RPackages with custom url: url -> urls=[url]

lib/spack/spack/build_systems/r.py

@@ -85,20 +85,28 @@ def homepage(cls):
             return "https://bioconductor.org/packages/" + cls.bioc
 
     @lang.classproperty
-    def url(cls):
+    def urls(cls):
         if cls.cran:
-            return (
+            return [
                 "https://cloud.r-project.org/src/contrib/"
-                + cls.cran
+                + f"{cls.cran}_{str(list(cls.versions)[0])}.tar.gz",
-                + "_"
+                "https://cloud.r-project.org/src/contrib/Archive/{cls.cran}/"
-                + str(list(cls.versions)[0])
+                + f"{cls.cran}_{str(list(cls.versions)[0])}.tar.gz",
-                + ".tar.gz"
+            ]
-            )
+        elif cls.bioc:
+            return [
+                "https://bioconductor.org/packages/release/bioc/src/contrib/"
+                + f"{cls.bioc}_{str(list(cls.versions)[0])}.tar.gz",
+                "https://bioconductor.org/packages/release/data/annotation/src/contrib/"
+                + f"{cls.bioc}_{str(list(cls.versions)[0])}.tar.gz",
+            ]
+        else:
+            return [cls.url]
 
     @lang.classproperty
     def list_url(cls):
         if cls.cran:
-            return "https://cloud.r-project.org/src/contrib/Archive/" + cls.cran + "/"
+            return "https://cloud.r-project.org/src/contrib/"
 
     @property
     def git(self):

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/phantompeakqualtools/package.py

@@ -11,7 +11,7 @@ class Phantompeakqualtools(RPackage):
     ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data."""
 
     homepage = "https://github.com/kundajelab/phantompeakqualtools"
-    url = "https://github.com/kundajelab/phantompeakqualtools/archive/1.2.tar.gz"
+    urls = ["https://github.com/kundajelab/phantompeakqualtools/archive/1.2.tar.gz"]
 
     version("1.2", sha256="86cbcca80b65f150b1cdbea673d8a47caba88c2db6b3b567a80f2c797c9a1668")
 

var/spack/repos/builtin/packages/qorts/package.py

@@ -17,7 +17,7 @@ class Qorts(RPackage):
     technology."""
 
     homepage = "https://github.com/hartleys/QoRTs"
-    url = "https://github.com/hartleys/QoRTs/releases/download/v1.2.42/QoRTs_1.2.42.tar.gz"
+    urls = ["https://github.com/hartleys/QoRTs/releases/download/v1.2.42/QoRTs_1.2.42.tar.gz"]
 
     version("1.2.42", sha256="c9f73ce8d5aac1036d13c50475458a61a24cbe5c0baf7ac65b87a7118c51ec08")
 

var/spack/repos/builtin/packages/r-bfastspatial/package.py

@@ -13,7 +13,7 @@ class RBfastspatial(RPackage):
     post-process the results."""
 
     homepage = "https://github.com/loicdtx/bfastSpatial"
-    url = "https://github.com/loicdtx/bfastSpatial/archive/0.6.2.tar.gz"
+    urls = ["https://github.com/loicdtx/bfastSpatial/archive/0.6.2.tar.gz"]
 
     version("0.6.2", sha256="2c6220a5d04d6e4531b0b022a015651e630433f8d6864fa8b820aed5af5c1897")
 

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-cmdstanr/package.py

@@ -17,7 +17,7 @@ class RCmdstanr(RPackage):
     fewer unexpected crashes in RStudio, and a more permissive license."""
 
     homepage = "https://mc-stan.org/cmdstanr/"
-    url = "https://github.com/stan-dev/cmdstanr/archive/refs/tags/v0.5.3.tar.gz"
+    urls = ["https://github.com/stan-dev/cmdstanr/archive/refs/tags/v0.5.3.tar.gz"]
 
     license("BSD-3-Clause")
 

var/spack/repos/builtin/packages/r-dada2/package.py

@@ -11,7 +11,7 @@ class RDada2(RPackage):
     resolution"""
 
     homepage = "https://benjjneb.github.io/dada2/"
-    url = "https://github.com/benjjneb/dada2/archive/v1.14.tar.gz"
+    urls = ["https://github.com/benjjneb/dada2/archive/v1.14.tar.gz"]
 
     license("LGPL-3.0-only")
 

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-ieugwasr/package.py

@@ -14,7 +14,7 @@ class RIeugwasr(RPackage):
     specific queries."""
 
     homepage = "https://github.com/MRCIEU/ieugwasr"
-    url = "https://github.com/MRCIEU/ieugwasr/archive/refs/tags/0.1.5.tar.gz"
+    urls = ["https://github.com/MRCIEU/ieugwasr/archive/refs/tags/0.1.5.tar.gz"]
 
     license("MIT")
 

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-libpressio/package.py

@@ -10,7 +10,7 @@ class RLibpressio(RPackage):
     """R package for libpressio"""
 
     homepage = "https://github.com/robertu94/libpressio-r"
-    url = "https://github.com/robertu94/libpressio-r/archive/0.0.1.tar.gz"
+    urls = ["https://github.com/robertu94/libpressio-r/archive/0.0.1.tar.gz"]
 
     maintainers("robertu94")
 

var/spack/repos/builtin/packages/r-mrinstruments/package.py

@@ -12,7 +12,7 @@ class RMrinstruments(RPackage):
     Datasets of eQTLs, GWAS catalogs, etc."""
 
     homepage = "https://github.com/MRCIEU/MRInstruments"
-    url = "https://github.com/MRCIEU/MRInstruments/archive/refs/tags/0.3.3.tar.gz"
+    urls = ["https://github.com/MRCIEU/MRInstruments/archive/refs/tags/0.3.3.tar.gz"]
 
     version("0.3.3", sha256="4ddbaf6335133e8f7baef469d6bc1f89212462b9f4062c9e4ddda37b12eb3486")
 

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-phantompeakqualtools/package.py

@@ -14,7 +14,7 @@ class RPhantompeakqualtools(RPackage):
     package."""
 
     homepage = "https://github.com/kundajelab/phantompeakqualtools"
-    url = "https://github.com/kundajelab/phantompeakqualtools/raw/master/spp_1.14.tar.gz"
+    urls = ["https://github.com/kundajelab/phantompeakqualtools/raw/master/spp_1.14.tar.gz"]
 
     version("1.14", sha256="d03be6163e82aed72298e54a92c181570f9975a395f57a69b21ac02b1001520b")
 

var/spack/repos/builtin/packages/r-twosamplemr/package.py

@@ -16,7 +16,7 @@ class RTwosamplemr(RPackage):
     serious work we strongly recommend using this R package."""
 
     homepage = "https://mrcieu.github.io/TwoSampleMR/"
-    url = "https://github.com/MRCIEU/TwoSampleMR/archive/refs/tags/v0.5.6.tar.gz"
+    urls = ["https://github.com/MRCIEU/TwoSampleMR/archive/refs/tags/v0.5.6.tar.gz"]
 
     license("MIT")
 

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")