Add top-level attributes for git R (Bioconductor) packages

var/spack/repos/builtin/packages/r-a4/package.py

@@ -29,9 +29,9 @@ class RA4(RPackage):
     """Automated Affymetrix Array Analysis Umbrella Package."""
 
     homepage = "https://www.bioconductor.org/packages/a4/"
-    url      = "https://git.bioconductor.org/packages/a4"
+    git      = "https://git.bioconductor.org/packages/a4.git"
-    list_url = homepage
+
-    version('1.24.0', git='https://git.bioconductor.org/packages/a4', commit='79b5143652176787c85a0d587b3bbfad6b4a19f4')
+    version('1.24.0', commit='79b5143652176787c85a0d587b3bbfad6b4a19f4')
 
     depends_on('r@3.4.0:3.4.9', when='@1.24.0')
     depends_on('r-a4base', type=('build', 'run'))

var/spack/repos/builtin/packages/r-a4base/package.py

@@ -29,9 +29,9 @@ class RA4base(RPackage):
     """Automated Affymetrix Array Analysis."""
 
     homepage = "https://www.bioconductor.org/packages/a4Base/"
-    url      = "'https://git.bioconductor.org/packages/a4Base'"
+    git      = "https://git.bioconductor.org/packages/a4Base.git"
-    list_url = homepage
+
-    version('1.24.0', git='https://git.bioconductor.org/packages/a4Base', commit='f674afe424a508df2c8ee6c87a06fbd4aa410ef6')
+    version('1.24.0', commit='f674afe424a508df2c8ee6c87a06fbd4aa410ef6')
 
     depends_on('r@3.4.0:3.4.9', when='@1.24.0')
     depends_on('r-biobase', type=('build', 'run'))

var/spack/repos/builtin/packages/r-a4classif/package.py

@@ -29,10 +29,9 @@ class RA4classif(RPackage):
     """Automated Affymetrix Array Analysis Classification Package."""
 
     homepage = "https://www.bioconductor.org/packages/a4Classif/"
-    url      = "https://git.bioconductor.org/packages/a4Classif"
+    git      = "https://git.bioconductor.org/packages/a4Classif.git"
-    list_url = homepage
 
-    version('1.24.0', git='https://git.bioconductor.org/packages/a4Classif', commit='ca06bf274c87a73fc12c29a6eea4b90289fe30b1')
+    version('1.24.0', commit='ca06bf274c87a73fc12c29a6eea4b90289fe30b1')
 
     depends_on('r@3.4.0:3.4.9', when='@1.24.0')
     depends_on('r-a4core', type=('build', 'run'))

var/spack/repos/builtin/packages/r-a4core/package.py

@@ -29,9 +29,9 @@ class RA4core(RPackage):
     """Automated Affymetrix Array Analysis Core Package."""
 
     homepage = "https://www.bioconductor.org/packages/a4Core/"
-    url      = "https://git.bioconductor.org/packages/a4Core"
+    git      = "https://git.bioconductor.org/packages/a4Core.git"
 
-    version('1.24.0', git='https://git.bioconductor.org/packages/a4Core', commit='c871faa3e1ab6be38a9ea3018816cf31b58b0ed3')
+    version('1.24.0', commit='c871faa3e1ab6be38a9ea3018816cf31b58b0ed3')
 
     depends_on('r@3.4.0:3.4.9', when='@1.24.0')
     depends_on('r-biobase', type=('build', 'run'))

var/spack/repos/builtin/packages/r-a4preproc/package.py

@@ -29,9 +29,9 @@ class RA4preproc(RPackage):
     """Automated Affymetrix Array Analysis Preprocessing Package."""
 
     homepage = "https://www.bioconductor.org/packages/a4Preproc/"
-    url      = "https://git.bioconductor.org/packages/a4Preproc"
+    git      = "https://git.bioconductor.org/packages/a4Preproc.git"
 
-    version('1.24.0', git='https://git.bioconductor.org/packages/a4Preproc', commit='651014b8102807aea4f1274e34e083e70b5e7ee7')
+    version('1.24.0', commit='651014b8102807aea4f1274e34e083e70b5e7ee7')
 
     depends_on('r@3.4.0:3.4.9', when='@1.24.0')
     depends_on('r-annotationdbi', type=('build', 'run'))

var/spack/repos/builtin/packages/r-a4reporting/package.py

@@ -29,9 +29,9 @@ class RA4reporting(RPackage):
     """Automated Affymetrix Array Analysis Reporting Package."""
 
     homepage = "https://www.bioconductor.org/packages/a4Reporting"
-    url      = "https://git.bioconductor.org/packages/a4Reporting"
+    git      = "https://git.bioconductor.org/packages/a4Reporting.git"
-    list_url = homepage
+
-    version('1.24.0', git='https://git.bioconductor.org/packages/a4Reporting', commit='bf22c4d50daf40fc9eaf8c476385bf4a24a5b5ce')
+    version('1.24.0', commit='bf22c4d50daf40fc9eaf8c476385bf4a24a5b5ce')
 
     depends_on('r@3.4.0:3.4.9', when='@1.24.0')
     depends_on('r-annaffy', type=('build', 'run'))

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

@@ -42,9 +42,9 @@ class RAbaenrichment(RPackage):
     user-defined brain regions."""
 
     homepage = "https://bioconductor.org/packages/ABAEnrichment/"
-    url      = "https://git.bioconductor.org/packages/ABAEnrichment"
+    git      = "https://git.bioconductor.org/packages/ABAEnrichment.git"
 
-    version('1.6.0', git='https://git.bioconductor.org/packages/ABAEnrichment', commit='d2a0467dcb7aa6e103e3b83dccd6510b0e142ac1')
+    version('1.6.0', commit='d2a0467dcb7aa6e103e3b83dccd6510b0e142ac1')
 
     depends_on('r@3.4.0:3.4.9', when='@1.6.0')
     depends_on('r-rcpp', type=('build', 'run'))

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

@@ -32,9 +32,9 @@ class RAbsseq(RPackage):
     of dispersion across expression level."""
 
     homepage = "https://www.bioconductor.org/packages/ABSSeq/"
-    url      = "https://git.bioconductor.org/packages/ABSSeq"
+    git      = "https://git.bioconductor.org/packages/ABSSeq.git"
 
-    version('1.22.8', git='https://git.bioconductor.org/packages/ABSSeq', commit='a67ba49bc156a4522092519644f3ec83d58ebd6a')
+    version('1.22.8', commit='a67ba49bc156a4522092519644f3ec83d58ebd6a')
 
     depends_on('r@3.4.0:3.4.9', when='@1.22.8')
     depends_on('r-locfit', type=('build', 'run'))

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

@@ -32,9 +32,9 @@ class RAcgh(RPackage):
     printing and plotting aCGH objects."""
 
     homepage = "https://www.bioconductor.org/packages/aCGH/"
-    url      = "https://git.bioconductor.org/packages/aCGH"
+    git      = "https://git.bioconductor.org/packages/aCGH.git"
 
-    version('1.54.0', git='https://git.bioconductor.org/packages/aCGH', commit='be2ed339449f55c8d218e10c435e4ad356683693')
+    version('1.54.0', commit='be2ed339449f55c8d218e10c435e4ad356683693')
 
     depends_on('r@3.4.0:3.4.9', when='@1.54.0')
     depends_on('r-cluster', type=('build', 'run'))

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

@@ -37,9 +37,9 @@ class RAcme(RPackage):
     experiments quite easily with enough memory."""
 
     homepage = "https://www.bioconductor.org/packages/ACME/"
-    url      = "https://git.bioconductor.org/packages/ACME"
+    git      = "https://git.bioconductor.org/packages/ACME.git"
 
-    version('2.32.0', git='https://git.bioconductor.org/packages/ACME', commit='76372255d7714a0c8128a11c028bf70214dac407')
+    version('2.32.0', commit='76372255d7714a0c8128a11c028bf70214dac407')
 
     depends_on('r@3.4.0:3.4.9', when='@2.32.0')
     depends_on('r-biobase', type=('build', 'run'))

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

@@ -32,9 +32,9 @@ class RAdsplit(RPackage):
     significance of the supporting gene set is determined."""
 
     homepage = "https://www.bioconductor.org/packages/adSplit/"
-    url      = "https://git.bioconductor.org/packages/adSplit"
+    git      = "https://git.bioconductor.org/packages/adSplit.git"
 
-    version('1.46.0', git='https://git.bioconductor.org/packages/adSplit', commit='7e81a83f34d371447f491b3a146bf6851e260c7c')
+    version('1.46.0', commit='7e81a83f34d371447f491b3a146bf6851e260c7c')
 
     depends_on('r@3.4.0:3.4.9', when='@1.46.0')
     depends_on('r-annotationdbi', type=('build', 'run'))

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

@@ -36,9 +36,8 @@ class RAffxparser(RPackage):
     from a set of CEL files into a convenient list structure."""
 
     homepage = "https://www.bioconductor.org/packages/affxparser/"
-    url      = "https://git.bioconductor.org/packages/affxparser"
+    git      = "https://git.bioconductor.org/packages/affxparser.git"
-    list_url = homepage
 
-    version('1.48.0', git='https://git.bioconductor.org/packages/affxparser', commit='2461ea88f310b59c4a9a997a4b3dadedbd65a4aa')
+    version('1.48.0', commit='2461ea88f310b59c4a9a997a4b3dadedbd65a4aa')
 
     depends_on('r@3.4.0:3.4.9', when='@1.48.0')

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

@@ -31,10 +31,9 @@ class RAffy(RPackage):
        functions. 'affy' is fully functional without it."""
 
