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

author: Adam J. Stewart <ajstewart426@gmail.com> 2018-07-23 21:56:48 -0500
committer: Todd Gamblin <tgamblin@llnl.gov> 2018-07-25 23:10:10 -0700
commit: a1572bb9991fc8fd8aa5a2d9a17f3b978a0d0bb6 (patch)
tree: 1782f43a822d9c9c6e35bb674b04d59ed4b9a4c5 /var
parent: 908d2dcd4d3e5aac2e5cc7f357015982247141ab (diff)
download: spack-a1572bb9991fc8fd8aa5a2d9a17f3b978a0d0bb6.tar.gz
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141 files changed, 307 insertions, 360 deletions
diff --git a/var/spack/repos/builtin/packages/r-a4/package.py b/var/spack/repos/builtin/packages/r-a4/package.py
index 312df82954..b32540f771 100644
--- a/var/spack/repos/builtin/packages/r-a4/package.py
+++ b/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"
-    list_url = homepage
-    version('1.24.0', git='https://git.bioconductor.org/packages/a4', commit='79b5143652176787c85a0d587b3bbfad6b4a19f4')
+    git      = "https://git.bioconductor.org/packages/a4.git"
+
+    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'))
diff --git a/var/spack/repos/builtin/packages/r-a4base/package.py b/var/spack/repos/builtin/packages/r-a4base/package.py
index 3eaf8fa1cf..7bc66f0db6 100644
--- a/var/spack/repos/builtin/packages/r-a4base/package.py
+++ b/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'"
-    list_url = homepage
-    version('1.24.0', git='https://git.bioconductor.org/packages/a4Base', commit='f674afe424a508df2c8ee6c87a06fbd4aa410ef6')
+    git      = "https://git.bioconductor.org/packages/a4Base.git"
+
+    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'))
diff --git a/var/spack/repos/builtin/packages/r-a4classif/package.py b/var/spack/repos/builtin/packages/r-a4classif/package.py
index 2f7d609d0c..75d87a3b0b 100644
--- a/var/spack/repos/builtin/packages/r-a4classif/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/a4Classif.git"
 
-    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'))
diff --git a/var/spack/repos/builtin/packages/r-a4core/package.py b/var/spack/repos/builtin/packages/r-a4core/package.py
index ab35a2f241..8079871158 100644
--- a/var/spack/repos/builtin/packages/r-a4core/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-a4preproc/package.py b/var/spack/repos/builtin/packages/r-a4preproc/package.py
index a03ce0e524..8517e776a5 100644
--- a/var/spack/repos/builtin/packages/r-a4preproc/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-a4reporting/package.py b/var/spack/repos/builtin/packages/r-a4reporting/package.py
index 091da1f5d1..7a02e9a800 100644
--- a/var/spack/repos/builtin/packages/r-a4reporting/package.py
+++ b/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"
-    list_url = homepage
-    version('1.24.0', git='https://git.bioconductor.org/packages/a4Reporting', commit='bf22c4d50daf40fc9eaf8c476385bf4a24a5b5ce')
+    git      = "https://git.bioconductor.org/packages/a4Reporting.git"
+
+    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'))
diff --git a/var/spack/repos/builtin/packages/r-abaenrichment/package.py b/var/spack/repos/builtin/packages/r-abaenrichment/package.py
index 50b2e64a69..7be6dbb13f 100644
--- a/var/spack/repos/builtin/packages/r-abaenrichment/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-absseq/package.py b/var/spack/repos/builtin/packages/r-absseq/package.py
index 72c825df6b..39cf5800d1 100644
--- a/var/spack/repos/builtin/packages/r-absseq/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-acgh/package.py b/var/spack/repos/builtin/packages/r-acgh/package.py
index ee941c33d2..a929fe6781 100644
--- a/var/spack/repos/builtin/packages/r-acgh/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-acme/package.py b/var/spack/repos/builtin/packages/r-acme/package.py
index d815249e48..ef04920ff0 100644
--- a/var/spack/repos/builtin/packages/r-acme/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-adsplit/package.py b/var/spack/repos/builtin/packages/r-adsplit/package.py
index 4405026fd2..0839856872 100644
--- a/var/spack/repos/builtin/packages/r-adsplit/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-affxparser/package.py b/var/spack/repos/builtin/packages/r-affxparser/package.py
index fc36c42cfa..1440802f23 100644
--- a/var/spack/repos/builtin/packages/r-affxparser/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/affxparser.git"
 
-    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')
diff --git a/var/spack/repos/builtin/packages/r-affy/package.py b/var/spack/repos/builtin/packages/r-affy/package.py
index 5b169f8175..2d1637673a 100644
--- a/var/spack/repos/builtin/packages/r-affy/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/affy.git"
 
-    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'))
diff --git a/var/spack/repos/builtin/packages/r-affycomp/package.py b/var/spack/repos/builtin/packages/r-affycomp/package.py
index 8d023f346e..d153ad2052 100644
--- a/var/spack/repos/builtin/packages/r-affycomp/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-affycompatible/package.py b/var/spack/repos/builtin/packages/r-affycompatible/package.py
index 3747cb7649..9499c20ab0 100644
--- a/var/spack/repos/builtin/packages/r-affycompatible/package.py
+++ b/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')
 
diff --git a/var/spack/repos/builtin/packages/r-affycontam/package.py b/var/spack/repos/builtin/packages/r-affycontam/package.py
index 1c39f1f357..994684e1c7 100644
--- a/var/spack/repos/builtin/packages/r-affycontam/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-affycoretools/package.py b/var/spack/repos/builtin/packages/r-affycoretools/package.py
index 1e838948b3..4156c9d460 100644
--- a/var/spack/repos/builtin/packages/r-affycoretools/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-affyexpress/package.py b/var/spack/repos/builtin/packages/r-affyexpress/package.py
index e5e591eb91..2077f01377 100644
--- a/var/spack/repos/builtin/packages/r-affyexpress/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-affyilm/package.py b/var/spack/repos/builtin/packages/r-affyilm/package.py
index 946785eb6f..5be8e7e95d 100644
--- a/var/spack/repos/builtin/packages/r-affyilm/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-affyio/package.py b/var/spack/repos/builtin/packages/r-affyio/package.py
index 5e3d66dbfb..2950776157 100644
--- a/var/spack/repos/builtin/packages/r-affyio/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/affyio.git"
+
+    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')
diff --git a/var/spack/repos/builtin/packages/r-affypdnn/package.py b/var/spack/repos/builtin/packages/r-affypdnn/package.py
index 24442119f6..e08b6a5bad 100644
--- a/var/spack/repos/builtin/packages/r-affypdnn/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-affyplm/package.py b/var/spack/repos/builtin/packages/r-affyplm/package.py
index 57f7c1ba44..ac52e2fba3 100644
--- a/var/spack/repos/builtin/packages/r-affyplm/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-affyqcreport/package.py b/var/spack/repos/builtin/packages/r-affyqcreport/package.py
index 8b87830561..d983861890 100644
--- a/var/spack/repos/builtin/packages/r-affyqcreport/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py b/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py
index d05f8965c6..0201cb6324 100644
--- a/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-agdex/package.py b/var/spack/repos/builtin/packages/r-agdex/package.py
index 64a9a4f229..6872f56642 100644
--- a/var/spack/repos/builtin/packages/r-agdex/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-agilp/package.py b/var/spack/repos/builtin/packages/r-agilp/package.py
index e4ab94f979..a89ef223d4 100644
--- a/var/spack/repos/builtin/packages/r-agilp/package.py
+++ b/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')
diff --git a/var/spack/repos/builtin/packages/r-agimicrorna/package.py b/var/spack/repos/builtin/packages/r-agimicrorna/package.py
index e5b17dc0ef..e311c4a32e 100644
--- a/var/spack/repos/builtin/packages/r-agimicrorna/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-aims/package.py b/var/spack/repos/builtin/packages/r-aims/package.py
index fc7883f7f7..e0b132f85d 100644
--- a/var/spack/repos/builtin/packages/r-aims/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-aldex2/package.py b/var/spack/repos/builtin/packages/r-aldex2/package.py
index 80a9fd07ba..6305c13b49 100644
--- a/var/spack/repos/builtin/packages/r-aldex2/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-allelicimbalance/package.py b/var/spack/repos/builtin/packages/r-allelicimbalance/package.py
index 961c07a0c8..b3440cd6fd 100644
--- a/var/spack/repos/builtin/packages/r-allelicimbalance/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-alpine/package.py b/var/spack/repos/builtin/packages/r-alpine/package.py
index 100008c502..9f7e5dc9b6 100644
--- a/var/spack/repos/builtin/packages/r-alpine/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-alsace/package.py b/var/spack/repos/builtin/packages/r-alsace/package.py
index aebffee9ac..401e2ce380 100644
--- a/var/spack/repos/builtin/packages/r-alsace/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-altcdfenvs/package.py b/var/spack/repos/builtin/packages/r-altcdfenvs/package.py
index 78d661cce6..e994ee1949 100644
--- a/var/spack/repos/builtin/packages/r-altcdfenvs/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-ampliqueso/package.py b/var/spack/repos/builtin/packages/r-ampliqueso/package.py
index d6f5b6899f..47239e3cef 100644
--- a/var/spack/repos/builtin/packages/r-ampliqueso/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-analysispageserver/package.py b/var/spack/repos/builtin/packages/r-analysispageserver/package.py
index 401cc4cedb..59f3d906e4 100644
--- a/var/spack/repos/builtin/packages/r-analysispageserver/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-anaquin/package.py b/var/spack/repos/builtin/packages/r-anaquin/package.py
index 21938a4ea3..2436acfd51 100644
--- a/var/spack/repos/builtin/packages/r-anaquin/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-aneufinder/package.py b/var/spack/repos/builtin/packages/r-aneufinder/package.py
index 9113851ff8..d01f13f333 100644
--- a/var/spack/repos/builtin/packages/r-aneufinder/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-aneufinderdata/package.py b/var/spack/repos/builtin/packages/r-aneufinderdata/package.py
index 7482c6c83a..f6c6279ad5 100644
--- a/var/spack/repos/builtin/packages/r-aneufinderdata/package.py
+++ b/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')
diff --git a/var/spack/repos/builtin/packages/r-annaffy/package.py b/var/spack/repos/builtin/packages/r-annaffy/package.py
index 4769d335c5..9968fcea04 100644
--- a/var/spack/repos/builtin/packages/r-annaffy/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-annotate/package.py b/var/spack/repos/builtin/packages/r-annotate/package.py
index dc07740c87..0f4960a4e6 100644
--- a/var/spack/repos/builtin/packages/r-annotate/package.py
+++ b/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"
-    list_url = homepage
-    version('1.54.0', git='https://git.bioconductor.org/packages/annotate', commit='860cc5b696795a31b18beaf4869f9c418d74549e')
+    git      = "https://git.bioconductor.org/packages/annotate.git"
+
+    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'))
diff --git a/var/spack/repos/builtin/packages/r-annotationdbi/package.py b/var/spack/repos/builtin/packages/r-annotationdbi/package.py
index da5b9d3186..28c833a33f 100644
--- a/var/spack/repos/builtin/packages/r-annotationdbi/package.py
+++ b/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"
-    list_url = homepage
-    version('1.38.2', git='https://git.bioconductor.org/packages/AnnotationDbi', commit='67d46facba8c15fa5f0eb47c4e39b53dbdc67c36')
+    git      = "https://git.bioconductor.org/packages/AnnotationDbi.git"
+
+    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'))
diff --git a/var/spack/repos/builtin/packages/r-annotationfilter/package.py b/var/spack/repos/builtin/packages/r-annotationfilter/package.py
index 072c43ab0d..3337589be8 100644
--- a/var/spack/repos/builtin/packages/r-annotationfilter/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/AnnotationFilter.git"
 
