Bioconductor package url change (#5797)

21 files changed, 54 insertions, 52 deletions

diff --git a/var/spack/repos/builtin/packages/r-affy/package.py b/var/spack/repos/builtin/packages/r-affy/package.py
index df6a61c644..6be405c38b 100644
--- a/var/spack/repos/builtin/packages/r-affy/package.py
+++ b/var/spack/repos/builtin/packages/r-affy/package.py
@@ -31,10 +31,10 @@ class RAffy(RPackage):
        functions. 'affy' is fully functional without it."""
 
     homepage = "https://bioconductor.org/packages/affy/"
-    url      = "https://bioconductor.org/packages/3.5/bioc/src/contrib/affy_1.54.0.tar.gz"
+    url      = "https://git.bioconductor.org/packages/affy"
     list_url = homepage
 
-    version('1.54.0', '84270de80ca61bb14b6127a6f5390100')
+    version('1.54.0', git='https://git.bioconductor.org/packages/affy', commit='a815f02906fcf491b28ed0a356d6fce95a6bd20e')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affyio/package.py b/var/spack/repos/builtin/packages/r-affyio/package.py
index 3ff6ca0829..ed1f9ff265 100644
--- a/var/spack/repos/builtin/packages/r-affyio/package.py
+++ b/var/spack/repos/builtin/packages/r-affyio/package.py
@@ -31,8 +31,9 @@ class RAffyio(RPackage):
        formats."""
 
     homepage = "https://bioconductor.org/packages/affyio/"
-    url      = "https://bioconductor.org/packages/3.5/bioc/src/contrib/affyio_1.46.0.tar.gz"
+    url      = "https://git.bioconductor.org/packages/affyio"
+    list_url = homepage
 
-    version('1.46.0', 'e1f7a89ae16940aa29b998a4dbdc0ef9')
+    version('1.46.0', git='https://git.bioconductor.org/packages/affyio', commit='977597f2772e08273d86579486f452170566c880')
     depends_on('r-zlibbioc', type=('build', 'run'))
     depends_on('r@3.4.0:3.4.9', when='@1.46.0')
diff --git a/var/spack/repos/builtin/packages/r-biobase/package.py b/var/spack/repos/builtin/packages/r-biobase/package.py
index 422e1a47a0..035d0ddcad 100644
--- a/var/spack/repos/builtin/packages/r-biobase/package.py
+++ b/var/spack/repos/builtin/packages/r-biobase/package.py
@@ -31,8 +31,10 @@ class RBiobase(RPackage):
  or which replace R functions."""
 
     homepage = "https://www.bioconductor.org/packages/Biobase/"
-    url      = "https://www.bioconductor.org/packages/release/bioc/src/contrib/Biobase_2.36.2.tar.gz"
+    url      = "https://git.bioconductor.org/packages/Biobase"
     list_url = homepage
-    version('2.36.2', '8854eb70acabb07b55d2953fb1ecff31')
+
+    version('2.36.2', git='https://git.bioconductor.org/packages/Biobase', commit='15f50912f3fa08ccb15c33b7baebe6b8a59ce075')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@2.36.2')
diff --git a/var/spack/repos/builtin/packages/r-biocgenerics/package.py b/var/spack/repos/builtin/packages/r-biocgenerics/package.py
index 5484eec53a..2d101b09e1 100644
--- a/var/spack/repos/builtin/packages/r-biocgenerics/package.py
+++ b/var/spack/repos/builtin/packages/r-biocgenerics/package.py
@@ -29,10 +29,9 @@ from spack import *
 class RBiocgenerics(RPackage):
     """S4 generic functions needed by many Bioconductor packages."""
     homepage = "https://www.bioconductor.org/packages/BiocGenerics/"
-    url      = "https://www.bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.22.0.tar.gz"
+    url      = "https://git.bioconductor.org/packages/BiocGenerics"
     list_url = homepage
 
-    version('0.22.1', '19759052960991f065e6542851d56efa')
-    version('0.22.0', 'ef910f2011c0652e1f5fdf3b14219490')
+    version('0.22.1', git='https://git.bioconductor.org/packages/BiocGenerics', commit='9c90bb8926885289d596a81ff318ee3745cbb6ad')
 
-    depends_on('r@3.4.0:3.4.9', when='@0.22.0:0.22.1')
+    depends_on('r@3.4.0:3.4.9', when='@0.22.1')
diff --git a/var/spack/repos/builtin/packages/r-biocinstaller/package.py b/var/spack/repos/builtin/packages/r-biocinstaller/package.py
index 3f158f5fd7..b2248f87ac 100644
--- a/var/spack/repos/builtin/packages/r-biocinstaller/package.py
+++ b/var/spack/repos/builtin/packages/r-biocinstaller/package.py
@@ -30,10 +30,9 @@ class RBiocinstaller(RPackage):
     and (some) github packages."""
 