     homepage = "https://bioconductor.org/packages/affy/"
-    url      = "https://git.bioconductor.org/packages/affy"
+    git      = "https://git.bioconductor.org/packages/affy.git"
-    list_url = homepage
 
-    version('1.54.0', git='https://git.bioconductor.org/packages/affy', commit='a815f02906fcf491b28ed0a356d6fce95a6bd20e')
+    version('1.54.0', commit='a815f02906fcf491b28ed0a356d6fce95a6bd20e')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))

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

@@ -30,9 +30,9 @@ class RAffycomp(RPackage):
     expression measures for Affymetrix Oligonucleotide Arrays."""
 
     homepage = "https://www.bioconductor.org/packages/affycomp/"
-    url      = "https://git.bioconductor.org/packages/affycomp"
+    git      = "https://git.bioconductor.org/packages/affycomp.git"
 
-    version('1.52.0', git='https://git.bioconductor.org/packages/affycomp', commit='1b97a1cb21ec93bf1e5c88d5d55b988059612790')
+    version('1.52.0', commit='1b97a1cb21ec93bf1e5c88d5d55b988059612790')
 
     depends_on('r@3.4.0:3.4.9', when='@1.52.0')
     depends_on('r-biobase', type=('build', 'run'))

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

@@ -34,7 +34,7 @@ class RAffycompatible(RPackage):
     (AGCC)-compatible sample annotation files."""
 
     homepage = "https://www.bioconductor.org/packages/AffyCompatible/"
-    git      = "https://git.bioconductor.org/packages/AffyCompatible"
+    git      = "https://git.bioconductor.org/packages/AffyCompatible.git"
 
     version('1.36.0', commit='dbbfd43a54ae1de6173336683a9461084ebf38c3')
 

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

@@ -30,9 +30,9 @@ class RAffycontam(RPackage):
     effectiveness."""
 
     homepage = "https://www.bioconductor.org/packages/affyContam/"
-    url      = "https://git.bioconductor.org/packages/affyContam"
+    git      = "https://git.bioconductor.org/packages/affyContam.git"
 
-    version('1.34.0', git='https://git.bioconductor.org/packages/affyContam', commit='03529f26d059c19e069cdda358dbf7789b6d4c40')
+    version('1.34.0', commit='03529f26d059c19e069cdda358dbf7789b6d4c40')
 
     depends_on('r@3.4.0:3.4.9', when=('@1.34.0'))
     depends_on('r-biobase', type=('build', 'run'))

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

@@ -30,9 +30,9 @@ class RAffycoretools(RPackage):
     the more common analyses that a core Biostatistician might see."""
 
     homepage = "https://www.bioconductor.org/packages/affycoretools/"
-    url      = "https://git.bioconductor.org/packages/affycoretools"
+    git      = "https://git.bioconductor.org/packages/affycoretools.git"
 
-    version('1.48.0', git='https://git.bioconductor.org/packages/affycoretools', commit='e0d52e34eead1ac45d3e60c59efd940e4889eb99')
+    version('1.48.0', commit='e0d52e34eead1ac45d3e60c59efd940e4889eb99')
 
     depends_on('r@3.4.0:3.4.9', when='@1.48.0')
     depends_on('r-biobase', type=('build', 'run'))

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

@@ -31,9 +31,9 @@ class RAffyexpress(RPackage):
     expressed genes in the Affymetrix gene expression data."""
 
     homepage = "https://www.bioconductor.org/packages/AffyExpress/"
-    url      = "https://git.bioconductor.org/packages/AffyExpress"
+    git      = "https://git.bioconductor.org/packages/AffyExpress.git"
 
-    version('1.42.0', git='https://git.bioconductor.org/packages/AffyExpress', commit='f5c5cf6173f4419e25f4aeff5e6b705a40abc371')
+    version('1.42.0', commit='f5c5cf6173f4419e25f4aeff5e6b705a40abc371')
 
     depends_on('r@3.4.0:3.4.9', when='@1.42.0')
     depends_on('r-affy', type=('build', 'run'))

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

@@ -33,9 +33,9 @@ class RAffyilm(RPackage):
     of the Langmuir model."""
 
     homepage = "https://www.bioconductor.org/packages/affyILM/"
-    url      = "https://git.bioconductor.org/packages/affyILM"
+    git      = "https://git.bioconductor.org/packages/affyILM.git"
 
-    version('1.28.0', git='https://git.bioconductor.org/packages/affyILM', commit='307bee3ebc599e0ea4a1d6fa8d5511ccf8bef7de')
+    version('1.28.0', commit='307bee3ebc599e0ea4a1d6fa8d5511ccf8bef7de')
 
     depends_on('r@3.4.0:3.4.9', when='@1.28.0')
     depends_on('r-gcrma', type=('build', 'run'))

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

@@ -31,9 +31,9 @@ class RAffyio(RPackage):
        formats."""
 
     homepage = "https://bioconductor.org/packages/affyio/"
-    url      = "https://git.bioconductor.org/packages/affyio"
+    git      = "https://git.bioconductor.org/packages/affyio.git"
-    list_url = homepage
+
+    version('1.46.0', commit='977597f2772e08273d86579486f452170566c880')
 
-    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')

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

@@ -30,9 +30,9 @@ class RAffypdnn(RPackage):
     described by Li Zhang et al."""
 
     homepage = "https://www.bioconductor.org/packages/affypdnn/"
-    url      = "https://git.bioconductor.org/packages/affypdnn"
+    git      = "https://git.bioconductor.org/packages/affypdnn.git"
 
-    version('1.50.0', git='https://git.bioconductor.org/packages/affypdnn', commit='97ff68e9f51f31333c0330435ea23b212b3ed18a')
+    version('1.50.0', commit='97ff68e9f51f31333c0330435ea23b212b3ed18a')
 
     depends_on('r@3.4.0:3.4.9', when='@1.50.0')
     depends_on('r-affy', type=('build', 'run'))

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

@@ -33,9 +33,9 @@ class RAffyplm(RPackage):
     PLM based quality assessment tools."""
 
     homepage = "https://www.bioconductor.org/packages/affyPLM/"
-    url      = "https://git.bioconductor.org/packages/affyPLM"
+    git      = "https://git.bioconductor.org/packages/affyPLM.git"
 
-    version('1.52.1', git='https://git.bioconductor.org/packages/affyPLM', commit='e8613a6018c4ee58045df6bf19128844f50a1f43')
+    version('1.52.1', commit='e8613a6018c4ee58045df6bf19128844f50a1f43')
 
     depends_on('r@3.4.0:3.4.9', when='@1.52.1')
     depends_on('r-biocgenerics', type=('build', 'run'))

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

@@ -31,9 +31,9 @@ class RAffyqcreport(RPackage):
     quality of a set of arrays in an AffyBatch object."""
 
     homepage = "https://www.bioconductor.org/packages/affyQCReport/"
-    url      = "https://git.bioconductor.org/packages/affyQCReport"
+    git      = "https://git.bioconductor.org/packages/affyQCReport.git"
 
-    version('1.54.0', git='https://git.bioconductor.org/packages/affyQCReport', commit='5572e9981dc874b78b4adebf58080cac3fbb69e1')
+    version('1.54.0', commit='5572e9981dc874b78b4adebf58080cac3fbb69e1')
 
     depends_on('r@3.4.0:3.4.9', when='@1.54.0')
     depends_on('r-biobase', type=('build', 'run'))

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

@@ -34,9 +34,9 @@ class RAffyrnadegradation(RPackage):
     by RNA degradation."""
 
     homepage = "https://www.bioconductor.org/packages/AffyRNADegradation/"
-    url      = "https://git.bioconductor.org/packages/AffyRNADegradation"
+    git      = "https://git.bioconductor.org/packages/AffyRNADegradation.git"
 
-    version('1.22.0', git='https://git.bioconductor.org/packages/AffyRNADegradation', commit='0fa78f8286494711a239ded0ba587b0de47c15d3')
+    version('1.22.0', commit='0fa78f8286494711a239ded0ba587b0de47c15d3')
 
     depends_on('r@3.4.0:3.4.9', when='@1.22.0')
     depends_on('r-affy', type=('build', 'run'))

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

@@ -30,9 +30,9 @@ class RAgdex(RPackage):
     for cross-species genomics."""
 
     homepage = "http://bioconductor.org/packages/AGDEX/"
-    url      = "https://git.bioconductor.org/packages/AGDEX"
+    git      = "https://git.bioconductor.org/packages/AGDEX.git"
 
-    version('1.24.0', git='https://git.bioconductor.org/packages/AGDEX', commit='29c6bcfa6919a5c6d8bcb36b44e75145a60ce7b5')
+    version('1.24.0', commit='29c6bcfa6919a5c6d8bcb36b44e75145a60ce7b5')
 
     depends_on('r@3.4.0:3.4.9', when='@1.24.0')
     depends_on('r-biobase', type=('build', 'run'))

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

@@ -29,8 +29,8 @@ class RAgilp(RPackage):
     """Agilent expression array processing package."""
 
     homepage = "http://bioconductor.org/packages/agilp/"
-    url      = "https://git.bioconductor.org/packages/agilp"
+    git      = "https://git.bioconductor.org/packages/agilp.git"
 
-    version('3.8.0', git='https://git.bioconductor.org/packages/agilp', commit='c772a802af1b4c0741f2edd78053a0425160ea53')
+    version('3.8.0', commit='c772a802af1b4c0741f2edd78053a0425160ea53')
 
     depends_on('r@3.4.0:3.4.9', when='@3.8.0')