-    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'))
diff --git a/var/spack/repos/builtin/packages/r-annotationforge/package.py b/var/spack/repos/builtin/packages/r-annotationforge/package.py
index 12555c1138..bb1f91a579 100644
--- a/var/spack/repos/builtin/packages/r-annotationforge/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-annotationhub/package.py b/var/spack/repos/builtin/packages/r-annotationhub/package.py
index e4a42dce9e..5d93003cce 100644
--- a/var/spack/repos/builtin/packages/r-annotationhub/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/AnnotationHub.git"
 
-    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'))
diff --git a/var/spack/repos/builtin/packages/r-bamsignals/package.py b/var/spack/repos/builtin/packages/r-bamsignals/package.py
index abc3b50d96..3c354bc342 100644
--- a/var/spack/repos/builtin/packages/r-bamsignals/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-biobase/package.py b/var/spack/repos/builtin/packages/r-biobase/package.py
index ef6a84d090..e3cb9530dc 100644
--- a/var/spack/repos/builtin/packages/r-biobase/package.py
+++ b/var/spack/repos/builtin/packages/r-biobase/package.py
@@ -28,14 +28,13 @@ from spack import *
 
 class RBiobase(RPackage):
     """Functions that are needed by many other packages
- or which replace R functions."""
+    or which replace R functions."""
 
     homepage = "https://www.bioconductor.org/packages/Biobase/"
-    url      = "https://git.bioconductor.org/packages/Biobase"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/Biobase.git"
 
-    version('2.38.0', git='https://git.bioconductor.org/packages/Biobase', commit='83f89829e0278ac014b0bc6664e621ac147ba424')
-    version('2.36.2', git='https://git.bioconductor.org/packages/Biobase', commit='15f50912f3fa08ccb15c33b7baebe6b8a59ce075')
+    version('2.38.0', commit='83f89829e0278ac014b0bc6664e621ac147ba424')
+    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:')
diff --git a/var/spack/repos/builtin/packages/r-biocgenerics/package.py b/var/spack/repos/builtin/packages/r-biocgenerics/package.py
index cba33db40d..3366eef19b 100644
--- a/var/spack/repos/builtin/packages/r-biocgenerics/package.py
+++ b/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
+    git      = "https://git.bioconductor.org/packages/BiocGenerics.git"
 
-    version('0.24.0', git='https://git.bioconductor.org/packages/BiocGenerics', commit='3db111e8c1f876267da89f4f0c5406a9d5c31cd1')
-    version('0.22.1', git='https://git.bioconductor.org/packages/BiocGenerics', commit='9c90bb8926885289d596a81ff318ee3745cbb6ad')
+    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:')
diff --git a/var/spack/repos/builtin/packages/r-biocinstaller/package.py b/var/spack/repos/builtin/packages/r-biocinstaller/package.py
index afc83961e6..3cf25e679e 100644
--- a/var/spack/repos/builtin/packages/r-biocinstaller/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/BiocInstaller.git"
 
-    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')
diff --git a/var/spack/repos/builtin/packages/r-biocparallel/package.py b/var/spack/repos/builtin/packages/r-biocparallel/package.py
index cb2ac2e9a6..07106ce5a6 100644
--- a/var/spack/repos/builtin/packages/r-biocparallel/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/BiocParallel.git"
 
-    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'))
diff --git a/var/spack/repos/builtin/packages/r-biocstyle/package.py b/var/spack/repos/builtin/packages/r-biocstyle/package.py
index 51c02c7615..630f7ddab7 100644
--- a/var/spack/repos/builtin/packages/r-biocstyle/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-biomart/package.py b/var/spack/repos/builtin/packages/r-biomart/package.py
index d327e47ee7..2936418e3b 100644
--- a/var/spack/repos/builtin/packages/r-biomart/package.py
+++ b/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('2.32.1', git='https://git.bioconductor.org/packages/biomaRt', commit='f84d74424fa599f6d08f8db4612ca09914a9087f')
+    version('2.34.2', commit='a7030915fbc6120cc6812aefdedba423a207459b')
+    version('2.32.1', 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-biomformat/package.py b/var/spack/repos/builtin/packages/r-biomformat/package.py
index 545a61e582..f428f41a5a 100644
--- a/var/spack/repos/builtin/packages/r-biomformat/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-biostrings/package.py b/var/spack/repos/builtin/packages/r-biostrings/package.py
index f28424421c..8803843ea6 100644
--- a/var/spack/repos/builtin/packages/r-biostrings/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/Biostrings.git"
 
-    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'))
diff --git a/var/spack/repos/builtin/packages/r-biovizbase/package.py b/var/spack/repos/builtin/packages/r-biovizbase/package.py
index 239bb12164..ed61008d26 100644
--- a/var/spack/repos/builtin/packages/r-biovizbase/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-bsgenome/package.py b/var/spack/repos/builtin/packages/r-bsgenome/package.py
index 35eaf00e21..84f458d37e 100644
--- a/var/spack/repos/builtin/packages/r-bsgenome/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/BSgenome.git"
 
-    version('1.46.0', git='https://git.bioconductor.org/packages/BSgenome', commit='bdfbd6d09820993585b8231ddea5e11c99008dc5')
-    version('1.44.2', git='https://git.bioconductor.org/packages/BSgenome', commit='105b00588a758d5ec7c347a7dff2756aea4516a0')
+    version('1.46.0', commit='bdfbd6d09820993585b8231ddea5e11c99008dc5')
+    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'))
diff --git a/var/spack/repos/builtin/packages/r-bumphunter/package.py b/var/spack/repos/builtin/packages/r-bumphunter/package.py
index 36b2797233..825be998e3 100644
--- a/var/spack/repos/builtin/packages/r-bumphunter/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/bumphunter.git"
 
-    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'))
diff --git a/var/spack/repos/builtin/packages/r-category/package.py b/var/spack/repos/builtin/packages/r-category/package.py
index 42f08d3fa6..a262a4e91f 100644
--- a/var/spack/repos/builtin/packages/r-category/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-clusterprofiler/package.py b/var/spack/repos/builtin/packages/r-clusterprofiler/package.py
index 558dbfeefc..8df5fccb70 100644
--- a/var/spack/repos/builtin/packages/r-clusterprofiler/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-cner/package.py b/var/spack/repos/builtin/packages/r-cner/package.py
index 3af527dec1..77fd5f0274 100644
--- a/var/spack/repos/builtin/packages/r-cner/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-complexheatmap/package.py b/var/spack/repos/builtin/packages/r-complexheatmap/package.py
index 5645c1a269..1897595a28 100644
--- a/var/spack/repos/builtin/packages/r-complexheatmap/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/ComplexHeatmap.git"
 
