Replace git-based Bioconductor R packages (#12005)

* Replace git-based Bioconductor R packages

The current collection of bioconductor packages tend to have scattered
dependencies and missing versions. This commit replaces git-based
packages with tool-generated Spack package recipes with correct
dependencies and descriptions in place.

* Fix some broken package names, add periods to title docstrings

* r-clue: new package at 0.3-57

* r-genomeinfodbdata: add 1.2.1

* r-gofuncr: new package at 1.4.0

* r-pfam-db: add 3.8.2

* Add missed package r-genelendatabase

* update r-goseq package

* update r-glimma package

* update r-rots package

* r-org-hs-eg-db: add 3.8.2

* r-vgam: fix incorrect R version

* r-rnaseqmap: new package at 2.42.0

* r-rhdf5lib: new package at 1.6.0

* r-scrime: new package at 1.3.5

* r-delayedmatrixstats: new package at 1.6.0

* r-hdf5array: new package at 1.12.1

* r-biocfilecache: new package at 1.8.0

* r-ctc: add new versions, dependencies

* r-genemeta: new package at 1.56.0

* r-scrime: fix flake8

* r-ensembldb: add missing dependencies

* Added missing dependencies to packages with certain DESCRIPTIONS

* r-mapplots: new package at 1.5.1

* r-beachmat: new package at 2.0.0

* r-beeswarm: new package at 0.2.3

* r-biocneighbors: new package at 1.2.0

* r-biocsingular: new package at 1.0.0

* r-ecp: new package at 3.1.1

* r-enrichplot: new package at 1.4.0

* r-europepmc: new package at 0.3

* r-ggbeeswarm: new package at 0.6.0

* r-ggplotify: new package at 0.0.3

* r-ggraph: new package at 1.0.2

* r-gridgraphics: new package at 0.4-1

* r-rcppannoy: new package at 0.0.12

* r-rcpphnsw: new package at 0.1.0

* r-rsvd: new package at 1.0.1

* r-scater: new package at 1.12.2

* r-singlecellexperiment: new package at 1.6.0

* r-tximport: new package at 1.12.3

* r-upsetr: new package at 1.4.0

* r-vioplot: new package at 0.3.2

* r-readr: add 1.3.1

* r-matrixstats: add 0.54.0

* r-ecp: flake8 fix

* r-biocmanager: new package at 1.30.4

* update bioconductor packages requiring BiocManager, new versions

* r-lambda-r: add 1.2.3

* r-vegan: add 2.5-5

* r-cner, r-rcppannoy, r-reportingtools, r-rsvd: add missing newlines at EOF

* r-chemometrics: flake8 fixes

* r-vgam: flake8 fixes

* CRAN packages: use cloud.r-project.org

* Use DESCRIPTION for R version constraints over bioconductor releases

* Update missed packages ABAData, acde, affydata

* Update remaining missed packages

* bio: Drop 'when' clause from first checksummed versions

* bio: improve package description generation logic

* r-genomeinfodbdata: use explicit sha256 sums

* r-pfam-db: update dependencies, add 3.10.0

* update r-org-hs-eg-db

* r-dirichletmultinomial: re-add gsl

* r-polyclip: new package at 1.10-0

* r-farver: new package at 1.1.0

* r-tweenr: new package at 1.0.1

* r-ggforce: new package at 0.3.1

* r-ggforce: remove redundant dep

* r-ggraph: add missing deps

* r-rcpphnsw: remove redundant depends_on

* r-reportingtools: re-add r-r-utils dep

* r-rhdf5: add gmake dep

* r-rhtslib: add system dependencies

* r-rsamtools: add gmake dep

* r-farver: remove redundant dep

* r-tweenr: remove redundant dep

* r-variantannotation: add gmake dep

* r-rgraphviz: add graphviz dep

* r-vsn: correct r-hexbin constraint

* r-scater: fix obsolete deps

* r-variantannotation: fix gmake dep type

* r-scater: tighten R version constraints

* r-rsamtools: fix gmake dep type

* r-rhtslib: fix gmake dep type

* r-rhtslib: use xz over lzma

* r-rhdf5: fix gmake dep type

* r-farver: replace with newer recipe for 2.0.1

* r-mzr: remove old dependency

* r-reportingtools: remove builtin dependency

* r-mzr: add gmake dep

* r-rhtslib: make system libraries link deps

* r-genomeinfodbdata: fix R version constraints

* r-geoquery: remove old deps from new versions

* r-genomicfeatures: tighten r-rmysql dep

* r-ensembldb: tighten r-annotationhub dep

* r-complexheatmap: fix r-dendextend dep

* r-cner: fix utils dep name

* r-clusterprofiler: fix r-gosemsim version req

* r-biostrings: fix r-iranges version reqs

* r-rhdf5lib: add gmake dep

* r-oligoclasses: fix r-biocinstaller dep range

* r-organismdbi: fix r-biocinstaller dep range

* r-hdf5array: add gmake dep

* r-gtrellis: tighten r-circlize version req

* r-gostats: fix r-graph version req

* r-glimma: fix old dependency ranges

* r-biostrings: syntax fix

* r-organismdbi: syntax fix

* r-dose: fix r-igraph dep

* r-dose: fix r-scales, r-rvcheck deps

* r-affy: fix r-biocinstaller dep

* r-ampliqueso: fix homepage

* r-aneufinder: fix r-biocgenerics dep

* r-beachmat: fix changed deps

* r-biocneighbors: fix old R constraint

* r-biocmanager: rewrite recipe for 1.30.10

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/r-oligoclasses/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