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

@@ -29,9 +29,9 @@ class RAgimicrorna(RPackage):
     """Processing and Analysis of Agilent microRNA data."""
 
     homepage = "https://www.bioconductor.org/packages/AgiMicroRna/"
-    url      = "https://git.bioconductor.org/packages/AgiMicroRna"
+    git      = "https://git.bioconductor.org/packages/AgiMicroRna.git"
 
-    version('2.26.0', git='https://git.bioconductor.org/packages/AgiMicroRna', commit='6dd74bae47986f2a23d03e3f1f9f78f701dd8053')
+    version('2.26.0', commit='6dd74bae47986f2a23d03e3f1f9f78f701dd8053')
 
     depends_on('r@3.4.0:3.4.9', when='@2.26.0')
     depends_on('r-affycoretools', type=('build', 'run'))

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

@@ -33,9 +33,9 @@ class RAims(RPackage):
     as well as on dataset of gene expression data."""
 
     homepage = "http://bioconductor.org/packages/AIMS/"
-    url      = "https://git.bioconductor.org/packages/AIMS"
+    git      = "https://git.bioconductor.org/packages/AIMS.git"
 
-    version('1.8.0', git='https://git.bioconductor.org/packages/AIMS', commit='86b866c20e191047492c51b43e3f73082c3f8357')
+    version('1.8.0', commit='86b866c20e191047492c51b43e3f73082c3f8357')
 
     depends_on('r@3.4.0:3.4.9', when='@1.8.0')
     depends_on('r-e1071', type=('build', 'run'))

var/spack/repos/builtin/packages/r-aldex2/package.py

@@ -39,9 +39,9 @@ class RAldex2(RPackage):
     and fdr values calculated by the Benjamini Hochberg correction."""
 
     homepage = "http://bioconductor.org/packages/ALDEx2/"
-    url      = "https://git.bioconductor.org/packages/ALDEx2"
+    git      = "https://git.bioconductor.org/packages/ALDEx2.git"
 
-    version('1.8.0', git='https://git.bioconductor.org/packages/ALDEx2', commit='24104824ca2402ad4f54fbf1ed9cee7fac2aaaf1')
+    version('1.8.0', commit='24104824ca2402ad4f54fbf1ed9cee7fac2aaaf1')
 
     depends_on('r@3.4.0:3.4.9', when='@1.8.0')
     depends_on('r-s4vectors', type=('build', 'run'))

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

@@ -30,9 +30,9 @@ class RAllelicimbalance(RPackage):
     investigation using RNA-seq data."""
 
     homepage = "http://bioconductor.org/packages/AllelicImbalance/"
-    url      = "https://git.bioconductor.org/packages/AllelicImbalance"
+    git      = "https://git.bioconductor.org/packages/AllelicImbalance.git"
 
-    version('1.14.0', git='https://git.bioconductor.org/packages/AllelicImbalance', commit='35958534945819baafde0e13d1eb4d05a514142c')
+    version('1.14.0', commit='35958534945819baafde0e13d1eb4d05a514142c')
 
     depends_on('r@3.4.0:3.4.9', when='@1.14.0')
     depends_on('r-genomicranges', type=('build', 'run'))

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

@@ -30,9 +30,9 @@ class RAlpine(RPackage):
     transcript abundance estimation."""
 
     homepage = "http://bioconductor.org/packages/alpine/"
-    url      = "https://git.bioconductor.org/packages/alpine"
+    git      = "https://git.bioconductor.org/packages/alpine.git"
 
-    version('1.2.0', git='https://git.bioconductor.org/packages/alpine', commit='896872e6071769e1ac2cf786974edb8b875c45eb')
+    version('1.2.0', commit='896872e6071769e1ac2cf786974edb8b875c45eb')
 
     depends_on('r@3.4.0:3.4.9', when='@1.2.0')
     depends_on('r-biostrings', type=('build', 'run'))

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

@@ -35,9 +35,9 @@ class RAlsace(RPackage):
     retention time correction, etcetera."""
 
     homepage = "https://www.bioconductor.org/packages/alsace/"
-    url      = "https://git.bioconductor.org/packages/alsace"
+    git      = "https://git.bioconductor.org/packages/alsace.git"
 
-    version('1.12.0', git='https://git.bioconductor.org/packages/alsace', commit='1364c65bbff05786d05c02799fd44fd57748fae3')
+    version('1.12.0', commit='1364c65bbff05786d05c02799fd44fd57748fae3')
 
     depends_on('r-als', type=('build', 'run'))
     depends_on('r-ptw', type=('build', 'run'))

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

@@ -29,9 +29,9 @@ class RAltcdfenvs(RPackage):
     """Convenience data structures and functions to handle cdfenvs."""
 
     homepage = "https://www.bioconductor.org/packages/altcdfenvs/"
-    url      = "https://git.bioconductor.org/packages/altcdfenvs"
+    git      = "https://git.bioconductor.org/packages/altcdfenvs.git"
 
-    version('2.38.0', git='https://git.bioconductor.org/packages/altcdfenvs', commit='2e92b9da76dbe50af4bf33c525134e29e9809291')
+    version('2.38.0', commit='2e92b9da76dbe50af4bf33c525134e29e9809291')
 
     depends_on('r@3.4.0:3.4.9', when='@2.38.0')
     depends_on('r-biocgenerics', type=('build', 'run'))

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

@@ -30,9 +30,9 @@ class RAmpliqueso(RPackage):
     amplicon sequencing panels, such as AmpliSeq."""
 
     homepage = "https://www.bioconductor.org/packages/ampliQueso/"
-    url      = "https://git.bioconductor.org/packages/ampliQueso"
+    git      = "https://git.bioconductor.org/packages/ampliQueso.git"
 
-    version('1.14.0', git='https://git.bioconductor.org/packages/ampliQueso', commit='9a4c26ec594171279aba8ab7fe59c4a2ea09b06b')
+    version('1.14.0', commit='9a4c26ec594171279aba8ab7fe59c4a2ea09b06b')
 
     depends_on('r@3.4.0:3.4.9', when='@1.14.0')
     depends_on('r-samr', type=('build', 'run'))

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

@@ -30,9 +30,9 @@ class RAnalysispageserver(RPackage):
     of customizable R analyses via the web."""
 
     homepage = "https://www.bioconductor.org/packages/AnalysisPageServer/"
-    url      = "https://git.bioconductor.org/packages/AnalysisPageServer"
+    git      = "https://git.bioconductor.org/packages/AnalysisPageServer.git"
 
-    version('1.10.0', git='https://git.bioconductor.org/packages/AnalysisPageServer', commit='876c87073be116fa15a1afdd407e21152eb80d50')
+    version('1.10.0', commit='876c87073be116fa15a1afdd407e21152eb80d50')
 
     depends_on('r@3.4.0:3.4.9', when='@1.10.0')
     depends_on('r-log4r', type=('build', 'run'))

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

@@ -33,9 +33,9 @@ class RAnaquin(RPackage):
     modelling and visualization of spike-in controls."""
 
     homepage = "https://www.bioconductor.org/packages/Anaquin/"
-    url      = "https://git.bioconductor.org/packages/Anaquin"
+    git      = "https://git.bioconductor.org/packages/Anaquin.git"
 
-    version('1.2.0', git='https://git.bioconductor.org/packages/Anaquin', commit='584d1970cc9dc1d354f9a6d7c1306bd7e8567119')
+    version('1.2.0', commit='584d1970cc9dc1d354f9a6d7c1306bd7e8567119')
 
     depends_on('r@3.4.0:3.4.9', when='@1.2.0')
     depends_on('r-deseq2', type=('build', 'run'))

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

@@ -30,9 +30,9 @@ class RAneufinder(RPackage):
     export and analysis from whole-genome single cell sequencing data."""
 
     homepage = "https://www.bioconductor.org/packages/AneuFinder/"
-    url      = "https://git.bioconductor.org/packages/AneuFinder"
+    git      = "https://git.bioconductor.org/packages/AneuFinder.git"
 
-    version('1.4.0', git='https://git.bioconductor.org/packages/AneuFinder', commit='e5bdf4d5e4f84ee5680986826ffed636ed853b8e')
+    version('1.4.0', commit='e5bdf4d5e4f84ee5680986826ffed636ed853b8e')
 
     depends_on('r@3.4.0:3.4.9', when='@1.4.0')
     depends_on('r-genomicranges', type=('build', 'run'))

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

@@ -30,8 +30,8 @@ class RAneufinderdata(RPackage):
     purposes in the AneuFinder package."""
 
     homepage = "https://www.bioconductor.org/packages/AneuFinderData/"
-    url      = "https://git.bioconductor.org/packages/AneuFinderData"
+    git      = "https://git.bioconductor.org/packages/AneuFinderData.git"
 
-    version('1.4.0', git='https://git.bioconductor.org/packages/AneuFinderData', commit='55c8807ee4a37a2eb6d0defafaf843f980b22c40')
+    version('1.4.0', commit='55c8807ee4a37a2eb6d0defafaf843f980b22c40')
 
     depends_on('r@3.4.0:3.4.9', when='@1.4.0')

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

@@ -35,9 +35,9 @@ class RAnnaffy(RPackage):
     using various criteria."""
 
     homepage = "https://www.bioconductor.org/packages/annaffy/"
-    url      = "https://git.bioconductor.org/packages/annaffy"
+    git      = "https://git.bioconductor.org/packages/annaffy.git"
 