-    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'))
diff --git a/var/spack/repos/builtin/packages/r-delayedarray/package.py b/var/spack/repos/builtin/packages/r-delayedarray/package.py
index 94aa4beeb2..0ffbd43dd7 100644
--- a/var/spack/repos/builtin/packages/r-delayedarray/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/DelayedArray.git"
 
-    version('0.4.1', git='https://git.bioconductor.org/packages/DelayedArray', commit='ffe932ef8c255614340e4856fc6e0b44128a27a1')
-    version('0.2.7', git='https://git.bioconductor.org/packages/DelayedArray', commit='909c2ce1665ebae2543172ead50abbe10bd42bc4')
+    version('0.4.1', commit='ffe932ef8c255614340e4856fc6e0b44128a27a1')
+    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')
diff --git a/var/spack/repos/builtin/packages/r-deseq/package.py b/var/spack/repos/builtin/packages/r-deseq/package.py
index d0d203b3ba..a9c378d294 100644
--- a/var/spack/repos/builtin/packages/r-deseq/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-deseq2/package.py b/var/spack/repos/builtin/packages/r-deseq2/package.py
index b9007190f2..ecdad2a563 100644
--- a/var/spack/repos/builtin/packages/r-deseq2/package.py
+++ b/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('1.16.1', git='https://git.bioconductor.org/packages/DESeq2', commit='0a815574382704a08ef8b906eceb0296f81cded5')
+    version('1.18.1', commit='ef65091d46436af68915124b752f5e1cc55e93a7')
+    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'))
diff --git a/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py b/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py
index 0414ef4fc3..2452277912 100644
--- a/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-dnacopy/package.py b/var/spack/repos/builtin/packages/r-dnacopy/package.py
index 5f19298098..b3428cd993 100644
--- a/var/spack/repos/builtin/packages/r-dnacopy/package.py
+++ b/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')
diff --git a/var/spack/repos/builtin/packages/r-dose/package.py b/var/spack/repos/builtin/packages/r-dose/package.py
index d55f02dd9b..aaeb05d532 100644
--- a/var/spack/repos/builtin/packages/r-dose/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-edger/package.py b/var/spack/repos/builtin/packages/r-edger/package.py
index 7eaf61ce86..a4840869b5 100644
--- a/var/spack/repos/builtin/packages/r-edger/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/edgeR.git"
 
-    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'))
diff --git a/var/spack/repos/builtin/packages/r-ensembldb/package.py b/var/spack/repos/builtin/packages/r-ensembldb/package.py
index 54928bafa2..3f02413dbc 100644
--- a/var/spack/repos/builtin/packages/r-ensembldb/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/ensembldb.git"
 
-    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'))
diff --git a/var/spack/repos/builtin/packages/r-fgsea/package.py b/var/spack/repos/builtin/packages/r-fgsea/package.py
index c3b7954b5c..da00f4b172 100644
--- a/var/spack/repos/builtin/packages/r-fgsea/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-gcrma/package.py b/var/spack/repos/builtin/packages/r-gcrma/package.py
index 9767371315..66a2e1f2e2 100644
--- a/var/spack/repos/builtin/packages/r-gcrma/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/gcrma.git"
 
-    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'))
diff --git a/var/spack/repos/builtin/packages/r-gdsfmt/package.py b/var/spack/repos/builtin/packages/r-gdsfmt/package.py
index 1e3aa44a6a..3df7379e38 100644
--- a/var/spack/repos/builtin/packages/r-gdsfmt/package.py
+++ b/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')
diff --git a/var/spack/repos/builtin/packages/r-genefilter/package.py b/var/spack/repos/builtin/packages/r-genefilter/package.py
index 65df911a9c..c7e1c13596 100644
--- a/var/spack/repos/builtin/packages/r-genefilter/package.py
+++ b/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"
-    list_url = homepage
-    version('1.58.1', git='https://git.bioconductor.org/packages/genefilter', commit='ace2556049677f60882adfe91f8cc96791556fc2')
+    git      = "https://git.bioconductor.org/packages/genefilter.git"
+
+    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'))
diff --git a/var/spack/repos/builtin/packages/r-geneplotter/package.py b/var/spack/repos/builtin/packages/r-geneplotter/package.py
index 1af12fddd0..a5b032a0c6 100644
--- a/var/spack/repos/builtin/packages/r-geneplotter/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-genie3/package.py b/var/spack/repos/builtin/packages/r-genie3/package.py
index 49dc72debc..cd61d010b7 100644
--- a/var/spack/repos/builtin/packages/r-genie3/package.py
+++ b/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',
-            commit='cafe6a1a85095cda6cc3c812eb6f53501fcbaf93')
+    version('1.2.0', commit='cafe6a1a85095cda6cc3c812eb6f53501fcbaf93')
 
     depends_on('r-reshape2', type=('build', 'run'))
     depends_on('r@3.5.0:', when='@1.2.0')
diff --git a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py
index 6619a0b59f..214f88e4d3 100644
--- a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/GenomeInfoDb.git"
 
-    version('1.14.0', git='https://git.bioconductor.org/packages/GenomeInfoDb', commit='4978308a57d887b764cc4ce83724ca1758f580f6')
-    version('1.12.3', git='https://git.bioconductor.org/packages/GenomeInfoDb', commit='2deef3f0571b7f622483257bc22d2509ab5a0369')
+    version('1.14.0', commit='4978308a57d887b764cc4ce83724ca1758f580f6')
+    version('1.12.3', commit='2deef3f0571b7f622483257bc22d2509ab5a0369')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-genomicalignments/package.py b/var/spack/repos/builtin/packages/r-genomicalignments/package.py
index 2c58758efb..1cf1580da5 100644
--- a/var/spack/repos/builtin/packages/r-genomicalignments/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/GenomicAlignments.git"
 
-    version('1.14.2', git='https://git.bioconductor.org/packages/GenomicAlignments', commit='57b0b35d8b36069d4d94af86af051f0129b28eef')
-    version('1.12.2', git='https://git.bioconductor.org/packages/GenomicAlignments', commit='b5d6f19e4a89b6c1c3e9e58e5ea4eb13870874ef')
+    version('1.14.2', commit='57b0b35d8b36069d4d94af86af051f0129b28eef')
+    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'))
diff --git a/var/spack/repos/builtin/packages/r-genomicfeatures/package.py b/var/spack/repos/builtin/packages/r-genomicfeatures/package.py
index 2b211c7c9f..06ff4cae60 100644
--- a/var/spack/repos/builtin/packages/r-genomicfeatures/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/GenomicFeatures.git"
 
-    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'))
diff --git a/var/spack/repos/builtin/packages/r-genomicranges/package.py b/var/spack/repos/builtin/packages/r-genomicranges/package.py
index d3941e81a6..2c3bd55ff1 100644
--- a/var/spack/repos/builtin/packages/r-genomicranges/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/GenomicRanges.git"
 
-    version('1.30.3', git='https://git.bioconductor.org/packages/GenomicRanges', commit='e99979054bc50ed8c0109bc54563036c1b368997')
-    version('1.28.6', git='https://git.bioconductor.org/packages/GenomicRanges', commit='197472d618f3ed04c795dc6ed435500c29619563')
+    version('1.30.3', commit='e99979054bc50ed8c0109bc54563036c1b368997')
+    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'))
diff --git a/var/spack/repos/builtin/packages/r-geoquery/package.py b/var/spack/repos/builtin/packages/r-geoquery/package.py
index b07978e7d4..1e5cd8469c 100644
--- a/var/spack/repos/builtin/packages/r-geoquery/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/GEOquery.git"
 
-    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'))
diff --git a/var/spack/repos/builtin/packages/r-ggbio/package.py b/var/spack/repos/builtin/packages/r-ggbio/package.py
index c10266a86c..9401e34441 100644
--- a/var/spack/repos/builtin/packages/r-ggbio/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/ggbio.git"
 
-    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'))
diff --git a/var/spack/repos/builtin/packages/r-gosemsim/package.py b/var/spack/repos/builtin/packages/r-gosemsim/package.py
index 9afc35eecb..c8861e4614 100644
--- a/var/spack/repos/builtin/packages/r-gosemsim/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-gostats/package.py b/var/spack/repos/builtin/packages/r-gostats/package.py
index 34388f93f1..b8ee160598 100644
--- a/var/spack/repos/builtin/packages/r-gostats/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-graph/package.py b/var/spack/repos/builtin/packages/r-graph/package.py
index 3368467674..0dbd4c25b6 100644
--- a/var/spack/repos/builtin/packages/r-graph/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-gseabase/package.py b/var/spack/repos/builtin/packages/r-gseabase/package.py
index a337d38e66..082d4ef382 100644
--- a/var/spack/repos/builtin/packages/r-gseabase/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-gtrellis/package.py b/var/spack/repos/builtin/packages/r-gtrellis/package.py
index b4a1d90fae..9fdc67a21e 100644
--- a/var/spack/repos/builtin/packages/r-gtrellis/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/gtrellis.git"
 
