From d38b4024bcb01abae5adbbac8eb75b8073a3d9f6 Mon Sep 17 00:00:00 2001 From: Wouter Deconinck Date: Tue, 20 Aug 2024 13:27:24 -0500 Subject: [PATCH] RPackages with bioc: remove redundant homepage and url --- .../repos/builtin/packages/bioconductor-dupradar/package.py | 2 -- .../repos/builtin/packages/bioconductor-ebseq/package.py | 3 +-- .../repos/builtin/packages/bioconductor-rsubread/package.py | 5 +---- .../repos/builtin/packages/bioconductor-tximeta/package.py | 3 --- .../packages/r-bsgenome-hsapiens-ucsc-hg19/package.py | 1 - var/spack/repos/builtin/packages/r-deseq2/package.py | 2 +- var/spack/repos/builtin/packages/r-do-db/package.py | 1 - .../packages/r-fdb-infiniummethylation-hg18/package.py | 1 - .../packages/r-fdb-infiniummethylation-hg19/package.py | 1 - .../repos/builtin/packages/r-genomeinfodbdata/package.py | 1 - var/spack/repos/builtin/packages/r-go-db/package.py | 1 - var/spack/repos/builtin/packages/r-hdo-db/package.py | 1 - .../package.py | 1 - .../r-illuminahumanmethylation450kmanifest/package.py | 1 - .../package.py | 1 - .../r-illuminahumanmethylationepicmanifest/package.py | 1 - var/spack/repos/builtin/packages/r-kegg-db/package.py | 1 - var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py | 1 - var/spack/repos/builtin/packages/r-pfam-db/package.py | 1 - .../packages/r-txdb-hsapiens-ucsc-hg18-knowngene/package.py | 1 - .../packages/r-txdb-hsapiens-ucsc-hg19-knowngene/package.py | 1 - 21 files changed, 3 insertions(+), 28 deletions(-) diff --git a/var/spack/repos/builtin/packages/bioconductor-dupradar/package.py b/var/spack/repos/builtin/packages/bioconductor-dupradar/package.py index 3eae761c401..3621ac2734a 100644 --- a/var/spack/repos/builtin/packages/bioconductor-dupradar/package.py +++ b/var/spack/repos/builtin/packages/bioconductor-dupradar/package.py @@ -9,8 +9,6 @@ class BioconductorDupradar(RPackage): """Assessment of duplication rates in RNA-Seq datasets""" - homepage = "https://bioconductor.org/packages/3.16/bioc/html/dupRadar.html" - url = "https://bioconductor.org/packages/release/bioc/src/contrib/dupRadar_1.30.0.tar.gz" maintainers("pabloaledo") bioc = "dupradar" diff --git a/var/spack/repos/builtin/packages/bioconductor-ebseq/package.py b/var/spack/repos/builtin/packages/bioconductor-ebseq/package.py index 7d54296fd42..508ba0b40f1 100644 --- a/var/spack/repos/builtin/packages/bioconductor-ebseq/package.py +++ b/var/spack/repos/builtin/packages/bioconductor-ebseq/package.py @@ -18,10 +18,9 @@ class BioconductorEbseq(RPackage): are the same as those required for gene-level analysis).""" homepage = "https://www.biostat.wisc.edu/~kendzior/EBSEQ/" - url = "https://bioconductor.org/packages/release/bioc/src/contrib/EBSeq_1.40.0.tar.gz" maintainers("pabloaledo") - bioc = "ebseq" + bioc = "EBSeq" version( "1.40.0", diff --git a/var/spack/repos/builtin/packages/bioconductor-rsubread/package.py b/var/spack/repos/builtin/packages/bioconductor-rsubread/package.py index 8ae22b208be..36422f3227d 100644 --- a/var/spack/repos/builtin/packages/bioconductor-rsubread/package.py +++ b/var/spack/repos/builtin/packages/bioconductor-rsubread/package.py @@ -9,10 +9,7 @@ class BioconductorRsubread(RPackage): """Mapping, quantification and variant analysis of sequencing data""" - homepage = "https://bioconductor.org/packages/3.16/bioc/html/Rsubread.html" - url = "https://bioconductor.org/packages/release/bioc/src/contrib/Rsubread_2.14.2.tar.gz" - - bioc = "rsubread" + bioc = "Rsubread" depends_on("r-matrix") depends_on("zlib-api") diff --git a/var/spack/repos/builtin/packages/bioconductor-tximeta/package.py b/var/spack/repos/builtin/packages/bioconductor-tximeta/package.py index