-    version('1.48.0', git='https://git.bioconductor.org/packages/annaffy', commit='89a03c64ac9df5d963ed60b87893a3fffa6798a0')
+    version('1.48.0', commit='89a03c64ac9df5d963ed60b87893a3fffa6798a0')
 
     depends_on('r@3.4.0:3.4.9', when='@1.48.0')
     depends_on('r-biobase', type=('build', 'run'))

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

@@ -29,9 +29,9 @@ class RAnnotate(RPackage):
     """Using R enviroments for annotation."""
 
     homepage = "https://www.bioconductor.org/packages/annotate/"
-    url      = "https://git.bioconductor.org/packages/annotate"
+    git      = "https://git.bioconductor.org/packages/annotate.git"
-    list_url = homepage
+
-    version('1.54.0', git='https://git.bioconductor.org/packages/annotate', commit='860cc5b696795a31b18beaf4869f9c418d74549e')
+    version('1.54.0', commit='860cc5b696795a31b18beaf4869f9c418d74549e')
 
     depends_on('r@3.4.0:3.4.9', when='@1.54.0')
     depends_on('r-annotationdbi', type=('build', 'run'))

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

@@ -22,8 +22,6 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-#
-#
 from spack import *
 
 
@@ -32,9 +30,9 @@ class RAnnotationdbi(RPackage):
     annotation data packages using SQLite data storage."""
 
     homepage = "https://www.bioconductor.org/packages/AnnotationDbi/"
-    url      = "https://git.bioconductor.org/packages/AnnotationDbi"
+    git      = "https://git.bioconductor.org/packages/AnnotationDbi.git"
-    list_url = homepage
+
-    version('1.38.2', git='https://git.bioconductor.org/packages/AnnotationDbi', commit='67d46facba8c15fa5f0eb47c4e39b53dbdc67c36')
+    version('1.38.2', commit='67d46facba8c15fa5f0eb47c4e39b53dbdc67c36')
 
     depends_on('r@3.4.0:3.4.9', when='@1.38.2')
     depends_on('r-biocgenerics', type=('build', 'run'))

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

@@ -32,10 +32,9 @@ class RAnnotationfilter(RPackage):
        packages."""
 
     homepage = "https://bioconductor.org/packages/AnnotationFilter/"
-    url      = "https://git.bioconductor.org/packages/AnnotationFilter"
+    git      = "https://git.bioconductor.org/packages/AnnotationFilter.git"
-    list_url = homepage
 
-    version('1.0.0', git='https://git.bioconductor.org/packages/AnnotationFilter', commit='a9f79b26defe3021eea60abe16ce1fa379813ec9')
+    version('1.0.0', commit='a9f79b26defe3021eea60abe16ce1fa379813ec9')
 
     depends_on('r-genomicranges', type=('build', 'run'))
     depends_on('r-lazyeval', type=('build', 'run'))

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

@@ -31,9 +31,9 @@ class RAnnotationforge(RPackage):
     with AnnotationDbi."""
 
     homepage = "https://www.bioconductor.org/packages/AnnotationForge/"
-    url      = "https://git.bioconductor.org/packages/AnnotationForge"
+    git      = "https://git.bioconductor.org/packages/AnnotationForge.git"
 
-    version('1.18.2', git='https://git.bioconductor.org/packages/AnnotationForge', commit='44ca3d4ef9e9825c14725ffdbbaa57ea059532e1')
+    version('1.18.2', commit='44ca3d4ef9e9825c14725ffdbbaa57ea059532e1')
 
     depends_on('r@3.4.0:3.4.9', when='@1.18.2')
     depends_on('r-biocgenerics', type=('build', 'run'))

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

@@ -36,10 +36,9 @@ class RAnnotationhub(RPackage):
        quick and reproducible access."""
 
     homepage = "https://bioconductor.org/packages/AnnotationHub/"
-    url      = "https://git.bioconductor.org/packages/AnnotationHub"
+    git      = "https://git.bioconductor.org/packages/AnnotationHub.git"
-    list_url = homepage
 
-    version('2.8.3', git='https://git.bioconductor.org/packages/AnnotationHub', commit='8aa9c64262a8d708d2bf1c82f82dfc3d7d4ccc0c')
+    version('2.8.3', commit='8aa9c64262a8d708d2bf1c82f82dfc3d7d4ccc0c')
 
     depends_on('r-rsqlite', type=('build', 'run'))
     depends_on('r-biocinstaller', type=('build', 'run'))

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

@@ -32,9 +32,9 @@ class RBamsignals(RPackage):
     profiles. It also handles paired-end data."""
 
     homepage = "https://www.bioconductor.org/packages/bamsignals/"
-    url      = "https://git.bioconductor.org/packages/bamsignals"
+    git      = "https://git.bioconductor.org/packages/bamsignals.git"
 
-    version('1.8.0', git='https://git.bioconductor.org/packages/bamsignals', commit='b123b83e8e026c9ec91209d4498aff3e95a5de23')
+    version('1.8.0', commit='b123b83e8e026c9ec91209d4498aff3e95a5de23')
 
     depends_on('r@3.4.0:3.4.9', when='@1.8.0')
     depends_on('r-biocgenerics', type=('build', 'run'))

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

@@ -31,11 +31,10 @@ class RBiobase(RPackage):
     or which replace R functions."""
 
     homepage = "https://www.bioconductor.org/packages/Biobase/"
-    url      = "https://git.bioconductor.org/packages/Biobase"
+    git      = "https://git.bioconductor.org/packages/Biobase.git"
-    list_url = homepage
 
-    version('2.38.0', git='https://git.bioconductor.org/packages/Biobase', commit='83f89829e0278ac014b0bc6664e621ac147ba424')
+    version('2.38.0', commit='83f89829e0278ac014b0bc6664e621ac147ba424')
-    version('2.36.2', git='https://git.bioconductor.org/packages/Biobase', commit='15f50912f3fa08ccb15c33b7baebe6b8a59ce075')
+    version('2.36.2', commit='15f50912f3fa08ccb15c33b7baebe6b8a59ce075')
 
     depends_on('r-biocgenerics@0.16.1:', type=('build', 'run'))
     depends_on('r@3.4.0:3.4.9', when='@2.36.2:')

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

@@ -22,17 +22,16 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-#
 from spack import *
 
 
 class RBiocgenerics(RPackage):
     """S4 generic functions needed by many Bioconductor packages."""
-    homepage = "https://www.bioconductor.org/packages/BiocGenerics/"
-    url      = "https://git.bioconductor.org/packages/BiocGenerics"
-    list_url = homepage
 
-    version('0.24.0', git='https://git.bioconductor.org/packages/BiocGenerics', commit='3db111e8c1f876267da89f4f0c5406a9d5c31cd1')
+    homepage = "https://www.bioconductor.org/packages/BiocGenerics/"
-    version('0.22.1', git='https://git.bioconductor.org/packages/BiocGenerics', commit='9c90bb8926885289d596a81ff318ee3745cbb6ad')
+    git      = "https://git.bioconductor.org/packages/BiocGenerics.git"
+
+    version('0.24.0', commit='3db111e8c1f876267da89f4f0c5406a9d5c31cd1')
+    version('0.22.1', commit='9c90bb8926885289d596a81ff318ee3745cbb6ad')
 
     depends_on('r@3.4.0:3.4.9', when='@0.22.1:')

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

@@ -30,9 +30,8 @@ class RBiocinstaller(RPackage):
     and (some) github packages."""
 
     homepage = "https://bioconductor.org/packages/BiocInstaller/"
-    url      = "https://git.bioconductor.org/packages/BiocInstaller"
+    git      = "https://git.bioconductor.org/packages/BiocInstaller.git"
-    list_url = homepage
 
-    version('1.26.1', git='https://git.bioconductor.org/packages/BiocInstaller', commit='9049b82a77aefa98e3f8e4dd7068317505d70e98')
+    version('1.26.1', commit='9049b82a77aefa98e3f8e4dd7068317505d70e98')
 
     depends_on('r@3.4.0:3.4.9', when='@1.26.1')

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

@@ -31,10 +31,9 @@ class RBiocparallel(RPackage):
        objects."""
 
     homepage = "https://bioconductor.org/packages/BiocParallel/"
-    url      = "https://git.bioconductor.org/packages/BiocParallel"
+    git      = "https://git.bioconductor.org/packages/BiocParallel.git"
-    list_url = homepage
 
-    version('1.10.1', git='https://git.bioconductor.org/packages/BiocParallel', commit='a76c58cf99fd585ba5ea33065649e68f1afe0a7d')
+    version('1.10.1', commit='a76c58cf99fd585ba5ea33065649e68f1afe0a7d')
 
     depends_on('r-futile-logger', type=('build', 'run'))
     depends_on('r-snow', type=('build', 'run'))

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

@@ -30,9 +30,9 @@ class RBiocstyle(RPackage):
     documents. Package vignettes illustrate use and functionality."""
 
     homepage = "https://www.bioconductor.org/packages/BiocStyle/"
-    url      = "https://git.bioconductor.org/packages/BiocStyle"
+    git      = "https://git.bioconductor.org/packages/BiocStyle.git"
 
-    version('2.4.1', git='https://git.bioconductor.org/packages/BiocStyle', commit='ef10764b68ac23a3a7a8ec3b6a6436187309c138')
+    version('2.4.1', commit='ef10764b68ac23a3a7a8ec3b6a6436187309c138')
 
     depends_on('r-bookdown', type=('build', 'run'))
     depends_on('r-knitr@1.12:', type=('build', 'run'))

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

@@ -40,10 +40,10 @@ class RBiomart(RPackage):
        online queries from gene annotation to database mining."""
 