     homepage = "https://bioconductor.org/packages/BiocInstaller/"
-    url      = "https://bioconductor.org/packages/3.5/bioc/src/contrib/BiocInstaller_1.26.1.tar.gz"
+    url      = "https://git.bioconductor.org/packages/BiocInstaller"
     list_url = homepage
 
-    version('1.26.1', 'ec0f8866639475bcd91179dcc840b5f4')
-    version('1.25.3', '6214770455a5122dca5544861f52c91d')
+    version('1.26.1', git='https://git.bioconductor.org/packages/BiocInstaller', commit='9049b82a77aefa98e3f8e4dd7068317505d70e98')
 
     depends_on('r@3.4.0:3.4.9', when='@1.26.1')
diff --git a/var/spack/repos/builtin/packages/r-biocparallel/package.py b/var/spack/repos/builtin/packages/r-biocparallel/package.py
index b49fd2e930..769c8b9b16 100644
--- a/var/spack/repos/builtin/packages/r-biocparallel/package.py
+++ b/var/spack/repos/builtin/packages/r-biocparallel/package.py
@@ -31,10 +31,10 @@ class RBiocparallel(RPackage):
        objects."""
 
     homepage = "https://bioconductor.org/packages/BiocParallel/"
-    url      = "https://bioconductor.org/packages/3.5/bioc/src/contrib/BiocParallel_1.10.1.tar.gz"
+    url      = "https://git.bioconductor.org/packages/BiocParallel"
     list_url = homepage
 
-    version('1.10.1', '0b587026c0e2c5945be1d84deb12d7dd')
+    version('1.10.1', git='https://git.bioconductor.org/packages/BiocParallel', commit='a76c58cf99fd585ba5ea33065649e68f1afe0a7d')
 
     depends_on('r-futile-logger', type=('build', 'run'))
     depends_on('r-snow', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-biomart/package.py b/var/spack/repos/builtin/packages/r-biomart/package.py
index 22856669e1..d9c15151bd 100644
--- a/var/spack/repos/builtin/packages/r-biomart/package.py
+++ b/var/spack/repos/builtin/packages/r-biomart/package.py
@@ -40,9 +40,9 @@ class RBiomart(RPackage):
        online queries from gene annotation to database mining."""
 
     homepage = "https://bioconductor.org/packages/biomaRt/"
-    url      = "https://bioconductor.org/packages/3.5/bioc/src/contrib/biomaRt_2.32.1.tar.gz"
+    url      = "https://git.bioconductor.org/packages/biomaRt"
 
-    version('2.32.1', '9c7f4547dbf4582fc88ca0c65f789328')
+    version('2.32.1', git='https://git.bioconductor.org/packages/biomaRt', commit='f84d74424fa599f6d08f8db4612ca09914a9087f')
 
     depends_on('r-xml', type=('build', 'run'))
     depends_on('r-rcurl', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-biostrings/package.py b/var/spack/repos/builtin/packages/r-biostrings/package.py
index 8c3740e9ce..fee137c11b 100644
--- a/var/spack/repos/builtin/packages/r-biostrings/package.py
+++ b/var/spack/repos/builtin/packages/r-biostrings/package.py
@@ -31,9 +31,10 @@ class RBiostrings(RPackage):
        or sets of sequences."""
 
     homepage = "https://bioconductor.org/packages/Biostrings/"
-    url      = "https://bioconductor.org/packages/3.5/bioc/src/contrib/Biostrings_2.44.2.tar.gz"
+    url      = "https://git.bioconductor.org/packages/Biostrings"
+    list_url = homepage
 
-    version('2.44.2', 'b30d8c116493ea160a0ca0a662666436')
+    version('2.44.2', git='https://git.bioconductor.org/packages/Biostrings', commit='e4a2b320fb21c5cab3ece7b3c6fecaedfb1e5200')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-delayedarray/package.py b/var/spack/repos/builtin/packages/r-delayedarray/package.py
index 35d8a30194..8cbeb0296b 100644
--- a/var/spack/repos/builtin/packages/r-delayedarray/package.py
+++ b/var/spack/repos/builtin/packages/r-delayedarray/package.py
@@ -43,9 +43,10 @@ class RDelayedarray(RPackage):
        frames."""
 