cafc8dccb49..3e1c6a9d208 100644 --- a/var/spack/repos/builtin/packages/bioconductor-tximeta/package.py +++ b/var/spack/repos/builtin/packages/bioconductor-tximeta/package.py @@ -14,9 +14,6 @@ class BioconductorTximeta(RPackage): metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility.""" - homepage = "https://bioconductor.org/packages/release/bioc/html/tximeta.html" - url = "https://bioconductor.org/packages/release/bioc/src/contrib/tximeta_1.18.1.tar.gz" - bioc = "tximeta" version( diff --git a/var/spack/repos/builtin/packages/r-bsgenome-hsapiens-ucsc-hg19/package.py b/var/spack/repos/builtin/packages/r-bsgenome-hsapiens-ucsc-hg19/package.py index 422fa08409a..7e4f90da4e0 100644 --- a/var/spack/repos/builtin/packages/r-bsgenome-hsapiens-ucsc-hg19/package.py +++ b/var/spack/repos/builtin/packages/r-bsgenome-hsapiens-ucsc-hg19/package.py @@ -15,7 +15,6 @@ class RBsgenomeHsapiensUcscHg19(RPackage): # This is a bioconductor package but there is no available git repo. bioc = "BSgenome.Hsapiens.UCSC.hg19" - url = "http://www.bioconductor.org/packages/release/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz" version( "1.4.3", diff --git a/var/spack/repos/builtin/packages/r-deseq2/package.py b/var/spack/repos/builtin/packages/r-deseq2/package.py index 5bb4ffe19da..d0f21fd34df 100644 --- a/var/spack/repos/builtin/packages/r-deseq2/package.py +++ b/var/spack/repos/builtin/packages/r-deseq2/package.py @@ -14,7 +14,7 @@ class RDeseq2(RPackage): sequencing assays and test for differential expression based on a model using the negative binomial distribution.""" - homepage = "https://bioconductor.org/packages/DESeq2" + bioc = "DESeq2" git = "https://git.bioconductor.org/packages/DESeq2.git" version("1.40.0", commit="c4962c3b16546e552fbc1a712258e4e21ff44241") diff --git a/var/spack/repos/builtin/packages/r-do-db/package.py b/var/spack/repos/builtin/packages/r-do-db/package.py index 7911c38f7ad..0eed7a5d326 100644 --- a/var/spack/repos/builtin/packages/r-do-db/package.py +++ b/var/spack/repos/builtin/packages/r-do-db/package.py @@ -14,7 +14,6 @@ class RDoDb(RPackage): # There is no git repository for this package. bioc = "DO.db" - url = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/DO.db_2.9.tar.gz" version("2.9", sha256="762bcb9b5188274fd81d82f785cf2846a5acc61fad55e2ff8ec1502282c27881") diff --git a/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg18/package.py b/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg18/package.py index ebbc94f2087..3e254154c45 100644 --- a/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg18/package.py +++ b/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg18/package.py @@ -13,7 +13,6 @@ class RFdbInfiniummethylationHg18(RPackage): # This is a bioconductor package but there is no available git repository bioc = "FDb.InfiniumMethylation.hg18" - url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/FDb.InfiniumMethylation.hg18_2.2.0.tar.gz" version("2.2.0", sha256="4a9028ac03c11fffbab731ea750bc7f9b0884fc43c6a8dac6eb2c644e4c79f6f") diff --git a/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg19/package.py b/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg19/package.py index e237ea1f07b..0e65ce5328e 100644 --- a/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg19/package.py +++ b/var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg19/package.py @@ -13,7 +13,6 @@ class RFdbInfiniummethylationHg19(RPackage): # No available git repository bioc = "FDb.InfiniumMethylation.hg19" - url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz" version("2.2.0", sha256="605aa3643588a2f40a942fa760b92662060a0dfedb26b4e4cd6f1a78b703093f") diff --git