     homepage = "https://bioconductor.org/packages/biomaRt/"
-    url      = "https://git.bioconductor.org/packages/biomaRt"
+    git      = "https://git.bioconductor.org/packages/biomaRt.git"
 
-    version('2.34.2', git='https://git.bioconductor.org/packages/biomaRt', commit='a7030915fbc6120cc6812aefdedba423a207459b')
+    version('2.34.2', commit='a7030915fbc6120cc6812aefdedba423a207459b')
-    version('2.32.1', git='https://git.bioconductor.org/packages/biomaRt', commit='f84d74424fa599f6d08f8db4612ca09914a9087f')
+    version('2.32.1', commit='f84d74424fa599f6d08f8db4612ca09914a9087f')
 
     depends_on('r-xml', type=('build', 'run'))
     depends_on('r-rcurl', type=('build', 'run'))

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

@@ -37,9 +37,9 @@ class RBiomformat(RPackage):
     as extensions of common core functions/methods."""
 
     homepage = "https://www.bioconductor.org/packages/biomformat/"
-    url      = "https://git.bioconductor.org/packages/biomformat"
+    git      = "https://git.bioconductor.org/packages/biomformat.git"
 
-    version('1.4.0', git='https://git.bioconductor.org/packages/biomformat', commit='83b4b1883bc56ea93a0a6ca90fc1b18712ef0f1a')
+    version('1.4.0', commit='83b4b1883bc56ea93a0a6ca90fc1b18712ef0f1a')
 
     depends_on('r-plyr', type=('build', 'run'))
     depends_on('r-jsonlite', type=('build', 'run'))

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

@@ -31,10 +31,9 @@ class RBiostrings(RPackage):
        or sets of sequences."""
 
     homepage = "https://bioconductor.org/packages/Biostrings/"
-    url      = "https://git.bioconductor.org/packages/Biostrings"
+    git      = "https://git.bioconductor.org/packages/Biostrings.git"
-    list_url = homepage
 
-    version('2.44.2', git='https://git.bioconductor.org/packages/Biostrings', commit='e4a2b320fb21c5cab3ece7b3c6fecaedfb1e5200')
+    version('2.44.2', commit='e4a2b320fb21c5cab3ece7b3c6fecaedfb1e5200')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))

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

@@ -33,9 +33,9 @@ class RBiovizbase(RPackage):
     and encourages consistency."""
 
     homepage = "http://bioconductor.org/packages/biovizBase/"
-    url      = "https://git.bioconductor.org/packages/biovizBase"
+    git      = "https://git.bioconductor.org/packages/biovizBase.git"
 
-    version('1.24.0', git='https://git.bioconductor.org/packages/biovizBase', commit='ae9cd2ff665b74a8f45ed9c1d17fc0a778b4af6c')
+    version('1.24.0', commit='ae9cd2ff665b74a8f45ed9c1d17fc0a778b4af6c')
 
     depends_on('r@3.4.0:3.4.9', when='@1.24.0')
     depends_on('r-scales', type=('build', 'run'))

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

@@ -30,11 +30,10 @@ class RBsgenome(RPackage):
        packages."""
 
     homepage = "https://www.bioconductor.org/packages/BSgenome/"
-    url      = "https://git.bioconductor.org/packages/BSgenome"
+    git      = "https://git.bioconductor.org/packages/BSgenome.git"
-    list_url = homepage
 
-    version('1.46.0', git='https://git.bioconductor.org/packages/BSgenome', commit='bdfbd6d09820993585b8231ddea5e11c99008dc5')
+    version('1.46.0', commit='bdfbd6d09820993585b8231ddea5e11c99008dc5')
-    version('1.44.2', git='https://git.bioconductor.org/packages/BSgenome', commit='105b00588a758d5ec7c347a7dff2756aea4516a0')
+    version('1.44.2', commit='105b00588a758d5ec7c347a7dff2756aea4516a0')
 
     depends_on('r-biocgenerics@0.13.8:', type=('build', 'run'))
     depends_on('r-s4vectors@0.9.36:', type=('build', 'run'))

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

@@ -29,10 +29,9 @@ class RBumphunter(RPackage):
     """Tools for finding bumps in genomic data"""
 
     homepage = "http://bioconductor.org/packages/bumphunter/"
-    url      = "https://git.bioconductor.org/packages/bumphunter"
+    git      = "https://git.bioconductor.org/packages/bumphunter.git"
-    list_url = homepage
 
-    version('1.16.0', git='https://git.bioconductor.org/packages/bumphunter', commit='1c3ab4d1fd2d75b1586ccef12665960b3602080a')
+    version('1.16.0', commit='1c3ab4d1fd2d75b1586ccef12665960b3602080a')
 
     depends_on('r-s4vectors', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))

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

@@ -29,9 +29,9 @@ class RCategory(RPackage):
     """A collection of tools for performing category analysis."""
 
     homepage = "https://www.bioconductor.org/packages/Category/"
-    url      = "https://git.bioconductor.org/packages/Category"
+    git      = "https://git.bioconductor.org/packages/Category.git"
 
-    version('2.42.1', git='https://git.bioconductor.org/packages/Category', commit='382c817a2371671a72f8f949dfb4050361ebabcd')
+    version('2.42.1', commit='382c817a2371671a72f8f949dfb4050361ebabcd')
 
     depends_on('r@3.4.0:3.4.9', when='@2.42.1')
     depends_on('r-biocgenerics', type=('build', 'run'))

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

@@ -30,9 +30,9 @@ class RClusterprofiler(RPackage):
     profiles (GO and KEGG) of gene and gene clusters."""
 
     homepage = "https://www.bioconductor.org/packages/clusterProfiler/"
-    url      = "https://git.bioconductor.org/packages/clusterProfiler"
+    git      = "https://git.bioconductor.org/packages/clusterProfiler.git"
 
-    version('3.4.4', git='https://git.bioconductor.org/packages/clusterProfiler', commit='b86b00e8405fe130e439362651a5567736e2d9d7')
+    version('3.4.4', commit='b86b00e8405fe130e439362651a5567736e2d9d7')
 
     depends_on('r@3.4.0:3.4.9', when='@3.4.4')
     depends_on('r-tidyr', type=('build', 'run'))

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

@@ -30,9 +30,9 @@ class RCner(RPackage):
         conserved noncoding elements."""
 
     homepage = "https://bioconductor.org/packages/CNEr/"
-    url      = "https://git.bioconductor.org/packages/CNEr"
+    git      = "https://git.bioconductor.org/packages/CNEr.git"
 
-    version('1.14.0', git='https://git.bioconductor.org/packages/CNEr', commit='b8634d65c51728c815127e22b45eba7c9b9db897')
+    version('1.14.0', commit='b8634d65c51728c815127e22b45eba7c9b9db897')
 
     depends_on('r-biostrings@2.33.4:', type=('build', 'run'))
     depends_on('r-dbi@0.7:', type=('build', 'run'))

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

@@ -32,10 +32,9 @@ class RComplexheatmap(RPackage):
        multiple heatmaps and supports self-defined annotation graphics."""
 
     homepage = "https://bioconductor.org/packages/ComplexHeatmap/"
-    url      = "https://git.bioconductor.org/packages/ComplexHeatmap"
+    git      = "https://git.bioconductor.org/packages/ComplexHeatmap.git"
-    list_url = homepage
 
-    version('1.14.0', git='https://git.bioconductor.org/packages/ComplexHeatmap', commit='0acd8974fb5cedde8cd96efea6dfa39324d25b34')
+    version('1.14.0', commit='0acd8974fb5cedde8cd96efea6dfa39324d25b34')
 
     depends_on('r-circlize', type=('build', 'run'))
     depends_on('r-getoptlong', type=('build', 'run'))

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

@@ -43,11 +43,10 @@ class RDelayedarray(RPackage):
        frames."""
 
     homepage = "https://bioconductor.org/packages/DelayedArray/"
-    url      = "https://git.bioconductor.org/packages/DelayedArray"
+    git      = "https://git.bioconductor.org/packages/DelayedArray.git"
-    list_url = homepage
 
-    version('0.4.1', git='https://git.bioconductor.org/packages/DelayedArray', commit='ffe932ef8c255614340e4856fc6e0b44128a27a1')
+    version('0.4.1', commit='ffe932ef8c255614340e4856fc6e0b44128a27a1')
-    version('0.2.7', git='https://git.bioconductor.org/packages/DelayedArray', commit='909c2ce1665ebae2543172ead50abbe10bd42bc4')
+    version('0.2.7', commit='909c2ce1665ebae2543172ead50abbe10bd42bc4')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-s4vectors@0.14.3:', type=('build', 'run'), when='@0.2.7')

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

@@ -32,9 +32,9 @@ class RDeseq(RPackage):
     distribution."""
 
     homepage = "https://www.bioconductor.org/packages/DESeq/"
-    url      = "https://git.bioconductor.org/packages/DESeq"
+    git      = "https://git.bioconductor.org/packages/DESeq.git"
 
-    version('1.28.0', git='https://git.bioconductor.org/packages/DESeq', commit='738371466e6ccf00179fd35b617c8ba0e1e91630')
+    version('1.28.0', commit='738371466e6ccf00179fd35b617c8ba0e1e91630')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))

var/spack/repos/builtin/packages/r-deseq2/package.py

@@ -32,10 +32,10 @@ class RDeseq2(RPackage):
     distribution."""
 
     homepage = "https://www.bioconductor.org/packages/DESeq2/"
-    url      = "https://git.bioconductor.org/packages/DESeq2"
+    git      = "https://git.bioconductor.org/packages/DESeq2.git"
 
