diff options
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/spack/repos/builtin | |
parent | 908d2dcd4d3e5aac2e5cc7f357015982247141ab (diff) | |
download | spack-a1572bb9991fc8fd8aa5a2d9a17f3b978a0d0bb6.tar.gz spack-a1572bb9991fc8fd8aa5a2d9a17f3b978a0d0bb6.tar.bz2 spack-a1572bb9991fc8fd8aa5a2d9a17f3b978a0d0bb6.tar.xz spack-a1572bb9991fc8fd8aa5a2d9a17f3b978a0d0bb6.zip |
Add top-level attributes for git R (Bioconductor) packages
Diffstat (limited to 'var/spack/repos/builtin')
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') |