a/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py b/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py index dde99a8f618..a47fc73dca9 100644 --- a/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py +++ b/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py @@ -11,7 +11,6 @@ class RGenomeinfodbdata(RPackage): in the GenomeInfoDb package.""" bioc = "GenomeInfoDbData" - url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/GenomeInfoDbData_0.99.0.tar.gz" version( "1.2.10", diff --git a/var/spack/repos/builtin/packages/r-go-db/package.py b/var/spack/repos/builtin/packages/r-go-db/package.py index be91be6ac28..392b7361f0a 100644 --- a/var/spack/repos/builtin/packages/r-go-db/package.py +++ b/var/spack/repos/builtin/packages/r-go-db/package.py @@ -13,7 +13,6 @@ class RGoDb(RPackage): Ontology assembled using data from GO.""" bioc = "GO.db" - url = "https://www.bioconductor.org/packages/release/data/annotation/src/contrib/GO.db_3.4.1.tar.gz" version( "3.17.0", diff --git a/var/spack/repos/builtin/packages/r-hdo-db/package.py b/var/spack/repos/builtin/packages/r-hdo-db/package.py index 49edc44d5f6..fd5adf87265 100644 --- a/var/spack/repos/builtin/packages/r-hdo-db/package.py +++ b/var/spack/repos/builtin/packages/r-hdo-db/package.py @@ -13,7 +13,6 @@ class RHdoDb(RPackage): assembled using data from DO. Its annotation data comes from https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology.""" - url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/HDO.db_0.99.1.tar.gz" bioc = "HDO.db" version("0.99.1", sha256="c17cf28d06621d91148a64d47fdeaa906d8621aba7a688715fb9571a55f7cf92") diff --git a/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kanno-ilmn12-hg19/package.py b/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kanno-ilmn12-hg19/package.py index 4d56732ad11..647ca63595c 100644 --- a/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kanno-ilmn12-hg19/package.py +++ b/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kanno-ilmn12-hg19/package.py @@ -14,7 +14,6 @@ class RIlluminahumanmethylation450kannoIlmn12Hg19(RPackage): # This package is available via bioconductor but there is no available git # repository. bioc = "IlluminaHumanMethylation450kanno.ilmn12.hg19" - url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0.tar.gz" version( "0.6.1", diff --git a/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kmanifest/package.py b/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kmanifest/package.py index cccadc46bee..305f516ebb0 100644 --- a/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kmanifest/package.py +++ b/var/spack/repos/builtin/packages/r-illuminahumanmethylation450kmanifest/package.py @@ -10,7 +10,6 @@ class RIlluminahumanmethylation450kmanifest(RPackage): """Annotation for Illumina's 450k methylation arrays.""" bioc = "IlluminaHumanMethylation450kmanifest" - url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/IlluminaHumanMethylation450kmanifest_0.4.0.tar.gz" version("0.4.0", sha256="41b2e54bac3feafc7646fe40bce3aa2b92c10871b0a13657c5736517792fa763") diff --git a/var/spack/repos/builtin/packages/r-illuminahumanmethylationepicanno-ilm10b4-hg19/package.py b/var/spack/repos/builtin/packages/r-illuminahumanmethylationepicanno-ilm10b4-hg19/package.py index 3cfbc85da9a..5e8cfab4b40 100644 --- a/var/spack/repos/builtin/packages/r-illuminahumanmethylationepicanno-ilm10b4-hg19/package.py +++ b/var/spack/repos/builtin/packages/r-illuminahumanmethylationepicanno-ilm10b4-hg19/package.py @@ -10,7 +10,6 @@ class RIlluminahumanmethylationepicannoIlm10b4Hg19(RPackage): """Annotation for Illumina's EPIC methylation arrays.""" bioc = "IlluminaHumanMethylationEPICanno.ilm10b4.hg19" - url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0.tar.gz" version("0.6.0", sha256="2c8128126b63e7fa805a5f3b02449367dca9c3be3eb5f6300acc718826590719") diff --git a/var/spack/repos/builtin/packages/r-illuminahumanmethylationepicmanifest/package.py b/var/spack/repos/builtin/packages/r-illuminahumanmethylationepicmanifest/package.py index 4c5884f132c..aefe11176d6 100644 --- a/var/spack/repos/builtin/packages/r-illuminahumanmethylationepicmanifest/package.py +++ b/var/spack/repos/builtin/packages/r-illuminahumanmethylationepicmanifest/package.py @@ -10,7 +10,6 @@ class RIlluminahumanmethylationepicmanifest(RPackage): """Manifest for Illumina's EPIC methylation arrays.""" bioc = "IlluminaHumanMethylationEPICmanifest" - url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz" version("0.3.0", sha256="e39a69d98486cec981e97c56f45bbe47d2ccb5bbb66a1b16fa0685575493902a") diff --git a/var/spack/repos/builtin/packages/r-kegg-db/package.py b/var/spack/repos/builtin/packages/r-kegg-db/package.py index 475b20f63de..649694b463a 100644 --- a/var/spack/repos/builtin/packages/r-kegg-db/package.py +++ b/var/spack/repos/builtin/packages/r-kegg-db/package.py @@ -14,7 +14,6 @@ class RKeggDb(RPackage): # NOTE: The KEGG.db package was removed in Bioconductor-3.13 bioc = "KEGG.db" - url = "https://www.bioconductor.org/packages/release/data/annotation/src/contrib/KEGG.db_3.2.3.tar.gz" version( "3.2.4", 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 3974775d0df..293853c80e8 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 @@ -13,7 +13,6 @@ class ROrgHsEgDb(RPackage): Gene identifiers.""" 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( "3.17.0", diff --git a/var/spack/repos/builtin/packages/r-pfam-db/package.py b/var/spack/repos/builtin/packages/r-pfam-db/package.py index b3a343c7091..e4d51e37f3e 100644 --- a/var/spack/repos/builtin/packages/r-pfam-db/package.py +++ b/var/spack/repos/builtin/packages/r-pfam-db/package.py @@ -13,7 +13,6 @@ class RPfamDb(RPackage): public repositories.""" bioc = "PFAM.db" - url = "https://www.bioconductor.org/packages/release/data/annotation/src/contrib/PFAM.db_3.4.1.tar.gz" version( "3.17.0", diff --git a/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg18-knowngene/package.py b/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg18-knowngene/package.py index 98b034b8b66..2cf6b588659 100644 --- a/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg18-knowngene/package.py +++ b/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg18-knowngene/package.py @@ -14,7 +14,6 @@ class RTxdbHsapiensUcscHg18Knowngene(RPackage): # This is a bioconductor package but ther is no available git repo bioc = "TxDb.Hsapiens.UCSC.hg18.knownGene" - url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2.tar.gz" version("3.2.2", sha256="bc9ca40b4eab87f5ca64a4b876d42502b9b8e9f5983d745bfe0ee349d97b69fa") diff --git a/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg19-knowngene/package.py b/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg19-knowngene/package.py index 6f578243fd4..ea2e2cf6589 100644 --- a/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg19-knowngene/package.py +++ b/var/spack/repos/builtin/packages/r-txdb-hsapiens-ucsc-hg19-knowngene/package.py @@ -14,7 +14,6 @@ class RTxdbHsapiensUcscHg19Knowngene(RPackage): # This is a bioconductor package but there is no available git repo. bioc = "TxDb.Hsapiens.UCSC.hg19.knownGene" - url = "https://bioconductor.org/packages/release/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz" version("3.2.2", sha256="063de2b1174782a0b2b8ab7f04a0bdf3c43252cb67c685a9f8ef2b8e318352e9")