-    version('1.18.1', git='https://git.bioconductor.org/packages/DESeq2', commit='ef65091d46436af68915124b752f5e1cc55e93a7')
+    version('1.18.1', commit='ef65091d46436af68915124b752f5e1cc55e93a7')
-    version('1.16.1', git='https://git.bioconductor.org/packages/DESeq2', commit='0a815574382704a08ef8b906eceb0296f81cded5')
+    version('1.16.1', commit='0a815574382704a08ef8b906eceb0296f81cded5')
 
     depends_on('r@3.4.0:3.4.9', when='@1.16.1:')
     depends_on("r-rcpparmadillo", type=('build', 'run'))

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

@@ -34,9 +34,9 @@ class RDirichletmultinomial(RPackage):
     further in the man page for this package, ?DirichletMultinomial."""
 
     homepage = "https://bioconductor.org/packages/DirichletMultinomial/"
-    url      = "https://git.bioconductor.org/packages/DirichletMultinomial"
+    git      = "https://git.bioconductor.org/packages/DirichletMultinomial.git"
 
-    version('1.20.0', git='https://git.bioconductor.org/packages/DirichletMultinomial', commit='251529f301da1482551142240aeb6baf8dab2272')
+    version('1.20.0', commit='251529f301da1482551142240aeb6baf8dab2272')
 
     depends_on('r-s4vectors', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))

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

@@ -31,6 +31,6 @@ class RDnacopy(RPackage):
     with abnormal copy number."""
 
     homepage = "https://www.bioconductor.org/packages/DNAcopy/"
-    url      = "https://git.bioconductor.org/packages/DNAcopy"
+    git      = "https://git.bioconductor.org/packages/DNAcopy.git"
 
-    version('1.50.1', git='https://git.bioconductor.org/packages/DNAcopy', commit='a20153029e28c009df813dbaf13d9f519fafa4e8')
+    version('1.50.1', commit='a20153029e28c009df813dbaf13d9f519fafa4e8')

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

@@ -34,9 +34,9 @@ class RDose(RPackage):
     biological data."""
 
     homepage = "https://www.bioconductor.org/packages/DOSE/"
-    url      = "https://git.bioconductor.org/packages/DOSE"
+    git      = "https://git.bioconductor.org/packages/DOSE.git"
 
-    version('3.2.0', git='https://git.bioconductor.org/packages/DOSE', commit='71f563fc39d02dfdf65184c94e0890a63b96b86b')
+    version('3.2.0', commit='71f563fc39d02dfdf65184c94e0890a63b96b86b')
 
     depends_on('r@3.4.0:3.4.9', when='@3.2.0')
     depends_on('r-scales', type=('build', 'run'))

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

@@ -35,10 +35,9 @@ class REdger(RPackage):
        SAGE and CAGE."""
 
     homepage = "https://bioconductor.org/packages/edgeR/"
-    url      = "https://git.bioconductor.org/packages/edgeR"
+    git      = "https://git.bioconductor.org/packages/edgeR.git"
-    list_url = homepage
 
-    version('3.18.1', git='https://git.bioconductor.org/packages/edgeR', commit='101106f3fdd9e2c45d4a670c88f64c12e97a0495')
+    version('3.18.1', commit='101106f3fdd9e2c45d4a670c88f64c12e97a0495')
 
     depends_on('r-limma', type=('build', 'run'))
     depends_on('r-locfit', type=('build', 'run'))

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

@@ -37,10 +37,9 @@ class REnsembldb(RPackage):
        region or transcript models of lincRNA genes."""
 
     homepage = "https://bioconductor.org/packages/ensembldb/"
-    url      = "https://git.bioconductor.org/packages/ensembldb"
+    git      = "https://git.bioconductor.org/packages/ensembldb.git"
-    list_url = homepage
 
-    version('2.0.4', git='https://git.bioconductor.org/packages/ensembldb', commit='514623d71e3cca7a4e547adb579b5a958702ef86')
+    version('2.0.4', commit='514623d71e3cca7a4e547adb579b5a958702ef86')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-genomicranges', type=('build', 'run'))

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

@@ -32,9 +32,9 @@ class RFgsea(RPackage):
     stantard approaches to multiple hypothesis correction."""
 
     homepage = "https://www.bioconductor.org/packages/fgsea/"
-    url      = "https://git.bioconductor.org/packages/fgsea"
+    git      = "https://git.bioconductor.org/packages/fgsea.git"
 
-    version('1.2.1', git='https://git.bioconductor.org/packages/fgsea', commit='99b04eef664204d0dca4b9f8027cd7eefb006b72')
+    version('1.2.1', commit='99b04eef664204d0dca4b9f8027cd7eefb006b72')
 
     depends_on('r@3.4.0:3.4.9', when='@1.2.1')
     depends_on('r-fastmatch', type=('build', 'run'))

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

@@ -29,10 +29,9 @@ class RGcrma(RPackage):
     """Background adjustment using sequence information"""
 
     homepage = "https://bioconductor.org/packages/gcrma/"
-    url      = "https://git.bioconductor.org/packages/gcrma"
+    git      = "https://git.bioconductor.org/packages/gcrma.git"
-    list_url = homepage
 
-    version('2.48.0', git='https://git.bioconductor.org/packages/gcrma', commit='3ea0eb0b5c15ffb24df76620667ae7996ed715b4')
+    version('2.48.0', commit='3ea0eb0b5c15ffb24df76620667ae7996ed715b4')
 
     depends_on('r-affy', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))

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

@@ -40,8 +40,8 @@ class RGdsfmt(RPackage):
        processes supported by the package parallel."""
 
     homepage = "http://bioconductor.org/packages/gdsfmt/"
-    url      = "https://git.bioconductor.org/packages/gdsfmt"
+    git      = "https://git.bioconductor.org/packages/gdsfmt.git"
 
-    version('1.14.1', git='https://git.bioconductor.org/packages/gdsfmt', commit='15743647b7eea5b82d3284858b4591fb6e59959d')
+    version('1.14.1', commit='15743647b7eea5b82d3284858b4591fb6e59959d')
 
     depends_on('r@3.4.0:3.4.9', when='@1.14.1')

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

@@ -29,9 +29,9 @@ class RGenefilter(RPackage):
     """Some basic functions for filtering genes"""
 
     homepage = "https://bioconductor.org/packages/genefilter/"
-    url      = "https://git.bioconductor.org/packages/genefilter"
+    git      = "https://git.bioconductor.org/packages/genefilter.git"
-    list_url = homepage
+
-    version('1.58.1', git='https://git.bioconductor.org/packages/genefilter', commit='ace2556049677f60882adfe91f8cc96791556fc2')
+    version('1.58.1', commit='ace2556049677f60882adfe91f8cc96791556fc2')
 
     depends_on('r@3.4.0:3.4.9', when='@1.58.1')
     depends_on('r-s4vectors', type=('build', 'run'))

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

@@ -29,9 +29,9 @@ class RGeneplotter(RPackage):
     """Functions for plotting genomic data."""
 
     homepage = "https://www.bioconductor.org/packages/geneplotter/"
-    url      = "https://git.bioconductor.org/packages/geneplotter"
+    git      = "https://git.bioconductor.org/packages/geneplotter.git"
 
-    version('1.54.0', git='https://git.bioconductor.org/packages/geneplotter', commit='efdd946e092e44e35fde1eb4bcc5ec1d52090940')
+    version('1.54.0', commit='efdd946e092e44e35fde1eb4bcc5ec1d52090940')
 
     depends_on('r@3.4.0:3.4.9', when='@1.54.0')
     depends_on('r-biobase', type=('build', 'run'))

var/spack/repos/builtin/packages/r-genie3/package.py

@@ -30,9 +30,9 @@ class RGenie3(RPackage):
     regulatory networks from expression data."""
 
     homepage = "https://bioconductor.org/packages/GENIE3/"
+    git      = "https://git.bioconductor.org/packages/GENIE3.git"
 
-    version('1.2.0', git='https://git.bioconductor.org/packages/GENIE3',
+    version('1.2.0', commit='cafe6a1a85095cda6cc3c812eb6f53501fcbaf93')
-            commit='cafe6a1a85095cda6cc3c812eb6f53501fcbaf93')
 
     depends_on('r-reshape2', type=('build', 'run'))
     depends_on('r@3.5.0:', when='@1.2.0')

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

@@ -32,11 +32,10 @@ class RGenomeinfodb(RPackage):
        names in their natural, rather than lexicographic, order."""
 
     homepage = "https://bioconductor.org/packages/GenomeInfoDb/"
-    url      = "https://git.bioconductor.org/packages/GenomeInfoDb"
+    git      = "https://git.bioconductor.org/packages/GenomeInfoDb.git"
-    list_url = homepage
 
-    version('1.14.0', git='https://git.bioconductor.org/packages/GenomeInfoDb', commit='4978308a57d887b764cc4ce83724ca1758f580f6')
+    version('1.14.0', commit='4978308a57d887b764cc4ce83724ca1758f580f6')
-    version('1.12.3', git='https://git.bioconductor.org/packages/GenomeInfoDb', commit='2deef3f0571b7f622483257bc22d2509ab5a0369')
+    version('1.12.3', commit='2deef3f0571b7f622483257bc22d2509ab5a0369')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))

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

@@ -32,11 +32,10 @@ class RGenomicalignments(RPackage):
     detection, and working with the nucleotide content of the alignments."""
 