-    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'))
diff --git a/var/spack/repos/builtin/packages/r-gviz/package.py b/var/spack/repos/builtin/packages/r-gviz/package.py
index 4498f0fcf5..2ec7adc275 100644
--- a/var/spack/repos/builtin/packages/r-gviz/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-hypergraph/package.py b/var/spack/repos/builtin/packages/r-hypergraph/package.py
index 3e9c634c51..579c32f1cb 100644
--- a/var/spack/repos/builtin/packages/r-hypergraph/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-illuminaio/package.py b/var/spack/repos/builtin/packages/r-illuminaio/package.py
index 2653ffa8df..abcd2713d3 100644
--- a/var/spack/repos/builtin/packages/r-illuminaio/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/illuminaio.git"
 
-    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')
diff --git a/var/spack/repos/builtin/packages/r-impute/package.py b/var/spack/repos/builtin/packages/r-impute/package.py
index 7fa3459467..233ce1b3f7 100644
--- a/var/spack/repos/builtin/packages/r-impute/package.py
+++ b/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')
diff --git a/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py b/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py
index afe36cd49e..74aff4a11f 100644
--- a/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/interactiveDisplayBase.git"
 
-    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'))
diff --git a/var/spack/repos/builtin/packages/r-iranges/package.py b/var/spack/repos/builtin/packages/r-iranges/package.py
index d4375d7f8b..caed7081fd 100644
--- a/var/spack/repos/builtin/packages/r-iranges/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/IRanges.git"
 
-    version('2.12.0', git='https://git.bioconductor.org/packages/IRanges', commit='1b1748655a8529ba87ad0f223f035ef0c08e7fcd')
-    version('2.10.5', git='https://git.bioconductor.org/packages/IRanges', commit='b00d1d5025e3c480d17c13100f0da5a0132b1614')
+    version('2.12.0', commit='1b1748655a8529ba87ad0f223f035ef0c08e7fcd')
+    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')
diff --git a/var/spack/repos/builtin/packages/r-irkernel/package.py b/var/spack/repos/builtin/packages/r-irkernel/package.py
index 5c4707165c..cfda326326 100644
--- a/var/spack/repos/builtin/packages/r-irkernel/package.py
+++ b/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', git='https://github.com/IRkernel/IRkernel.git',
-        tag='0.7')
+    version('master', tag='0.7')
 
     depends_on('r-repr', type=('build', 'run'))
     depends_on('r-irdisplay', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-jaspar2018/package.py b/var/spack/repos/builtin/packages/r-jaspar2018/package.py
index 1e9e92afb8..a82aa89e8a 100644
--- a/var/spack/repos/builtin/packages/r-jaspar2018/package.py
+++ b/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:')
diff --git a/var/spack/repos/builtin/packages/r-kegggraph/package.py b/var/spack/repos/builtin/packages/r-kegggraph/package.py
index ba883e7e3c..579ce11f52 100644
--- a/var/spack/repos/builtin/packages/r-kegggraph/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-keggrest/package.py b/var/spack/repos/builtin/packages/r-keggrest/package.py
index 8f3c311265..573ca54a64 100644
--- a/var/spack/repos/builtin/packages/r-keggrest/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/KEGGREST.git"
 
-    version('1.18.1', git='https://git.bioconductor.org/packages/KEGGREST', commit='f6e6f1987e4db9d977a75609fab0cb710be2e2e4')
-    version('1.2.0', git='https://git.bioconductor.org/packages/KEGGREST', commit='ed48de0def57a909894e237fa4731c4a052d8849')
+    version('1.18.1', commit='f6e6f1987e4db9d977a75609fab0cb710be2e2e4')
+    version('1.2.0',  commit='ed48de0def57a909894e237fa4731c4a052d8849')
 
     depends_on('r-httr', type=('build', 'run'))
     depends_on('r-png', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-limma/package.py b/var/spack/repos/builtin/packages/r-limma/package.py
index 78d513b80c..f9fc1de8b0 100644
--- a/var/spack/repos/builtin/packages/r-limma/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/limma.git"
 
-    version('3.34.9', git='https://git.bioconductor.org/packages/limma', commit='6755278a929f942a49e2441fb002a3ed393e1139')
-    version('3.32.10', git='https://git.bioconductor.org/packages/limma', commit='593edf28e21fe054d64137ae271b8a52ab05bc60')
-    version('3.32.6', 'df5dc2b85189a24e939efa3a8e6abc41')
+    version('3.34.9',  commit='6755278a929f942a49e2441fb002a3ed393e1139')
+    version('3.32.10', commit='593edf28e21fe054d64137ae271b8a52ab05bc60')
 
     depends_on('r@3.4.0:3.4.9', when='@3.32.10:')
diff --git a/var/spack/repos/builtin/packages/r-makecdfenv/package.py b/var/spack/repos/builtin/packages/r-makecdfenv/package.py
index 749801b0d8..e78c88d9ee 100644
--- a/var/spack/repos/builtin/packages/r-makecdfenv/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-mergemaid/package.py b/var/spack/repos/builtin/packages/r-mergemaid/package.py
index bfec39da95..8a4dd4dcbf 100644
--- a/var/spack/repos/builtin/packages/r-mergemaid/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-minfi/package.py b/var/spack/repos/builtin/packages/r-minfi/package.py
index d659b95500..bb5d305752 100644
--- a/var/spack/repos/builtin/packages/r-minfi/package.py
+++ b/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"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/minfi.git"
 
-    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'))
diff --git a/var/spack/repos/builtin/packages/r-mlinterfaces/package.py b/var/spack/repos/builtin/packages/r-mlinterfaces/package.py
index c1d2c5cbcd..709a3754b7 100644
--- a/var/spack/repos/builtin/packages/r-mlinterfaces/package.py
+++ b/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'))
diff --git a/var/spack/repos/builtin/packages/r-msnbase/package.py b/var/spack/repos/builtin/packages/r-msnbase/package.py
index 7f20505f7b..d59737a8a9 100644
--- a/var/spack/repos/builtin/packages/r-msnbase/package.py
+++ b/var/spack/repos/builtin/packages/r-msnbase/package.py
@@ -30,9 +30,9 @@ class RMsnbase(RPackage):
        proteomics data."""
 
     homepage = "https://www.bioconductor.org/packages/MSnbase/"
-    url      = "https://git.bioconductor.org/packages/MSnbase"
+    git      = "https://git.bioconductor.org/packages/MSnbase.git"
 
-    version('2.2.0', git='https://git.bioconductor.org/packages/MSnbase', commit='d6e8fb7f106d05096fa9074da0f829ac8f02c197')
+    version('2.2.0', commit='d6e8fb7f106d05096fa9074da0f829ac8f02c197')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-multtest/package.py b/var/spack/repos/builtin/packages/r-multtest/package.py
index aa6676bffd..89739c78b7 100644
--- a/var/spack/repos/builtin/packages/r-multtest/package.py
+++ b/var/spack/repos/builtin/packages/r-multtest/package.py
@@ -29,9 +29,9 @@ class RMulttest(RPackage):
     """Resampling-based multiple hypothesis testing"""
 
     homepage = "https://www.bioconductor.org/packages/multtest/"
-    url      = "https://git.bioconductor.org/packages/multtest"
+    git      = "https://git.bioconductor.org/packages/multtest.git"
 
-    version('2.32.0', git='https://git.bioconductor.org/packages/multtest', commit='c5e890dfbffcc3a3f107303a24b6085614312f4a')
+    version('2.32.0', commit='c5e890dfbffcc3a3f107303a24b6085614312f4a')
 
     depends_on('r@3.4.0:3.4.9', when='@2.32.0')
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-mzid/package.py b/var/spack/repos/builtin/packages/r-mzid/package.py
index 3a866ff705..9abc4465c9 100644
--- a/var/spack/repos/builtin/packages/r-mzid/package.py
+++ b/var/spack/repos/builtin/packages/r-mzid/package.py
@@ -33,9 +33,9 @@ class RMzid(RPackage):
        supply an mzIdentML file so the problems can be fixed quickly."""
 
     homepage = "https://www.bioconductor.org/packages/mzID/"
-    url      = "https://git.bioconductor.org/packages/mzID"
+    git      = "https://git.bioconductor.org/packages/mzID.git"
 
-    version('1.14.0', git='https://git.bioconductor.org/packages/mzID', commit='1c53aa6523ae61d3ebb13381381fc119d6cc6115')
+    version('1.14.0', commit='1c53aa6523ae61d3ebb13381381fc119d6cc6115')
 
     depends_on('r-xml', type=('build', 'run'))
     depends_on('r-plyr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-mzr/package.py b/var/spack/repos/builtin/packages/r-mzr/package.py
index c429c9c97a..18c65bb1e3 100644
--- a/var/spack/repos/builtin/packages/r-mzr/package.py
+++ b/var/spack/repos/builtin/packages/r-mzr/package.py
@@ -34,9 +34,9 @@ class RMzr(RPackage):
        reading code has previously been used in XCMS."""
 
