diff --git a/BioArchLinux/r-adverscarial/PKGBUILD b/BioArchLinux/r-adverscarial/PKGBUILD index 331ae7370f..5109a254f9 100644 --- a/BioArchLinux/r-adverscarial/PKGBUILD +++ b/BioArchLinux/r-adverscarial/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.0.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc="adverSCarial, generate and analyze the vulnerability of scRNA-seq classifiers to adversarial attacks" +pkgdesc="generate and analyze the vulnerability of scRNA-seq classifiers to adversarial attacks" arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(MIT) diff --git a/BioArchLinux/r-adverscarial/lilac.yaml b/BioArchLinux/r-adverscarial/lilac.yaml index e6925146d1..558ff4e2bd 100644 --- a/BioArchLinux/r-adverscarial/lilac.yaml +++ b/BioArchLinux/r-adverscarial/lilac.yaml @@ -15,3 +15,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-biodb/PKGBUILD b/BioArchLinux/r-biodb/PKGBUILD index 7c8cba7793..8ede549b6b 100644 --- a/BioArchLinux/r-biodb/PKGBUILD +++ b/BioArchLinux/r-biodb/PKGBUILD @@ -6,7 +6,7 @@ _pkgver=1.10.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=3 -pkgdesc="biodb, a library and a development framework for connecting to chemical and biological databases" +pkgdesc="a library and a development framework for connecting to chemical and biological databases" arch=(x86_64) url="https://bioconductor.org/packages/$_pkgname" license=(AGPL3) diff --git a/BioArchLinux/r-biodb/lilac.yaml b/BioArchLinux/r-biodb/lilac.yaml index f129abbf04..f7f421c129 100644 --- a/BioArchLinux/r-biodb/lilac.yaml +++ b/BioArchLinux/r-biodb/lilac.yaml @@ -31,4 +31,4 @@ update_on: md5: true - alias: r - source: manual - manual: 1 + manual: 2 diff --git a/BioArchLinux/r-biodbexpasy/PKGBUILD b/BioArchLinux/r-biodbexpasy/PKGBUILD index c0aa6e9d59..c4e86f80e7 100644 --- a/BioArchLinux/r-biodbexpasy/PKGBUILD +++ b/BioArchLinux/r-biodbexpasy/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.6.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc="biodbExpasy, a library for connecting to Expasy ENZYME database." +pkgdesc="a library for connecting to Expasy ENZYME database." arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(AGPL3) diff --git a/BioArchLinux/r-biodbexpasy/lilac.yaml b/BioArchLinux/r-biodbexpasy/lilac.yaml index a337da48e7..fb407456fe 100644 --- a/BioArchLinux/r-biodbexpasy/lilac.yaml +++ b/BioArchLinux/r-biodbexpasy/lilac.yaml @@ -15,3 +15,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-biodbhmdb/PKGBUILD b/BioArchLinux/r-biodbhmdb/PKGBUILD index 764b89f36c..07aa8850e5 100644 --- a/BioArchLinux/r-biodbhmdb/PKGBUILD +++ b/BioArchLinux/r-biodbhmdb/PKGBUILD @@ -6,7 +6,7 @@ _pkgver=1.8.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc="biodbHmdb, a library for connecting to the HMDB Database" +pkgdesc="a library for connecting to the HMDB Database" arch=(x86_64) url="https://bioconductor.org/packages/$_pkgname" license=(AGPL3) diff --git a/BioArchLinux/r-biodbhmdb/lilac.yaml b/BioArchLinux/r-biodbhmdb/lilac.yaml index 26b6fa3b14..ad27275ab6 100644 --- a/BioArchLinux/r-biodbhmdb/lilac.yaml +++ b/BioArchLinux/r-biodbhmdb/lilac.yaml @@ -16,3 +16,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-biodbncbi/PKGBUILD b/BioArchLinux/r-biodbncbi/PKGBUILD index fd203e83cd..8102f8c4eb 100644 --- a/BioArchLinux/r-biodbncbi/PKGBUILD +++ b/BioArchLinux/r-biodbncbi/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.6.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc="biodbNcbi, a library for connecting to NCBI Databases." +pkgdesc="a library for connecting to NCBI Databases." arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(AGPL3) diff --git a/BioArchLinux/r-biodbncbi/lilac.yaml b/BioArchLinux/r-biodbncbi/lilac.yaml index 2ef7503622..035b61436f 100644 --- a/BioArchLinux/r-biodbncbi/lilac.yaml +++ b/BioArchLinux/r-biodbncbi/lilac.yaml @@ -15,3 +15,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-biodbnci/PKGBUILD b/BioArchLinux/r-biodbnci/PKGBUILD index 06d2cae8b2..eb3c468de6 100644 --- a/BioArchLinux/r-biodbnci/PKGBUILD +++ b/BioArchLinux/r-biodbnci/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.6.