RPackages with bioc: remove redundant homepage and url

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"

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",

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"
+    bioc = "Rsubread"
-    url = "https://bioconductor.org/packages/release/bioc/src/contrib/Rsubread_2.14.2.tar.gz"
-
-    bioc = "rsubread"
 
     depends_on("r-matrix")
     depends_on("zlib-api")

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(

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",

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")

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")
 

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")
 

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")
 

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",

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",

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")

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",

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")
 

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")
 

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")
 

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",

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",

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",

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")
 

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")