     homepage = "https://www.bioconductor.org/packages/mzR/"
-    url      = "https://git.bioconductor.org/packages/mzR"
+    git      = "https://git.bioconductor.org/packages/mzR.git"
 
-    version('2.10.0', git='https://git.bioconductor.org/packages/mzR', commit='a6168b68e48c281e88de9647254a8db1e21df388')
+    version('2.10.0', commit='a6168b68e48c281e88de9647254a8db1e21df388')
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-oligoclasses/package.py b/var/spack/repos/builtin/packages/r-oligoclasses/package.py
index 694277b30d..aee2afeb96 100644
--- a/var/spack/repos/builtin/packages/r-oligoclasses/package.py
+++ b/var/spack/repos/builtin/packages/r-oligoclasses/package.py
@@ -31,9 +31,9 @@ class ROligoclasses(RPackage):
     crlmm packages."""
 
     homepage = "https://www.bioconductor.org/packages/oligoClasses/"
-    url      = "https://git.bioconductor.org/packages/oligoClasses"
+    git      = "https://git.bioconductor.org/packages/oligoClasses.git"
 
-    version('1.38.0', git='https://git.bioconductor.org/packages/oligoClasses', commit='fe2bb7f02c7ed3cbd338254c27ceba6ff829a962')
+    version('1.38.0', commit='fe2bb7f02c7ed3cbd338254c27ceba6ff829a962')
 
     depends_on('r@3.4.0:3.4.9', when='@1.38.0')
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-organismdbi/package.py b/var/spack/repos/builtin/packages/r-organismdbi/package.py
index 7b6672122a..35a83281b2 100644
--- a/var/spack/repos/builtin/packages/r-organismdbi/package.py
+++ b/var/spack/repos/builtin/packages/r-organismdbi/package.py
@@ -31,10 +31,9 @@ class ROrganismdbi(RPackage):
        fact that each of these packages implements a select methods."""
 
     homepage = "https://bioconductor.org/packages/OrganismDbi/"
-    url      = "https://git.bioconductor.org/packages/OrganismDbi"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/OrganismDbi.git"
 
-    version('1.18.1', git='https://git.bioconductor.org/packages/OrganismDbi', commit='ba2d1237256805e935d9534a0c6f1ded07b42e95')
+    version('1.18.1', commit='ba2d1237256805e935d9534a0c6f1ded07b42e95')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-annotationdbi', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-pathview/package.py b/var/spack/repos/builtin/packages/r-pathview/package.py
index df01a762bb..d8539ccf7e 100644
--- a/var/spack/repos/builtin/packages/r-pathview/package.py
+++ b/var/spack/repos/builtin/packages/r-pathview/package.py
@@ -36,9 +36,9 @@ class RPathview(RPackage):
     tools for large-scale and fully automated analysis."""
 
     homepage = "https://www.bioconductor.org/packages/pathview/"
-    url      = "https://git.bioconductor.org/packages/pathview"
+    git      = "https://git.bioconductor.org/packages/pathview.git"
 
-    version('1.16.7', git='https://git.bioconductor.org/packages/pathview', commit='fc560ed15ef7393a73d35e714716cc24dc835339')
+    version('1.16.7', commit='fc560ed15ef7393a73d35e714716cc24dc835339')
 
     depends_on('r-keggrest', type=('build', 'run'))
     depends_on('r-png', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-pcamethods/package.py b/var/spack/repos/builtin/packages/r-pcamethods/package.py
index 46fb07ba13..7578de6421 100644
--- a/var/spack/repos/builtin/packages/r-pcamethods/package.py
+++ b/var/spack/repos/builtin/packages/r-pcamethods/package.py
@@ -37,9 +37,9 @@ class RPcamethods(RPackage):
        Physiology, Golm, Germany."""
 
     homepage = "http://bioconductor.org/packages/pcaMethods/"
-    url      = "https://git.bioconductor.org/packages/pcaMethods"
-    list_url = homepage
-    version('1.68.0', git='https://git.bioconductor.org/packages/pcaMethods', commit='c8d7c93dcaf7ef728f3d089ae5d55771b320bdab')
+    git      = "https://git.bioconductor.org/packages/pcaMethods.git"
+
+    version('1.68.0', commit='c8d7c93dcaf7ef728f3d089ae5d55771b320bdab')
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-phyloseq/package.py b/var/spack/repos/builtin/packages/r-phyloseq/package.py
index ee6be01977..b71670dc87 100644
--- a/var/spack/repos/builtin/packages/r-phyloseq/package.py
+++ b/var/spack/repos/builtin/packages/r-phyloseq/package.py
@@ -30,9 +30,9 @@ class RPhyloseq(RPackage):
     storage, analysis, and graphical display of microbiome census data."""
 
     homepage = "https://www.bioconductor.org/packages/phyloseq/"
-    url      = "https://git.bioconductor.org/packages/phyloseq"
+    git      = "https://git.bioconductor.org/packages/phyloseq.git"
 
-    version('1.20.0', git='https://git.bioconductor.org/packages/phyloseq', commit='107d1d5e3437a6e33982c06a548d3cc91df2a7e0')
+    version('1.20.0', commit='107d1d5e3437a6e33982c06a548d3cc91df2a7e0')
 
     depends_on('r@3.4.0:3.4.9', when='@1.20.0')
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-preprocesscore/package.py b/var/spack/repos/builtin/packages/r-preprocesscore/package.py
index b053574b48..3200115cc6 100644
--- a/var/spack/repos/builtin/packages/r-preprocesscore/package.py
+++ b/var/spack/repos/builtin/packages/r-preprocesscore/package.py
@@ -29,9 +29,8 @@ class RPreprocesscore(RPackage):
     """A library of core preprocessing routines"""
 
     homepage = "https://bioconductor.org/packages/preprocessCore/"
-    url      = "https://git.bioconductor.org/packages/preprocessCore"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/preprocessCore.git"
 
-    version('1.38.1', git='https://git.bioconductor.org/packages/preprocessCore', commit='c58cb4c720eda0f1c733b989b14912093a7c5fbc')
+    version('1.38.1', commit='c58cb4c720eda0f1c733b989b14912093a7c5fbc')
 
     depends_on('r@3.4.0:3.4.9', when='@1.38.1')
diff --git a/var/spack/repos/builtin/packages/r-protgenerics/package.py b/var/spack/repos/builtin/packages/r-protgenerics/package.py
index 4fbd0c4f63..c6f0c92322 100644
--- a/var/spack/repos/builtin/packages/r-protgenerics/package.py
+++ b/var/spack/repos/builtin/packages/r-protgenerics/package.py
@@ -29,9 +29,8 @@ class RProtgenerics(RPackage):
     """S4 generic functions needed by Bioconductor proteomics packages."""
 
     homepage = "https://bioconductor.org/packages/ProtGenerics/"
-    url      = "https://git.bioconductor.org/packages/ProtGenerics"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/ProtGenerics.git"
 
-    version('1.8.0', git='https://git.bioconductor.org/packages/ProtGenerics', commit='b2b3bb0938e20f58fca905f6870de7dbc9dfd7a3')
+    version('1.8.0', commit='b2b3bb0938e20f58fca905f6870de7dbc9dfd7a3')
 
     depends_on('r@3.4.0:3.4.9', when='@1.8.0')
diff --git a/var/spack/repos/builtin/packages/r-quantro/package.py b/var/spack/repos/builtin/packages/r-quantro/package.py
index 23b52f25f4..d8cbf0e8b2 100644
--- a/var/spack/repos/builtin/packages/r-quantro/package.py
+++ b/var/spack/repos/builtin/packages/r-quantro/package.py
@@ -34,10 +34,9 @@ class RQuantro(RPackage):
        user-defined groups."""
 
     homepage = "https://www.bioconductor.org/packages/quantro/"
-    url      = "https://git.bioconductor.org/packages/quantro"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/quantro.git"
 
-    version('1.10.0', git='https://git.bioconductor.org/packages/quantro', commit='111337c0aba052aa49c3d2e2d3042794b28858c9')
+    version('1.10.0', commit='111337c0aba052aa49c3d2e2d3042794b28858c9')
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-minfi', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-qvalue/package.py b/var/spack/repos/builtin/packages/r-qvalue/package.py
index d7e16d0634..e7a1b86400 100644
--- a/var/spack/repos/builtin/packages/r-qvalue/package.py
+++ b/var/spack/repos/builtin/packages/r-qvalue/package.py
@@ -41,9 +41,9 @@ class RQvalue(RPackage):
     and data mining."""
 
     homepage = "https://www.bioconductor.org/packages/qvalue/"
-    url      = "https://git.bioconductor.org/packages/qvalue"
+    git      = "https://git.bioconductor.org/packages/qvalue.git"
 
-    version('2.8.0', git='https://git.bioconductor.org/packages/qvalue', commit='c7bf3315619d42d800f57a36670c25a7495ded72')
+    version('2.8.0', commit='c7bf3315619d42d800f57a36670c25a7495ded72')
 
     depends_on('r@3.4.0:3.4.9', when='@2.8.0')
     depends_on('r-ggplot2', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rbgl/package.py b/var/spack/repos/builtin/packages/r-rbgl/package.py
index 235cc7b49b..c6c48d6973 100644
--- a/var/spack/repos/builtin/packages/r-rbgl/package.py
+++ b/var/spack/repos/builtin/packages/r-rbgl/package.py
@@ -30,9 +30,9 @@ class RRbgl(RPackage):
     algorithms contained in the BOOST library."""
 