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc="biodbNci, a library for connecting to biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database" +pkgdesc="a library for connecting to the National Cancer Institute (USA) CACTUS Database" arch=(x86_64) url="https://bioconductor.org/packages/$_pkgname" license=(AGPL3) diff --git a/BioArchLinux/r-biodbnci/lilac.py b/BioArchLinux/r-biodbnci/lilac.py index b5cdb057c5..013b1650aa 100644 --- a/BioArchLinux/r-biodbnci/lilac.py +++ b/BioArchLinux/r-biodbnci/lilac.py @@ -7,7 +7,10 @@ sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) from lilac_r_utils import r_pre_build def pre_build(): - r_pre_build(_G) + r_pre_build( + _G, + expect_title = "biodbNci, a library for connecting to biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database", + ) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-biodbnci/lilac.yaml b/BioArchLinux/r-biodbnci/lilac.yaml index 71f5055c76..9f2c0c6df8 100644 --- a/BioArchLinux/r-biodbnci/lilac.yaml +++ b/BioArchLinux/r-biodbnci/lilac.yaml @@ -16,3 +16,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-ccimpute/PKGBUILD b/BioArchLinux/r-ccimpute/PKGBUILD index f867a22a37..f69d323ce6 100644 --- a/BioArchLinux/r-ccimpute/PKGBUILD +++ b/BioArchLinux/r-ccimpute/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.4.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc="ccImpute: an accurate and scalable consensus clustering based approach to impute dropout events in the single-cell RNA-seq data (https://doi.org/10.1186/s12859-022-04814-8)" +pkgdesc="an accurate and scalable consensus clustering based approach to impute dropout events in the single-cell RNA-seq data" arch=(x86_64) url="https://bioconductor.org/packages/$_pkgname" license=(GPL3) diff --git a/BioArchLinux/r-ccimpute/lilac.py b/BioArchLinux/r-ccimpute/lilac.py index b5cdb057c5..94d7c23960 100644 --- a/BioArchLinux/r-ccimpute/lilac.py +++ b/BioArchLinux/r-ccimpute/lilac.py @@ -7,7 +7,10 @@ sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) from lilac_r_utils import r_pre_build def pre_build(): - r_pre_build(_G) + r_pre_build( + _G, + expect_title = "ccImpute: an accurate and scalable consensus clustering based approach to impute dropout events in the single-cell RNA-seq data (https://doi.org/10.1186/s12859-022-04814-8)", + ) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-ccimpute/lilac.yaml b/BioArchLinux/r-ccimpute/lilac.yaml index ddd7797262..0336940ea6 100644 --- a/BioArchLinux/r-ccimpute/lilac.yaml +++ b/BioArchLinux/r-ccimpute/lilac.yaml @@ -16,3 +16,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-compspot/PKGBUILD b/BioArchLinux/r-compspot/PKGBUILD index dac3c072a8..410bcd3066 100644 --- a/BioArchLinux/r-compspot/PKGBUILD +++ b/BioArchLinux/r-compspot/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.0.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc="compSPOT: Tool for identifying and comparing significantly mutated genomic hotspots" +pkgdesc="Tool for identifying and comparing significantly mutated genomic hotspots" arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(Artistic2.0) diff --git a/BioArchLinux/r-compspot/lilac.yaml b/BioArchLinux/r-compspot/lilac.yaml index 289339db96..4f1df18f7b 100644 --- a/BioArchLinux/r-compspot/lilac.yaml +++ b/BioArchLinux/r-compspot/lilac.yaml @@ -17,3 +17,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-deming/lilac.py b/BioArchLinux/r-deming/lilac.py index b5cdb057c5..416db00f81 100644 --- a/BioArchLinux/r-deming/lilac.py +++ b/BioArchLinux/r-deming/lilac.py @@ -7,7 +7,10 @@ sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) from lilac_r_utils import r_pre_build def pre_build(): - r_pre_build(_G) + r_pre_build( + _G, + expect_title = "Deming, Theil-Sen, Passing-Bablock and Total Least Squares Regression", + ) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-despace/PKGBUILD b/BioArchLinux/r-despace/PKGBUILD index 176f2db282..10cdb3ea6a 100644 --- a/BioArchLinux/r-despace/PKGBUILD +++ b/BioArchLinux/r-despace/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.2.