     homepage = "https://bioconductor.org/packages/DelayedArray/"
-    url      = "https://bioconductor.org/packages/3.5/bioc/src/contrib/DelayedArray_0.2.7.tar.gz"
+    url      = "https://git.bioconductor.org/packages/DelayedArray"
+    list_url = homepage
 
-    version('0.2.7', 'a03b9a92745b7bcac4c0ed44ed6b2272')
+    version('0.2.7', git='https://git.bioconductor.org/packages/DelayedArray', commit='909c2ce1665ebae2543172ead50abbe10bd42bc4')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-edger/package.py b/var/spack/repos/builtin/packages/r-edger/package.py
index 1d8a08c454..2d9da861db 100644
--- a/var/spack/repos/builtin/packages/r-edger/package.py
+++ b/var/spack/repos/builtin/packages/r-edger/package.py
@@ -35,10 +35,10 @@ class REdger(RPackage):
        SAGE and CAGE."""
 
     homepage = "https://bioconductor.org/packages/edgeR/"
-    url      = "https://bioconductor.org/packages/3.5/bioc/src/contrib/edgeR_3.18.1.tar.gz"
+    url      = "https://git.bioconductor.org/packages/edgeR"
     list_url = homepage
 
-    version('3.18.1', 'f074fe4d8f220efe27d61c0666e4b270')
+    version('3.18.1', git='https://git.bioconductor.org/packages/edgeR', commit='101106f3fdd9e2c45d4a670c88f64c12e97a0495')
 
     depends_on('r-limma', type=('build', 'run'))
     depends_on('r-locfit', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-gcrma/package.py b/var/spack/repos/builtin/packages/r-gcrma/package.py
index 603d7d55ef..b54315796a 100644
--- a/var/spack/repos/builtin/packages/r-gcrma/package.py
+++ b/var/spack/repos/builtin/packages/r-gcrma/package.py
@@ -29,10 +29,10 @@ class RGcrma(RPackage):
     """Background adjustment using sequence information"""
 
     homepage = "https://bioconductor.org/packages/gcrma/"
-    url      = "https://bioconductor.org/packages/3.5/bioc/src/contrib/gcrma_2.48.0.tar.gz"
+    url      = "https://git.bioconductor.org/packages/gcrma"
     list_url = homepage
 
-    version('2.48.0', 'c3a2f21c6f93458d1a123594e437a210')
+    version('2.48.0', git='https://git.bioconductor.org/packages/gcrma', commit='3ea0eb0b5c15ffb24df76620667ae7996ed715b4')
 
     depends_on('r-affy', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py
index 90e44682c3..85a161a01b 100644
--- a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py
+++ b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py
@@ -32,15 +32,14 @@ class RGenomeinfodb(RPackage):
        names in their natural, rather than lexicographic, order."""
 
     homepage = "https://bioconductor.org/packages/GenomeInfoDb/"
-    url      = "https://bioconductor.org/packages/3.5/bioc/src/contrib/GenomeInfoDb_1.12.2.tar.gz"
+    url      = "https://git.bioconductor.org/packages/GenomeInfoDb"
     list_url = homepage
 
-    version('1.12.3', '035e120026904df964a79617a8b3e6c6')
-    version('1.12.2', '55b5399d9c8c58b093dfa5f69f8ce2cc')
+    version('1.12.3', git='https://git.bioconductor.org/packages/GenomeInfoDb', commit='2deef3f0571b7f622483257bc22d2509ab5a0369')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
     depends_on('r-rcurl', type=('build', 'run'))
     depends_on('r-genomeinfodbdata', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@1.12.2:1.12.3')
+    depends_on('r@3.4.0:3.4.9', when='@1.12.3')
diff --git a/var/spack/repos/builtin/packages/r-genomicranges/package.py b/var/spack/repos/builtin/packages/r-genomicranges/package.py
index 41f21dff35..bd3f685acd 100644
--- a/var/spack/repos/builtin/packages/r-genomicranges/package.py
+++ b/var/spack/repos/builtin/packages/r-genomicranges/package.py
@@ -38,15 +38,14 @@ class RGenomicranges(RPackage):
        infrastructure."""
 
     homepage = "https://bioconductor.org/packages/GenomicRanges/"
-    url      = "https://bioconductor.org/packages/3.5/bioc/src/contrib/GenomicRanges_1.28.5.tar.gz"
+    url      = "https://git.bioconductor.org/packages/GenomicRanges"
     list_url = homepage
 