     homepage = "https://www.bioconductor.org/packages/RBGL/"
-    url      = "https://git.bioconductor.org/packages/RBGL"
+    git      = "https://git.bioconductor.org/packages/RBGL.git"
 
-    version('1.52.0', git='https://git.bioconductor.org/packages/RBGL', commit='93e8fcfafec8f1cd5638fe30dc0f9506d15b49c0')
+    version('1.52.0', commit='93e8fcfafec8f1cd5638fe30dc0f9506d15b49c0')
 
     depends_on('r@3.4.0:3.4.9', when='@1.52.0')
     depends_on('r-graph', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-reportingtools/package.py b/var/spack/repos/builtin/packages/r-reportingtools/package.py
index 6a0835a129..e5b7962e5b 100644
--- a/var/spack/repos/builtin/packages/r-reportingtools/package.py
+++ b/var/spack/repos/builtin/packages/r-reportingtools/package.py
@@ -40,9 +40,9 @@ class RReportingtools(RPackage):
     site: http:// research-pub.gene.com/ReportingTools."""
 
     homepage = "https://bioconductor.org/packages/ReportingTools/"
-    url      = "https://git.bioconductor.org/packages/ReportingTools"
+    git      = "https://git.bioconductor.org/packages/ReportingTools.git"
 
-    version('2.16.0', git='https://git.bioconductor.org/packages/ReportingTools', commit='b1aa0ea302da7f2993ce8087b1d09c11ddf03663')
+    version('2.16.0', commit='b1aa0ea302da7f2993ce8087b1d09c11ddf03663')
 
     depends_on('r@3.4.0:3.4.9', when='@2.16.0')
     depends_on('r-knitr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rgraphviz/package.py b/var/spack/repos/builtin/packages/r-rgraphviz/package.py
index be4f12d535..1e9dd09edb 100644
--- a/var/spack/repos/builtin/packages/r-rgraphviz/package.py
+++ b/var/spack/repos/builtin/packages/r-rgraphviz/package.py
@@ -30,9 +30,9 @@ class RRgraphviz(RPackage):
     R graph objects from the graph package."""
 
     homepage = "http://bioconductor.org/packages/Rgraphviz/"
-    url      = "https://git.bioconductor.org/packages/Rgraphviz"
+    git      = "https://git.bioconductor.org/packages/Rgraphviz.git"
 
-    version('2.20.0', git='https://git.bioconductor.org/packages/Rgraphviz', commit='eface6298150667bb22eac672f1a45e52fbf8c90')
+    version('2.20.0', commit='eface6298150667bb22eac672f1a45e52fbf8c90')
 
     depends_on('r@3.4.0:3.4.9', when='@2.20.0')
     depends_on('r-graph', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rhdf5/package.py b/var/spack/repos/builtin/packages/r-rhdf5/package.py
index 24e9e7b81f..1fac7872d8 100644
--- a/var/spack/repos/builtin/packages/r-rhdf5/package.py
+++ b/var/spack/repos/builtin/packages/r-rhdf5/package.py
@@ -35,9 +35,9 @@ class RRhdf5(RPackage):
     applications work on datasets that are larger than the available RAM."""
 
     homepage = "https://www.bioconductor.org/packages/rhdf5/"
-    url      = "https://git.bioconductor.org/packages/rhdf5"
+    git      = "https://git.bioconductor.org/packages/rhdf5.git"
 
-    version('2.20.0', git='https://git.bioconductor.org/packages/rhdf5', commit='37b5165325062728bbec9167f89f5f4b794f30bc')
+    version('2.20.0', commit='37b5165325062728bbec9167f89f5f4b794f30bc')
 
     depends_on('r@3.4.0:3.4.9', when='@2.20.0')
     depends_on('r-zlibbioc', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rsamtools/package.py b/var/spack/repos/builtin/packages/r-rsamtools/package.py
index 0491c77933..0789fd3580 100644
--- a/var/spack/repos/builtin/packages/r-rsamtools/package.py
+++ b/var/spack/repos/builtin/packages/r-rsamtools/package.py
@@ -32,10 +32,9 @@ class RRsamtools(RPackage):
        indexed tab-delimited (tabix) files."""
 
     homepage = "https://bioconductor.org/packages/Rsamtools/"
-    url      = "https://git.bioconductor.org/packages/Rsamtools"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/Rsamtools.git"
 
-    version('1.28.0', git='https://git.bioconductor.org/packages/Rsamtools', commit='dfa5b6abef68175586f21add7927174786412472')
+    version('1.28.0', 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-rtracklayer/package.py b/var/spack/repos/builtin/packages/r-rtracklayer/package.py
index 171a49de82..3737eb5205 100644
--- a/var/spack/repos/builtin/packages/r-rtracklayer/package.py
+++ b/var/spack/repos/builtin/packages/r-rtracklayer/package.py
@@ -34,10 +34,9 @@ class RRtracklayer(RPackage):
        current viewport."""
 
     homepage = "http://bioconductor.org/packages/rtracklayer/"
-    url      = "https://git.bioconductor.org/packages/rtracklayer"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/rtracklayer.git"
 
-    version('1.36.6', git='https://git.bioconductor.org/packages/rtracklayer', commit='8c0ac7230f94e0c5a981acbb178c8de70e968131')
+    version('1.36.6', commit='8c0ac7230f94e0c5a981acbb178c8de70e968131')
 
     depends_on('r-xml', type=('build', 'run'))
     depends_on('r-biocgenerics', 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 d6b6293f99..d5d0e216ba 100644
--- a/var/spack/repos/builtin/packages/r-s4vectors/package.py
+++ b/var/spack/repos/builtin/packages/r-s4vectors/package.py
@@ -36,11 +36,10 @@ class RS4vectors(RPackage):
        package and in other Bioconductor infrastructure packages)."""
 
     homepage = "https://bioconductor.org/packages/S4Vectors/"
-    url      = "https://git.bioconductor.org/packages/S4Vectors"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/S4Vectors.git"
 
-    version('0.16.0', git='https://git.bioconductor.org/packages/S4Vectors', commit='00fec03fcbcb7cff37917fab0da28d91fdf9dc3d')
-    version('0.14.7', git='https://git.bioconductor.org/packages/S4Vectors', commit='40af17fe0b8e93b6a72fc787540d2961773b8e23')
+    version('0.16.0', commit='00fec03fcbcb7cff37917fab0da28d91fdf9dc3d')
+    version('0.14.7', commit='40af17fe0b8e93b6a72fc787540d2961773b8e23')
 
     depends_on('r-biocgenerics@0.21.1:', type=('build', 'run'), when='@0.14.7')
     depends_on('r-biocgenerics@0.23.3:', type=('build', 'run'), when='@0.16.0')
diff --git a/var/spack/repos/builtin/packages/r-seqlogo/package.py b/var/spack/repos/builtin/packages/r-seqlogo/package.py
index 07207b2b80..88d30f4e73 100644
--- a/var/spack/repos/builtin/packages/r-seqlogo/package.py
+++ b/var/spack/repos/builtin/packages/r-seqlogo/package.py
@@ -31,8 +31,8 @@ class RSeqlogo(RPackage):
        Stephens (1990)."""
 
     homepage = "https://bioconductor.org/packages/seqLogo/"
-    url      = "https://git.bioconductor.org/packages/seqLogo"
+    git      = "https://git.bioconductor.org/packages/seqLogo.git"
 
-    version('1.44.0', git='https://git.bioconductor.org/packages/seqLogo', commit='4cac14ff29f413d6de1a9944eb5d21bfe5045fac')
+    version('1.44.0', commit='4cac14ff29f413d6de1a9944eb5d21bfe5045fac')
 
     depends_on('r@3.4.3:3.4.9', when='@1.44.0')
diff --git a/var/spack/repos/builtin/packages/r-shortread/package.py b/var/spack/repos/builtin/packages/r-shortread/package.py
index b5a53d4c7c..db5dcc2877 100644
--- a/var/spack/repos/builtin/packages/r-shortread/package.py
+++ b/var/spack/repos/builtin/packages/r-shortread/package.py
@@ -34,9 +34,9 @@ class RShortread(RPackage):
     for early single-end, ungapped alignment formats."""
 
     homepage = "https://www.bioconductor.org/packages/ShortRead/"
-    url      = "https://git.bioconductor.org/packages/ShortRead"
+    git      = "https://git.bioconductor.org/packages/ShortRead.git"
 
-    version('1.34.2', git='https://git.bioconductor.org/packages/ShortRead', commit='25daac63b301df66a8ef6e98cc2977522c6786cd')
+    version('1.34.2', commit='25daac63b301df66a8ef6e98cc2977522c6786cd')
 
     depends_on('r@3.4.0:3.4.9', when='@1.34.2')
     depends_on('r-latticeextra', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-siggenes/package.py b/var/spack/repos/builtin/packages/r-siggenes/package.py
index b3f7786a18..8dec8aac97 100644
--- a/var/spack/repos/builtin/packages/r-siggenes/package.py
+++ b/var/spack/repos/builtin/packages/r-siggenes/package.py
@@ -32,10 +32,9 @@ class RSiggenes(RPackage):
        (EBAM)."""
 