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc="DESpace: a framework to discover spatially variable genes" +pkgdesc="a framework to discover spatially variable genes" arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(GPL3) diff --git a/BioArchLinux/r-despace/lilac.yaml b/BioArchLinux/r-despace/lilac.yaml index 640ec1867d..0bfe4161b2 100644 --- a/BioArchLinux/r-despace/lilac.yaml +++ b/BioArchLinux/r-despace/lilac.yaml @@ -29,3 +29,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-epimix/PKGBUILD b/BioArchLinux/r-epimix/PKGBUILD index f5983a833d..c64f0df2d9 100644 --- a/BioArchLinux/r-epimix/PKGBUILD +++ b/BioArchLinux/r-epimix/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.4.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc="EpiMix: an integrative tool for the population-level analysis of DNA methylation" +pkgdesc="an integrative tool for the population-level analysis of DNA methylation" arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(GPL3) diff --git a/BioArchLinux/r-epimix/lilac.yaml b/BioArchLinux/r-epimix/lilac.yaml index 994999261b..14cf298870 100644 --- a/BioArchLinux/r-epimix/lilac.yaml +++ b/BioArchLinux/r-epimix/lilac.yaml @@ -44,3 +44,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-featseekr/PKGBUILD b/BioArchLinux/r-featseekr/PKGBUILD index bda3ce9a79..6a262f81d6 100644 --- a/BioArchLinux/r-featseekr/PKGBUILD +++ b/BioArchLinux/r-featseekr/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.2.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc="FeatSeekR an R package for unsupervised feature selection" +pkgdesc="an R package for unsupervised feature selection" arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(GPL3) diff --git a/BioArchLinux/r-featseekr/lilac.py b/BioArchLinux/r-featseekr/lilac.py index b5cdb057c5..725108321a 100644 --- a/BioArchLinux/r-featseekr/lilac.py +++ b/BioArchLinux/r-featseekr/lilac.py @@ -7,7 +7,10 @@ sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) from lilac_r_utils import r_pre_build def pre_build(): - r_pre_build(_G) + r_pre_build( + _G, + expect_title = "FeatSeekR an R package for unsupervised feature selection", + ) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-featseekr/lilac.yaml b/BioArchLinux/r-featseekr/lilac.yaml index c6ac3a1f1f..a76c74add6 100644 --- a/BioArchLinux/r-featseekr/lilac.yaml +++ b/BioArchLinux/r-featseekr/lilac.yaml @@ -14,3 +14,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-flowcore/PKGBUILD b/BioArchLinux/r-flowcore/PKGBUILD index 61c180e231..6d28c8f70a 100644 --- a/BioArchLinux/r-flowcore/PKGBUILD +++ b/BioArchLinux/r-flowcore/PKGBUILD @@ -7,7 +7,7 @@ _pkgver=2.14.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=3 -pkgdesc="flowCore: Basic structures for flow cytometry data" +pkgdesc="Basic structures for flow cytometry data" arch=(x86_64) url="https://bioconductor.org/packages/$_pkgname" license=(Artistic2.0) diff --git a/BioArchLinux/r-flowcore/lilac.yaml b/BioArchLinux/r-flowcore/lilac.yaml index 25b2a10cfb..e5fee1328b 100644 --- a/BioArchLinux/r-flowcore/lilac.yaml +++ b/BioArchLinux/r-flowcore/lilac.yaml @@ -21,5 +21,7 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 update_on_build: - pkgbase: r-cytolib diff --git a/BioArchLinux/r-gdrtestdata/PKGBUILD b/BioArchLinux/r-gdrtestdata/PKGBUILD index 2f123171f3..5ab77b8816 100644 --- a/BioArchLinux/r-gdrtestdata/PKGBUILD +++ b/BioArchLinux/r-gdrtestdata/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.0.