     homepage = "https://bioconductor.org/packages/GenomicAlignments/"
-    url      = "https://git.bioconductor.org/packages/GenomicAlignments"
+    git      = "https://git.bioconductor.org/packages/GenomicAlignments.git"
-    list_url = homepage
 
-    version('1.14.2', git='https://git.bioconductor.org/packages/GenomicAlignments', commit='57b0b35d8b36069d4d94af86af051f0129b28eef')
+    version('1.14.2', commit='57b0b35d8b36069d4d94af86af051f0129b28eef')
-    version('1.12.2', git='https://git.bioconductor.org/packages/GenomicAlignments', commit='b5d6f19e4a89b6c1c3e9e58e5ea4eb13870874ef')
+    version('1.12.2', commit='b5d6f19e4a89b6c1c3e9e58e5ea4eb13870874ef')
 
     depends_on('r-biocgenerics@0.15.3:', type=('build', 'run'))
     depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))

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

@@ -36,10 +36,9 @@ class RGenomicfeatures(RPackage):
        desired features in a convenient format."""
 
     homepage = "http://bioconductor.org/packages/GenomicFeatures/"
-    url      = "https://git.bioconductor.org/packages/GenomicFeatures"
+    git      = "https://git.bioconductor.org/packages/GenomicFeatures.git"
-    list_url = homepage
 
-    version('1.28.5', git='https://git.bioconductor.org/packages/GenomicFeatures', commit='ba92381ae93cb1392dad5e6acfab8f6c1d744834')
+    version('1.28.5', commit='ba92381ae93cb1392dad5e6acfab8f6c1d744834')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))

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

@@ -38,11 +38,10 @@ class RGenomicranges(RPackage):
        infrastructure."""
 
     homepage = "https://bioconductor.org/packages/GenomicRanges/"
-    url      = "https://git.bioconductor.org/packages/GenomicRanges"
+    git      = "https://git.bioconductor.org/packages/GenomicRanges.git"
-    list_url = homepage
 
-    version('1.30.3', git='https://git.bioconductor.org/packages/GenomicRanges', commit='e99979054bc50ed8c0109bc54563036c1b368997')
+    version('1.30.3', commit='e99979054bc50ed8c0109bc54563036c1b368997')
-    version('1.28.6', git='https://git.bioconductor.org/packages/GenomicRanges', commit='197472d618f3ed04c795dc6ed435500c29619563')
+    version('1.28.6', commit='197472d618f3ed04c795dc6ed435500c29619563')
 
     depends_on('r-biocgenerics@0.21.2:', type=('build', 'run'))
     depends_on('r-s4vectors@0.9.47:', type=('build', 'run'))

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

@@ -32,10 +32,9 @@ class RGeoquery(RPackage):
        GEOquery is the bridge between GEO and BioConductor."""
 
     homepage = "https://bioconductor.org/packages/GEOquery/"
-    url      = "https://git.bioconductor.org/packages/GEOquery"
+    git      = "https://git.bioconductor.org/packages/GEOquery.git"
-    list_url = homepage
 
-    version('2.42.0', git='https://git.bioconductor.org/packages/GEOquery', commit='c26adef8d3ddbd6932a3170f2f84f6e4327641fb')
+    version('2.42.0', commit='c26adef8d3ddbd6932a3170f2f84f6e4327641fb')
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-xml', type=('build', 'run'))

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

@@ -37,10 +37,9 @@ class RGgbio(RPackage):
        and several splicing summaries."""
 
     homepage = "http://bioconductor.org/packages/ggbio/"
-    url      = "https://git.bioconductor.org/packages/ggbio"
+    git      = "https://git.bioconductor.org/packages/ggbio.git"
-    list_url = homepage
 
-    version('1.24.1', git='https://git.bioconductor.org/packages/ggbio', commit='ef04c1bca1330f37152bcc21080cbde94849a094')
+    version('1.24.1', commit='ef04c1bca1330f37152bcc21080cbde94849a094')
 
     depends_on('r-gridextra', type=('build', 'run'))
     depends_on('r-scales', type=('build', 'run'))

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

@@ -35,9 +35,9 @@ class RGosemsim(RPackage):
     Schlicker, Jiang, Lin and Wang respectively."""
 
     homepage = "https://www.bioconductor.org/packages/GOSemSim/"
-    url      = "https://git.bioconductor.org/packages/GOSemSim"
+    git      = "https://git.bioconductor.org/packages/GOSemSim.git"
 
-    version('2.2.0', git='https://git.bioconductor.org/packages/GOSemSim', commit='247434790e6c8cf99e5643f569390362b8c87c52')
+    version('2.2.0', commit='247434790e6c8cf99e5643f569390362b8c87c52')
 
     depends_on('r@3.4.0:3.4.9', when='@2.2.0')
     depends_on('r-annotationdbi', type=('build', 'run'))

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

@@ -31,9 +31,9 @@ class RGostats(RPackage):
     testing and other simple calculations."""
 
     homepage = "https://www.bioconductor.org/packages/GOstats/"
-    url      = "https://git.bioconductor.org/packages/GOstats"
+    git      = "https://git.bioconductor.org/packages/GOstats.git"
 
-    version('2.42.0', git='https://git.bioconductor.org/packages/GOstats', commit='8b29709064a3b66cf1d963b2be0c996fb48c873e')
+    version('2.42.0', commit='8b29709064a3b66cf1d963b2be0c996fb48c873e')
 
     depends_on('r@3.4.1:3.4.9', when='@2.42.0')
     depends_on('r-biobase', type=('build', 'run'))

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

@@ -29,9 +29,9 @@ class RGraph(RPackage):
     """A package that implements some simple graph handling capabilities."""
 
     homepage = "https://www.bioconductor.org/packages/graph/"
-    url      = "https://git.bioconductor.org/packages/graph"
+    git      = "https://git.bioconductor.org/packages/graph.git"
 
-    version('1.54.0', git='https://git.bioconductor.org/packages/graph', commit='2a8b08520096241620421078fc1098f4569c7301')
+    version('1.54.0', commit='2a8b08520096241620421078fc1098f4569c7301')
 
     depends_on('r@3.4.0:3.4.9', when='@1.54.0')
     depends_on('r-biocgenerics', type=('build', 'run'))

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

@@ -30,9 +30,9 @@ class RGseabase(RPackage):
     Set Enrichment Analysis (GSEA)."""
 
     homepage = "https://www.bioconductor.org/packages/GSEABase/"
-    url      = "https://git.bioconductor.org/packages/GSEABase"
+    git      = "https://git.bioconductor.org/packages/GSEABase.git"
 
-    version('1.38.2', git='https://git.bioconductor.org/packages/GSEABase', commit='84c9f10c316163118ca990900a7a67555b96e75b')
+    version('1.38.2', commit='84c9f10c316163118ca990900a7a67555b96e75b')
 
     depends_on('r@3.4.0:3.4.9', when='@1.38.2')
     depends_on('r-biocgenerics', type=('build', 'run'))

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

@@ -34,10 +34,9 @@ class RGtrellis(RPackage):
        graphics in the plot."""
 
     homepage = "https://bioconductor.org/packages/gtrellis/"
-    url      = "https://git.bioconductor.org/packages/gtrellis"
+    git      = "https://git.bioconductor.org/packages/gtrellis.git"
-    list_url = homepage
 
-    version('1.8.0', git='https://git.bioconductor.org/packages/gtrellis', commit='f813b420a008c459f63a2a13e5e64c5507c4c472')
+    version('1.8.0', commit='f813b420a008c459f63a2a13e5e64c5507c4c472')
 
     depends_on('r-iranges', type=('build', 'run'))
     depends_on('r-genomicranges', type=('build', 'run'))

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

@@ -35,9 +35,9 @@ class RGviz(RPackage):
     together with your data."""
 
     homepage = "http://bioconductor.org/packages/Gviz/"
-    url      = "https://git.bioconductor.org/packages/Gviz"
+    git      = "https://git.bioconductor.org/packages/Gviz.git"
 
-    version('1.20.0', git='https://git.bioconductor.org/packages/Gviz', commit='299b8255e1b03932cebe287c3690d58c88f5ba5c')
+    version('1.20.0', commit='299b8255e1b03932cebe287c3690d58c88f5ba5c')
 
     depends_on('r@3.4.0:3.4.9', when='@1.20.0')
     depends_on('r-s4vectors', type=('build', 'run'))

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

@@ -30,9 +30,9 @@ class RHypergraph(RPackage):
     representing and manipulating hypergraphs."""
 
     homepage = "https://www.bioconductor.org/packages/hypergraph/"
-    url      = "https://git.bioconductor.org/packages/hypergraph"
+    git      = "https://git.bioconductor.org/packages/hypergraph.git"
 
-    version('1.48.0', git='https://git.bioconductor.org/packages/hypergraph', commit='a4c19ea0b5f15204f706a7bfdea5363706382820')
+    version('1.48.0', commit='a4c19ea0b5f15204f706a7bfdea5363706382820')
 
     depends_on('r@3.4.0:3.4.9', when='@1.48.0')
     depends_on('r-graph', type=('build', 'run'))

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

@@ -30,10 +30,9 @@ class RIlluminaio(RPackage):
        IDAT."""
 
     homepage = "http://bioconductor.org/packages/illuminaio/"
-    url      = "https://git.bioconductor.org/packages/illuminaio"
+    git      = "https://git.bioconductor.org/packages/illuminaio.git"
-    list_url = homepage
 