     homepage = "http://bioconductor.org/packages/siggenes/"
-    url      = "https://git.bioconductor.org/packages/siggenes"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/siggenes.git"
 
-    version('1.50.0', git='https://git.bioconductor.org/packages/siggenes', commit='b1818f26e1449005ffd971df6bda8da0303080bc')
+    version('1.50.0', commit='b1818f26e1449005ffd971df6bda8da0303080bc')
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-multtest', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-simpleaffy/package.py b/var/spack/repos/builtin/packages/r-simpleaffy/package.py
index 627e8982c5..04e13e1913 100644
--- a/var/spack/repos/builtin/packages/r-simpleaffy/package.py
+++ b/var/spack/repos/builtin/packages/r-simpleaffy/package.py
@@ -33,10 +33,9 @@ class RSimpleaffy(RPackage):
        for generating high resolution journal figures..."""
 
     homepage = "http://bioconductor.org/packages/simpleaffy/"
-    url      = "https://git.bioconductor.org/packages/simpleaffy"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/simpleaffy.git"
 
-    version('2.52.0', git='https://git.bioconductor.org/packages/simpleaffy', commit='f2b43fb9b8e6fa4c03fe28b4efb3144a0a42a385')
+    version('2.52.0', 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-snprelate/package.py b/var/spack/repos/builtin/packages/r-snprelate/package.py
index ed97780f8a..5c5126b14e 100644
--- a/var/spack/repos/builtin/packages/r-snprelate/package.py
+++ b/var/spack/repos/builtin/packages/r-snprelate/package.py
@@ -44,9 +44,9 @@ class RSnprelate(RPackage):
        structural variation calls."""
 
     homepage = "https://bioconductor.org/packages/SNPRelate"
-    url      = "https://git.bioconductor.org/packages/SNPRelate"
+    git      = "https://git.bioconductor.org/packages/SNPRelate.git"
 
-    version('1.12.2', git='https://git.bioconductor.org/packages/SNPRelate', commit='dce2e2b6f36483a9f905bb5df6ae834a9f1136fe')
+    version('1.12.2', commit='dce2e2b6f36483a9f905bb5df6ae834a9f1136fe')
 
     depends_on('r@3.4.0:3.4.9', when='@1.12.2')
     depends_on('r-gdsfmt@1.8.3:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-somaticsignatures/package.py b/var/spack/repos/builtin/packages/r-somaticsignatures/package.py
index 7f3d2a9b58..cebb1f70e5 100644
--- a/var/spack/repos/builtin/packages/r-somaticsignatures/package.py
+++ b/var/spack/repos/builtin/packages/r-somaticsignatures/package.py
@@ -32,10 +32,9 @@ class RSomaticsignatures(RPackage):
        flexibility in the matrix decomposition algorithms."""
 
     homepage = "https://bioconductor.org/packages/SomaticSignatures/"
-    url      = "https://git.bioconductor.org/packages/SomaticSignatures"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/SomaticSignatures.git"
 
-    version('2.12.1', git='https://git.bioconductor.org/packages/SomaticSignatures', commit='932298c6877d076004de5541cec85a14e819517a')
+    version('2.12.1', commit='932298c6877d076004de5541cec85a14e819517a')
 
     depends_on('r-variantannotation', type=('build', 'run'))
     depends_on('r-genomicranges', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-spem/package.py b/var/spack/repos/builtin/packages/r-spem/package.py
index bcc7e4716e..b2c9761c95 100644
--- a/var/spack/repos/builtin/packages/r-spem/package.py
+++ b/var/spack/repos/builtin/packages/r-spem/package.py
@@ -30,10 +30,9 @@ class RSpem(RPackage):
     series data"""
 
     homepage = "https://bioconductor.org/packages/SPEM/"
-    url      = "https://git.bioconductor.org/packages/SPEM"
+    git      = "https://git.bioconductor.org/packages/SPEM.git"
 
-    version('1.18.0', git='https://git.bioconductor.org/packages/SPEM',
-            commit='3ab425dd9889885eac328d26b73366a875cd250b')
+    version('1.18.0', commit='3ab425dd9889885eac328d26b73366a875cd250b')
 
     depends_on('r-rsolnp', 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 f06523e96d..080765caeb 100644
--- a/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py
+++ b/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py
@@ -32,11 +32,10 @@ class RSummarizedexperiment(RPackage):
        represent samples."""
 
     homepage = "https://bioconductor.org/packages/SummarizedExperiment/"
-    url      = "https://git.bioconductor.org/packages/SummarizedExperiment"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/SummarizedExperiment.git"
 
-    version('1.8.1', git='https://git.bioconductor.org/packages/SummarizedExperiment', commit='9d8a29aa9c78bbc7dcc6472537e13fc0d11dc1f7')
-    version('1.6.5', git='https://git.bioconductor.org/packages/SummarizedExperiment', commit='ec69cd5cfbccaef148a9f6abdfb3e22e888695d0')
+    version('1.8.1', commit='9d8a29aa9c78bbc7dcc6472537e13fc0d11dc1f7')
+    version('1.6.5', commit='ec69cd5cfbccaef148a9f6abdfb3e22e888695d0')
 
     depends_on('r-genomicranges@1.27.22:', type=('build', 'run'), when='@1.6.5')
     depends_on('r-genomicranges@1.29.14:', type=('build', 'run'), when='@1.8.1')
diff --git a/var/spack/repos/builtin/packages/r-sva/package.py b/var/spack/repos/builtin/packages/r-sva/package.py
index 01531d8a01..60f4add8a2 100644
--- a/var/spack/repos/builtin/packages/r-sva/package.py
+++ b/var/spack/repos/builtin/packages/r-sva/package.py
@@ -29,9 +29,9 @@ class RSva(RPackage):
     """Surrogate Variable Analysis."""
 
     homepage = "https://www.bioconductor.org/packages/sva/"
-    url      = "https://git.bioconductor.org/packages/sva"
+    git      = "https://git.bioconductor.org/packages/sva.git"
 
-    version('3.24.4', git='https://git.bioconductor.org/packages/sva', commit='ed2ebb6e33374dc9ec50e6ea97cc1d9aef836c73')
+    version('3.24.4', commit='ed2ebb6e33374dc9ec50e6ea97cc1d9aef836c73')
 
     depends_on('r@3.4.0:3.4.9', when='@3.24.4')
     depends_on('r-mgcv', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-tfbstools/package.py b/var/spack/repos/builtin/packages/r-tfbstools/package.py
index 655b7a4044..0f65c3baef 100644
--- a/var/spack/repos/builtin/packages/r-tfbstools/package.py
+++ b/var/spack/repos/builtin/packages/r-tfbstools/package.py
@@ -41,9 +41,9 @@ class RTfbstools(RPackage):
        of de novo motif discovery software."""
 
     homepage = "http://bioconductor.org/packages/TFBSTools/"
-    url      = "https://git.bioconductor.org/packages/TFBSTools"
+    git      = "https://git.bioconductor.org/packages/TFBSTools.git"
 
-    version('1.16.0', git='https://git.bioconductor.org/packages/TFBSTools', commit='565436a5a674d4dea7279e796a20c5bd2034f65a')
+    version('1.16.0', commit='565436a5a674d4dea7279e796a20c5bd2034f65a')
 
     depends_on('r-biobase@2.28:', type=('build', 'run'))
     depends_on('r-biostrings@2.36.4:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-tmixclust/package.py b/var/spack/repos/builtin/packages/r-tmixclust/package.py
index d36787c8b9..cef3ccd5f3 100644
--- a/var/spack/repos/builtin/packages/r-tmixclust/package.py
+++ b/var/spack/repos/builtin/packages/r-tmixclust/package.py
@@ -33,10 +33,9 @@ class RTmixclust(RPackage):
     series datasets."""
 
     homepage = "https://bioconductor.org/packages/TMixClust/"
-    url      = "https://git.bioconductor.org/packages/TMixClust"
+    git      = "https://git.bioconductor.org/packages/TMixClust.git"
 
-    version('1.0.1', git='https://git.bioconductor.org/packages/TMixClust',
-            commit='0ac800210e3eb9da911767a80fb5582ab33c0cad')
+    version('1.0.1', commit='0ac800210e3eb9da911767a80fb5582ab33c0cad')
 
     depends_on('r-gss', type=('build', 'run'))
     depends_on('r-mvtnorm', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-topgo/package.py b/var/spack/repos/builtin/packages/r-topgo/package.py
index bf901d7a3a..c03a557806 100644
--- a/var/spack/repos/builtin/packages/r-topgo/package.py
+++ b/var/spack/repos/builtin/packages/r-topgo/package.py
@@ -32,10 +32,10 @@ class RTopgo(RPackage):
     between GO terms can be implemented and applied."""
 