-    version('1.28.6', '84c5a40e846b35e98d019ca39783cfe6')
-    version('1.28.5', '5b11897331c4371e09133ea3be125c03')
+    version('1.28.6', git='https://git.bioconductor.org/packages/GenomicRanges', commit='197472d618f3ed04c795dc6ed435500c29619563')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
     depends_on('r-genomeinfodb', type=('build', 'run'))
     depends_on('r-xvector', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@1.28.5:1.28.6')
+    depends_on('r@3.4.0:3.4.9', when='@1.28.6')
diff --git a/var/spack/repos/builtin/packages/r-preprocesscore/package.py b/var/spack/repos/builtin/packages/r-preprocesscore/package.py
index cf36d00cc7..95ce33d8c3 100644
--- a/var/spack/repos/builtin/packages/r-preprocesscore/package.py
+++ b/var/spack/repos/builtin/packages/r-preprocesscore/package.py
@@ -29,8 +29,9 @@ class RPreprocesscore(RPackage):
     """A library of core preprocessing routines"""
 
     homepage = "https://bioconductor.org/packages/preprocessCore/"
-    url      = "https://bioconductor.org/packages/3.5/bioc/src/contrib/preprocessCore_1.38.1.tar.gz"
+    url      = "https://git.bioconductor.org/packages/preprocessCore"
     list_url = homepage
 
-    version('1.38.1', '5085ba98cbab4686f1eb86971f1eecd6')
+    version('1.38.1', git='https://git.bioconductor.org/packages/preprocessCore', commit='c58cb4c720eda0f1c733b989b14912093a7c5fbc')
+
     depends_on('r@3.4.0:3.4.9', when='@1.38.1')
diff --git a/var/spack/repos/builtin/packages/r-rsamtools/package.py b/var/spack/repos/builtin/packages/r-rsamtools/package.py
index 96fbff92b1..41b08a95c7 100644
--- a/var/spack/repos/builtin/packages/r-rsamtools/package.py
+++ b/var/spack/repos/builtin/packages/r-rsamtools/package.py
@@ -32,10 +32,10 @@ class RRsamtools(RPackage):
        indexed tab-delimited (tabix) files."""
 
     homepage = "https://bioconductor.org/packages/Rsamtools/"
-    url      = "https://bioconductor.org/packages/3.5/bioc/src/contrib/Rsamtools_1.28.0.tar.gz"
+    url      = "https://git.bioconductor.org/packages/Rsamtools"
     list_url = homepage
 
-    version('1.28.0', '313bceac68edec07f2ee466520461d35')
+    version('1.28.0', git='https://git.bioconductor.org/packages/Rsamtools', commit='dfa5b6abef68175586f21add7927174786412472')
 
     depends_on('r-genomeinfodb', type=('build', 'run'))
     depends_on('r-genomicranges', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-s4vectors/package.py b/var/spack/repos/builtin/packages/r-s4vectors/package.py
index 09b5759256..84ee43cdfe 100644
--- a/var/spack/repos/builtin/packages/r-s4vectors/package.py
+++ b/var/spack/repos/builtin/packages/r-s4vectors/package.py
@@ -36,12 +36,10 @@ class RS4vectors(RPackage):
        package and in other Bioconductor infrastructure packages)."""
 
     homepage = "https://bioconductor.org/packages/S4Vectors/"
-    url      = "https://bioconductor.org/packages/3.5/bioc/src/contrib/S4Vectors_0.14.4.tar.gz"
+    url      = "https://git.bioconductor.org/packages/S4Vectors"
     list_url = homepage
 
-    version('0.14.7', '3d7cc843d8fd56ec983d511f27a4ed57')
-    version('0.14.6', 'e40ba5de581fc54d70bd5c049415973c')
-    version('0.14.4', '08ccc46e6d39f3aa9091f868ecec1f70')
+    version('0.14.7', git='https://git.bioconductor.org/packages/S4Vectors', commit='40af17fe0b8e93b6a72fc787540d2961773b8e23')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@0.14.4:0.14.7')
+    depends_on('r@3.4.0:3.4.9', when='@0.14.7')
diff --git a/var/spack/repos/builtin/packages/r-simpleaffy/package.py b/var/spack/repos/builtin/packages/r-simpleaffy/package.py
index 1288b37342..36d616fa8c 100644
--- a/var/spack/repos/builtin/packages/r-simpleaffy/package.py
+++ b/var/spack/repos/builtin/packages/r-simpleaffy/package.py
@@ -33,9 +33,10 @@ class RSimpleaffy(RPackage):
        for generating high resolution journal figures..."""
 