-    version('0.18.0', git='https://git.bioconductor.org/packages/illuminaio', commit='e6b8ab1f8eacb760aebdb4828e9cfbf07da06eda')
+    version('0.18.0', commit='e6b8ab1f8eacb760aebdb4828e9cfbf07da06eda')
 
     depends_on('r-base64', type=('build', 'run'))
     depends_on('r@3.4.0:3.4.9', when='@0.18.0')

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

@@ -29,8 +29,8 @@ class RImpute(RPackage):
     """Imputation for microarray data (currently KNN only)."""
 
     homepage = "https://www.bioconductor.org/packages/impute/"
-    url      = "https://git.bioconductor.org/packages/impute"
+    git      = "https://git.bioconductor.org/packages/impute.git"
 
-    version('1.50.1', git='https://git.bioconductor.org/packages/impute', commit='31d1cc141797afdc83743e1d95aab8a90ee19b71')
+    version('1.50.1', commit='31d1cc141797afdc83743e1d95aab8a90ee19b71')
 
     depends_on('r@3.4.0:3.4.9', when='@1.50.1')

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

@@ -31,10 +31,9 @@ class RInteractivedisplaybase(RPackage):
        Bioconductor objects."""
 
     homepage = "https://bioconductor.org/packages/interactiveDisplayBase/"
-    url      = "https://git.bioconductor.org/packages/interactiveDisplayBase"
+    git      = "https://git.bioconductor.org/packages/interactiveDisplayBase.git"
-    list_url = homepage
 
-    version('1.14.0', git='https://git.bioconductor.org/packages/interactiveDisplayBase', commit='e2ccc7eefdd904e3b1032dc6b3f4a28d08c1cd40')
+    version('1.14.0', commit='e2ccc7eefdd904e3b1032dc6b3f4a28d08c1cd40')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-shiny', type=('build', 'run'))

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

@@ -38,11 +38,10 @@ class RIranges(RPackage):
     i.e., collections of atomic vectors and DataFrames."""
 
     homepage = "https://www.bioconductor.org/packages/IRanges/"
-    url      = "https://git.bioconductor.org/packages/IRanges"
+    git      = "https://git.bioconductor.org/packages/IRanges.git"
-    list_url = homepage
 
-    version('2.12.0', git='https://git.bioconductor.org/packages/IRanges', commit='1b1748655a8529ba87ad0f223f035ef0c08e7fcd')
+    version('2.12.0', commit='1b1748655a8529ba87ad0f223f035ef0c08e7fcd')
-    version('2.10.5', git='https://git.bioconductor.org/packages/IRanges', commit='b00d1d5025e3c480d17c13100f0da5a0132b1614')
+    version('2.10.5', commit='b00d1d5025e3c480d17c13100f0da5a0132b1614')
 
     depends_on('r-biocgenerics@0.21.1:', type=('build', 'run'), when='@2.10.5')
     depends_on('r-biocgenerics@0.23.3:', type=('build', 'run'), when='@2.12.0')

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

@@ -30,10 +30,9 @@ class RIrkernel(RPackage):
     """R kernel for Jupyter"""
 
     homepage = "https://irkernel.github.io/"
+    git      = "https://github.com/IRkernel/IRkernel.git"
 
-    # Git repository
+    version('master', tag='0.7')
-    version('master', git='https://github.com/IRkernel/IRkernel.git',
-        tag='0.7')
 
     depends_on('r-repr', type=('build', 'run'))
     depends_on('r-irdisplay', type=('build', 'run'))

var/spack/repos/builtin/packages/r-jaspar2018/package.py

@@ -30,8 +30,8 @@ class RJaspar2018(RPackage):
     please use the package TFBSTools (>= 1.15.6)."""
 
     homepage = "http://jaspar.genereg.net/"
-    url      = "https://git.bioconductor.org/packages/JASPAR2018"
+    git      = "https://git.bioconductor.org/packages/JASPAR2018.git"
 
-    version('1.0.0', git='https://git.bioconductor.org/packages/JASPAR2018', commit='4c84092b3737bb1c57ab56f4321f2f5e4b0efeaa')
+    version('1.0.0', commit='4c84092b3737bb1c57ab56f4321f2f5e4b0efeaa')
 
     depends_on('r@3.4.0:')

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

@@ -34,9 +34,9 @@ class RKegggraph(RPackage):
     etc."""
 
     homepage = "https://www.bioconductor.org/packages/KEGGgraph/"
-    url      = "https://git.bioconductor.org/packages/KEGGgraph"
+    git      = "https://git.bioconductor.org/packages/KEGGgraph.git"
 
-    version('1.38.1', git='https://git.bioconductor.org/packages/KEGGgraph', commit='dd31665beb36d5aad8ed09ed56c603633b6b2292')
+    version('1.38.1', commit='dd31665beb36d5aad8ed09ed56c603633b6b2292')
 
     depends_on('r-graph', type=('build', 'run'))
     depends_on('r-xml', type=('build', 'run'))

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

@@ -34,11 +34,10 @@ class RKeggrest(RPackage):
        catalogue) are provided."""
 
     homepage = "http://bioconductor.org/packages/KEGGREST"
-    url      = "https://git.bioconductor.org/packages/KEGGREST"
+    git      = "https://git.bioconductor.org/packages/KEGGREST.git"
-    list_url = homepage
 
-    version('1.18.1', git='https://git.bioconductor.org/packages/KEGGREST', commit='f6e6f1987e4db9d977a75609fab0cb710be2e2e4')
+    version('1.18.1', commit='f6e6f1987e4db9d977a75609fab0cb710be2e2e4')
-    version('1.2.0', git='https://git.bioconductor.org/packages/KEGGREST', commit='ed48de0def57a909894e237fa4731c4a052d8849')
+    version('1.2.0',  commit='ed48de0def57a909894e237fa4731c4a052d8849')
 
     depends_on('r-httr', type=('build', 'run'))
     depends_on('r-png', type=('build', 'run'))

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

@@ -30,11 +30,9 @@ class RLimma(RPackage):
     for microarray data."""
 
     homepage = "https://www.bioconductor.org/packages/limma/"
-    url      = "https://git.bioconductor.org/packages/limma"
+    git      = "https://git.bioconductor.org/packages/limma.git"
-    list_url = homepage
 
-    version('3.34.9', git='https://git.bioconductor.org/packages/limma', commit='6755278a929f942a49e2441fb002a3ed393e1139')
+    version('3.34.9',  commit='6755278a929f942a49e2441fb002a3ed393e1139')
-    version('3.32.10', git='https://git.bioconductor.org/packages/limma', commit='593edf28e21fe054d64137ae271b8a52ab05bc60')
+    version('3.32.10', commit='593edf28e21fe054d64137ae271b8a52ab05bc60')
-    version('3.32.6', 'df5dc2b85189a24e939efa3a8e6abc41')
 
     depends_on('r@3.4.0:3.4.9', when='@3.32.10:')

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

@@ -33,9 +33,9 @@ class RMakecdfenv(RPackage):
     that environment."""
 
     homepage = "https://www.bioconductor.org/packages/makecdfenv/"
-    url      = "https://git.bioconductor.org/packages/makecdfenv"
+    git      = "https://git.bioconductor.org/packages/makecdfenv.git"
 
-    version('1.52.0', git='https://git.bioconductor.org/packages/makecdfenv', commit='b88a3e93e3b7feeeca69eda7c1fc5a0826c81120')
+    version('1.52.0', commit='b88a3e93e3b7feeeca69eda7c1fc5a0826c81120')
 
     depends_on('r@3.4.0:3.4.9', when='@1.52.0')
     depends_on('r-affyio', type=('build', 'run'))

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

@@ -38,9 +38,9 @@ class RMergemaid(RPackage):
        cross-validate associations of gene expression data with survival."""
 
     homepage = "https://www.bioconductor.org/packages/MergeMaid/"
-    url      = "https://git.bioconductor.org/packages/MergeMaid"
+    git      = "https://git.bioconductor.org/packages/MergeMaid.git"
 
-    version('2.48.0', git='https://git.bioconductor.org/packages/MergeMaid', commit='aee89c523fcafff4c166ff3db4fff90df16a1ed4')
+    version('2.48.0', commit='aee89c523fcafff4c166ff3db4fff90df16a1ed4')
 
     depends_on('r-survival', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))

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

@@ -29,10 +29,9 @@ class RMinfi(RPackage):
     """Tools to analyze & visualize Illumina Infinium methylation arrays."""
 
     homepage = "https://bioconductor.org/packages/minfi/"
-    url      = "https://git.bioconductor.org/packages/minfi"
+    git      = "https://git.bioconductor.org/packages/minfi.git"
-    list_url = homepage
 
-    version('1.22.1', git='https://git.bioconductor.org/packages/minfi', commit='b2faf84bcbb291e32d470a0e029450093527545b')
+    version('1.22.1', commit='b2faf84bcbb291e32d470a0e029450093527545b')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-genomicranges', type=('build', 'run'))

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

@@ -30,9 +30,9 @@ class RMlinterfaces(RPackage):
     code for data in R and Bioconductor containers."""
 
     homepage = "https://www.bioconductor.org/packages/MLInterfaces/"
-    url      = "https://git.bioconductor.org/packages/MLInterfaces"
+    git      = "https://git.bioconductor.org/packages/MLInterfaces.git"
 
-    version('1.56.0', git='https://git.bioconductor.org/packages/MLInterfaces', commit='31fe6fb20d859fcb01d5552f42bca6bab16cc67f')
+    version('1.56.0', commit='31fe6fb20d859fcb01d5552f42bca6bab16cc67f')
 
     depends_on('r@3.4.0:3.4.9', when='@1.56.0')
     depends_on('r-biocgenerics', type=('build', 'run'))