     homepage = "https://www.bioconductor.org/packages/topGO/"
-    url      = "https://git.bioconductor.org/packages/topGO"
+    git      = "https://git.bioconductor.org/packages/topGO.git"
 
-    version('2.30.1', git='https://git.bioconductor.org/packages/topGO', commit='b1469ce1d198ccb73ef79ca22cab81659e16dbaa')
-    version('2.28.0', git='https://git.bioconductor.org/packages/topGO', commit='066a975d460046cce33fb27e74e6a0ebc33fd716')
+    version('2.30.1', commit='b1469ce1d198ccb73ef79ca22cab81659e16dbaa')
+    version('2.28.0', commit='066a975d460046cce33fb27e74e6a0ebc33fd716')
 
     depends_on('r@3.4.0:3.4.9')
     depends_on('r-dbi', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-variantannotation/package.py b/var/spack/repos/builtin/packages/r-variantannotation/package.py
index 66b4ff014d..e4fd563f54 100644
--- a/var/spack/repos/builtin/packages/r-variantannotation/package.py
+++ b/var/spack/repos/builtin/packages/r-variantannotation/package.py
@@ -30,10 +30,9 @@ class RVariantannotation(RPackage):
        outcomes."""
 
     homepage = "https://www.bioconductor.org/packages/VariantAnnotation/"
-    url      = "https://git.bioconductor.org/packages/VariantAnnotation"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/VariantAnnotation.git"
 
-    version('1.22.3', git='https://git.bioconductor.org/packages/VariantAnnotation', commit='3a91b6d4297aa416d5f056dec6f8925eb1a8eaee')
+    version('1.22.3', commit='3a91b6d4297aa416d5f056dec6f8925eb1a8eaee')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-genomeinfodb', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-vsn/package.py b/var/spack/repos/builtin/packages/r-vsn/package.py
index 20a761b1f9..b98a9db1bb 100644
--- a/var/spack/repos/builtin/packages/r-vsn/package.py
+++ b/var/spack/repos/builtin/packages/r-vsn/package.py
@@ -40,9 +40,9 @@ class RVsn(RPackage):
        differential transcription."""
 
     homepage = "https://www.bioconductor.org/packages/vsn/"
-    url      = "https://git.bioconductor.org/packages/vsn"
+    git      = "https://git.bioconductor.org/packages/vsn.git"
 
-    version('3.44.0', git='https://git.bioconductor.org/packages/vsn', commit='e54513fcdd07ccfb8094359e93cef145450f0ee0')
+    version('3.44.0', commit='e54513fcdd07ccfb8094359e93cef145450f0ee0')
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-affy', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-xde/package.py b/var/spack/repos/builtin/packages/r-xde/package.py
index baac09e451..f48b174e25 100644
--- a/var/spack/repos/builtin/packages/r-xde/package.py
+++ b/var/spack/repos/builtin/packages/r-xde/package.py
@@ -30,9 +30,9 @@ class RXde(RPackage):
        expression."""
 
     homepage = "https://www.bioconductor.org/packages/XDE/"
-    url      = "https://git.bioconductor.org/packages/XDE"
+    git      = "https://git.bioconductor.org/packages/XDE.git"
 
-    version('2.22.0', git='https://git.bioconductor.org/packages/XDE', commit='25bcec965ae42a410dd285a9db9be46d112d8e81')
+    version('2.22.0', commit='25bcec965ae42a410dd285a9db9be46d112d8e81')
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-xmapbridge/package.py b/var/spack/repos/builtin/packages/r-xmapbridge/package.py
index d36f6d4922..c098824fb4 100644
--- a/var/spack/repos/builtin/packages/r-xmapbridge/package.py
+++ b/var/spack/repos/builtin/packages/r-xmapbridge/package.py
@@ -30,9 +30,8 @@ class RXmapbridge(RPackage):
        exports plotting files in a suitable format."""
 
     homepage = "https://www.bioconductor.org/packages/xmapbridge/"
-    url      = "https://git.bioconductor.org/packages/xmapbridge"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/xmapbridge.git"
 
-    version('1.34.0', git='https://git.bioconductor.org/packages/xmapbridge', commit='f162e1f72ead5f5a1aede69032d5771a6572d965')
+    version('1.34.0', commit='f162e1f72ead5f5a1aede69032d5771a6572d965')
 
     depends_on('r@3.4.0:3.4.9', when='@1.34.0')
diff --git a/var/spack/repos/builtin/packages/r-xvector/package.py b/var/spack/repos/builtin/packages/r-xvector/package.py
index e30f302403..50b75182e1 100644
--- a/var/spack/repos/builtin/packages/r-xvector/package.py
+++ b/var/spack/repos/builtin/packages/r-xvector/package.py
@@ -30,10 +30,9 @@ class RXvector(RPackage):
        an R external pointer, or on disk)."""
 
     homepage = "https://bioconductor.org/packages/XVector/"
-    url      = "https://git.bioconductor.org/packages/XVector"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/XVector.git"
 
-    version('0.16.0', git='https://git.bioconductor.org/packages/XVector', commit='54615888e1a559da4a81de33e934fc0f1c3ad99f')
+    version('0.16.0', 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-yapsa/package.py b/var/spack/repos/builtin/packages/r-yapsa/package.py
index ffe5067227..99df404e06 100644
--- a/var/spack/repos/builtin/packages/r-yapsa/package.py
+++ b/var/spack/repos/builtin/packages/r-yapsa/package.py
@@ -34,10 +34,9 @@ class RYapsa(RPackage):
        catalogue) are provided."""
 
     homepage = "http://bioconductor.org/packages/YAPSA/"
-    url      = "https://git.bioconductor.org/packages/YAPSA"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/YAPSA.git"
 
-    version('1.2.0', git='https://git.bioconductor.org/packages/YAPSA', commit='320809b69e470e30a777a383f8341f93064ec24d')
+    version('1.2.0', commit='320809b69e470e30a777a383f8341f93064ec24d')
 
     depends_on('r-genomicranges', type=('build', 'run'))
     depends_on('r-ggplot2', 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 5d34329f90..f645ef4d4c 100644
--- a/var/spack/repos/builtin/packages/r-yaqcaffy/package.py
+++ b/var/spack/repos/builtin/packages/r-yaqcaffy/package.py
@@ -31,10 +31,9 @@ class RYaqcaffy(RPackage):
        reference datasets."""
 
     homepage = "http://bioconductor.org/packages/yaqcaffy/"
-    url      = "https://git.bioconductor.org/packages/yaqcaffy"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/yaqcaffy.git"
 
-    version('1.36.0', git='https://git.bioconductor.org/packages/yaqcaffy', commit='4d46fe77b2c8de2230a77b0c07dd5dd726e3abd6')
+    version('1.36.0', 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-yarn/package.py b/var/spack/repos/builtin/packages/r-yarn/package.py
index 6744f9cde1..16208137de 100644
--- a/var/spack/repos/builtin/packages/r-yarn/package.py
+++ b/var/spack/repos/builtin/packages/r-yarn/package.py
@@ -34,10 +34,9 @@ class RYarn(RPackage):
        sparsity found in very large RNA-seq experiments."""
 
     homepage = "https://bioconductor.org/packages/yarn/"
-    url      = "https://git.bioconductor.org/packages/yarn"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/yarn.git"
 
-    version('1.2.0', git='https://git.bioconductor.org/packages/yarn', commit='28af616ef8c27dcadf6568e276dea8465486a697')
+    version('1.2.0', commit='28af616ef8c27dcadf6568e276dea8465486a697')
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-biomart', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-zlibbioc/package.py b/var/spack/repos/builtin/packages/r-zlibbioc/package.py
index 408609875b..6ee69c0455 100644
--- a/var/spack/repos/builtin/packages/r-zlibbioc/package.py
+++ b/var/spack/repos/builtin/packages/r-zlibbioc/package.py
@@ -33,8 +33,8 @@ class RZlibbioc(RPackage):
        on use."""
 
     homepage = "http://bioconductor.org/packages/release/bioc/html/Zlibbioc.html"
-    url      = "https://git.bioconductor.org/packages/zlibbioc"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/zlibbioc.git"
+
+    version('1.22.0', commit='30377f830af2bc1ff17bbf3fdd2cb6442015fea5')
 
-    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')
author	Adam J. Stewart <ajstewart426@gmail.com>	2018-07-23 21:56:48 -0500
committer	Todd Gamblin <tgamblin@llnl.gov>	2018-07-25 23:10:10 -0700
commit	a1572bb9991fc8fd8aa5a2d9a17f3b978a0d0bb6 (patch)
tree	1782f43a822d9c9c6e35bb674b04d59ed4b9a4c5 /var
parent	908d2dcd4d3e5aac2e5cc7f357015982247141ab (diff)
download	spack-a1572bb9991fc8fd8aa5a2d9a17f3b978a0d0bb6.tar.gz spack-a1572bb9991fc8fd8aa5a2d9a17f3b978a0d0bb6.tar.bz2 spack-a1572bb9991fc8fd8aa5a2d9a17f3b978a0d0bb6.tar.xz spack-a1572bb9991fc8fd8aa5a2d9a17f3b978a0d0bb6.zip