1 files changed, 34 insertions, 25 deletions

diff --git a/var/spack/repos/builtin/packages/r-rtracklayer/package.py b/var/spack/repos/builtin/packages/r-rtracklayer/package.py
index e272d6a80d..a83f1ea5ec 100644
--- a/var/spack/repos/builtin/packages/r-rtracklayer/package.py
+++ b/var/spack/repos/builtin/packages/r-rtracklayer/package.py
@@ -7,39 +7,48 @@ from spack import *
 
 
 class RRtracklayer(RPackage):
-    """Extensible framework for interacting with multiple genome browsers
+    """R interface to genome annotation files and the UCSC genome browser.
+
+       Extensible framework for interacting with multiple genome browsers
        (currently UCSC built-in) and manipulating annotation tracks in various
        formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
        built-in). The user may export/import tracks to/from the supported
        browsers, as well as query and modify the browser state, such as the
        current viewport."""
 
-    homepage = "http://bioconductor.org/packages/rtracklayer/"
+    homepage = "https://bioconductor.org/packages/rtracklayer"
     git      = "https://git.bioconductor.org/packages/rtracklayer.git"
 
-    version('1.40.5', commit='4e5b06daccd0bca1ddcd93052deca896ade58fd6')
+    version('1.44.4', commit='aec96e85daf53b5c5eb2e89250d2755352be4de3')
+    version('1.42.2', commit='76702f671faea736807d54aeecfbadcd152d94c5')
+    version('1.40.6', commit='ba9a6e711504a702147383bc7abfcc36eb304df7')
+    version('1.38.3', commit='f20db703c09dc7e808c09e9b78c15aec9e546248')
     version('1.36.6', commit='8c0ac7230f94e0c5a981acbb178c8de70e968131')
 
-    depends_on('r-xml', type=('build', 'run'))
-    depends_on('r-biocgenerics', type=('build', 'run'))
-    depends_on('r-biocgenerics@0.25.1:', when='@1.40.5', type=('build', 'run'))
-    depends_on('r-s4vectors', type=('build', 'run'))
-    depends_on('r-s4vectors@0.17.25:', when='@1.40.5', type=('build', 'run'))
-    depends_on('r-iranges', type=('build', 'run'))
-    depends_on('r-iranges@2.13.13:', when='@1.40.5', type=('build', 'run'))
-    depends_on('r-xvector', type=('build', 'run'))
-    depends_on('r-xvector@0.19.7:', when='@1.40.5', type=('build', 'run'))
-    depends_on('r-genomeinfodb', type=('build', 'run'))
-    depends_on('r-genomeinfodb@1.15.2:', when='@1.40.5', type=('build', 'run'))
-    depends_on('r-biostrings', type=('build', 'run'))
-    depends_on('r-biostrings@2.47.6:', when='@1.40.5', type=('build', 'run'))
+    depends_on('r@3.3:', type=('build', 'run'))
+    depends_on('r-genomicranges@1.21.20:', type=('build', 'run'))
+    depends_on('r-xml@1.98-0:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.13.8:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
+    depends_on('r-iranges@2.3.7:', type=('build', 'run'))
+    depends_on('r-xvector@0.9.4:', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.3.14:', type=('build', 'run'))
+    depends_on('r-biostrings@2.43.7:', type=('build', 'run'))
     depends_on('r-zlibbioc', type=('build', 'run'))
-    depends_on('r-rcurl', type=('build', 'run'))
-    depends_on('r-rsamtools', type=('build', 'run'))
-    depends_on('r-rsamtools@1.31.2:', when='@1.40.5', type=('build', 'run'))
-    depends_on('r-genomicalignments', type=('build', 'run'))
-    depends_on('r-genomicalignments@1.15.6:', when='@1.40.5', type=('build', 'run'))
-    depends_on('r-genomicranges@1.21.20:', when='@1.36.3', type=('build', 'run'))
-    depends_on('r-genomicranges@1.31.8:', when='@1.40.5', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@1.36.6', type=('build', 'run'))
-    depends_on('r@3.5.0:3.5.9', when='@1.40.5', type=('build', 'run'))
+    depends_on('r-rcurl@1.4-2:', type=('build', 'run'))
+    depends_on('r-rsamtools@1.17.8:', type=('build', 'run'))
+    depends_on('r-genomicalignments@1.5.4:', type=('build', 'run'))
+
+    depends_on('r-iranges@2.11.12:', when='@1.38.3:', type=('build', 'run'))
+
+    depends_on('r-genomicranges@1.31.8:', when='@1.40.6:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.25.1:', when='@1.40.6:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.25:', when='@1.40.6:', type=('build', 'run'))
+    depends_on('r-iranges@2.13.13:', when='@1.40.6:', type=('build', 'run'))
+    depends_on('r-xvector@0.19.7:', when='@1.40.6:', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.15.2:', when='@1.40.6:', type=('build', 'run'))
+    depends_on('r-biostrings@2.47.6:', when='@1.40.6:', type=('build', 'run'))
+    depends_on('r-rsamtools@1.31.2:', when='@1.40.6:', type=('build', 'run'))
+    depends_on('r-genomicalignments@1.15.6:', when='@1.40.6:', type=('build', 'run'))
+
+    depends_on('r-s4vectors@0.19.22:', when='@1.42.2:', type=('build', 'run'))