     homepage = "http://bioconductor.org/packages/simpleaffy/"
-    url      = "https://bioconductor.org/packages/3.5/bioc/src/contrib/simpleaffy_2.52.0.tar.gz"
+    url      = "https://git.bioconductor.org/packages/simpleaffy"
+    list_url = homepage
 
-    version('2.52.0', 'aa305099a57b3d868be53dc8c539b74e')
+    version('2.52.0', git='https://git.bioconductor.org/packages/simpleaffy', commit='f2b43fb9b8e6fa4c03fe28b4efb3144a0a42a385')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py b/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py
index 39523e7c7b..104a61cb8c 100644
--- a/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py
+++ b/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py
@@ -32,10 +32,10 @@ class RSummarizedexperiment(RPackage):
        represent samples."""
 
     homepage = "https://bioconductor.org/packages/SummarizedExperiment/"
-    url      = "https://bioconductor.org/packages/3.5/bioc/src/contrib/SummarizedExperiment_1.6.5.tar.gz"
+    url      = "https://git.bioconductor.org/packages/SummarizedExperiment"
     list_url = homepage
 
-    version('1.6.5', '8f7d534e37cfda1e3e145ec7609c61f5')
+    version('1.6.5', git='https://git.bioconductor.org/packages/SummarizedExperiment', commit='ec69cd5cfbccaef148a9f6abdfb3e22e888695d0')
 
     depends_on('r-genomicranges', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-xvector/package.py b/var/spack/repos/builtin/packages/r-xvector/package.py
index 1961b69003..4018422c18 100644
--- a/var/spack/repos/builtin/packages/r-xvector/package.py
+++ b/var/spack/repos/builtin/packages/r-xvector/package.py
@@ -30,10 +30,10 @@ class RXvector(RPackage):
        an R external pointer, or on disk)."""
 
     homepage = "https://bioconductor.org/packages/XVector/"
-    url      = "https://bioconductor.org/packages/3.5/bioc/src/contrib/XVector_0.16.0.tar.gz"
+    url      = "https://git.bioconductor.org/packages/XVector"
     list_url = homepage
 
-    version('0.16.0', '839426de12cbb570c85f27f8e7afb144')
+    version('0.16.0', git='https://git.bioconductor.org/packages/XVector', commit='54615888e1a559da4a81de33e934fc0f1c3ad99f')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-yaqcaffy/package.py b/var/spack/repos/builtin/packages/r-yaqcaffy/package.py
index d866b5811e..1901990927 100644
--- a/var/spack/repos/builtin/packages/r-yaqcaffy/package.py
+++ b/var/spack/repos/builtin/packages/r-yaqcaffy/package.py
@@ -31,10 +31,10 @@ class RYaqcaffy(RPackage):
        reference datasets."""
 
     homepage = "http://bioconductor.org/packages/yaqcaffy/"
-    url      = "https://bioconductor.org/packages/3.5/bioc/src/contrib/yaqcaffy_1.36.0.tar.gz"
+    url      = "https://git.bioconductor.org/packages/yaqcaffy"
     list_url = homepage
 
-    version('1.36.0', '73bea4305aa6b1fc9d49881b95bcda42')
+    version('1.36.0', git='https://git.bioconductor.org/packages/yaqcaffy', commit='4d46fe77b2c8de2230a77b0c07dd5dd726e3abd6')
 
     depends_on('r-simpleaffy', type=('build', 'run'))
     depends_on('r@3.4.0:3.4.9', when='@1.36.0')
diff --git a/var/spack/repos/builtin/packages/r-zlibbioc/package.py b/var/spack/repos/builtin/packages/r-zlibbioc/package.py
index db155fb9bd..280c7da3de 100644
--- a/var/spack/repos/builtin/packages/r-zlibbioc/package.py
+++ b/var/spack/repos/builtin/packages/r-zlibbioc/package.py
@@ -33,7 +33,8 @@ class RZlibbioc(RPackage):
        on use."""
 
     homepage = "http://bioconductor.org/packages/release/bioc/html/Zlibbioc.html"
-    url      = "https://bioconductor.org/packages/3.5/bioc/src/contrib/zlibbioc_1.22.0.tar.gz"
+    url      = "https://git.bioconductor.org/packages/zlibbioc"
+    list_url = homepage
 
-    version('1.22.0', '2e9496b860270d2e73d1305b8c6c69a5')
+    version('1.22.0', git='https://git.bioconductor.org/packages/zlibbioc', commit='30377f830af2bc1ff17bbf3fdd2cb6442015fea5')
     depends_on('r@3.4.0:3.4.9', when='@1.22.0')