 additions & 0 deletions repos/spack_repo/builtin/packages/r_org_dr_eg_db/package.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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"))
37 changes: 31 additions & 6 deletions repos/spack_repo/builtin/packages/r_org_hs_eg_db/package.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -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"))
39 changes: 39 additions & 0 deletions repos/spack_repo/builtin/packages/r_org_mm_eg_db/package.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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"))
Loading