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc="gDRtestData - R data package with testing dose reponse data" +pkgdesc="R data package with testing dose reponse data" arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(Artistic2.0) diff --git a/BioArchLinux/r-gdrtestdata/lilac.yaml b/BioArchLinux/r-gdrtestdata/lilac.yaml index ede5a13c7c..1d1349d0e2 100644 --- a/BioArchLinux/r-gdrtestdata/lilac.yaml +++ b/BioArchLinux/r-gdrtestdata/lilac.yaml @@ -12,3 +12,5 @@ update_on: repo: bioc-data-experiment md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-geoexplorer/PKGBUILD b/BioArchLinux/r-geoexplorer/PKGBUILD index 8351c3a19c..cbb170f177 100644 --- a/BioArchLinux/r-geoexplorer/PKGBUILD +++ b/BioArchLinux/r-geoexplorer/PKGBUILD @@ -6,7 +6,7 @@ _pkgver=1.8.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc="GEOexplorer: a webserver for gene expression analysis and visualisation" +pkgdesc="a webserver for gene expression analysis and visualisation" arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(GPL3) diff --git a/BioArchLinux/r-geoexplorer/lilac.yaml b/BioArchLinux/r-geoexplorer/lilac.yaml index 7f3dba73b3..6957de12f0 100644 --- a/BioArchLinux/r-geoexplorer/lilac.yaml +++ b/BioArchLinux/r-geoexplorer/lilac.yaml @@ -41,3 +41,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-granie/PKGBUILD b/BioArchLinux/r-granie/PKGBUILD index 915be74e5f..6a4a8ac067 100644 --- a/BioArchLinux/r-granie/PKGBUILD +++ b/BioArchLinux/r-granie/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.6.1 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc="GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data" +pkgdesc="Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data" arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(Artistic2.0) diff --git a/BioArchLinux/r-granie/lilac.yaml b/BioArchLinux/r-granie/lilac.yaml index 3e3dbaf3c8..b7a5bdab35 100644 --- a/BioArchLinux/r-granie/lilac.yaml +++ b/BioArchLinux/r-granie/lilac.yaml @@ -45,3 +45,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-hgu95av2cdf/PKGBUILD b/BioArchLinux/r-hgu95av2cdf/PKGBUILD index f1e34b4451..0de4cd8d34 100644 --- a/BioArchLinux/r-hgu95av2cdf/PKGBUILD +++ b/BioArchLinux/r-hgu95av2cdf/PKGBUILD @@ -6,7 +6,7 @@ _pkgver=2.18.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=5 -pkgdesc="hgu95av2cdf" +pkgdesc="A package containing an environment representing the HG_U95Av2.CDF file" arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=('LGPL-2.0-or-later') diff --git a/BioArchLinux/r-hgu95av2cdf/lilac.py b/BioArchLinux/r-hgu95av2cdf/lilac.py index b5cdb057c5..46a3195af3 100644 --- a/BioArchLinux/r-hgu95av2cdf/lilac.py +++ b/BioArchLinux/r-hgu95av2cdf/lilac.py @@ -7,7 +7,10 @@ sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) from lilac_r_utils import r_pre_build def pre_build(): - r_pre_build(_G) + r_pre_build( + _G, + expect_title = "hgu95av2cdf", + ) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-hgu95av2cdf/lilac.yaml b/BioArchLinux/r-hgu95av2cdf/lilac.yaml index d255e72df0..47c430752c 100644 --- a/BioArchLinux/r-hgu95av2cdf/lilac.yaml +++ b/BioArchLinux/r-hgu95av2cdf/lilac.yaml @@ -11,4 +11,4 @@ update_on: md5: true - alias: r - source: manual - manual: 1 + manual: 2 diff --git a/BioArchLinux/r-hicool/PKGBUILD b/BioArchLinux/r-hicool/PKGBUILD index 71d660ff2b..50626a6bdf 100644 --- a/BioArchLinux/r-hicool/PKGBUILD +++ b/BioArchLinux/r-hicool/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.2.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc="HiCool" +pkgdesc="Processing Hi-C raw data within R" arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(MIT) diff --git a/BioArchLinux/r-hicool/lilac.py b/BioArchLinux/r-hicool/lilac.py index b5cdb057c5..d1b976f30e 100644 --- a/BioArchLinux/r-hicool/lilac.py +++ b/BioArchLinux/r-hicool/lilac.py @@ -7,7 +7,10 @@ sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) from lilac_r_utils import r_pre_build def pre_build(): - r_pre_build(_G) + r_pre_build( + _G, + expect_title = "HiCool", + ) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-hicool/lilac.yaml b/BioArchLinux/r-hicool/lilac.yaml index cc4262a02d..64bb3dccbe 100644 --- a/BioArchLinux/r-hicool/lilac.yaml +++ b/BioArchLinux/r-hicool/lilac.yaml @@ -24,3 +24,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-isobayes/PKGBUILD b/BioArchLinux/r-isobayes/PKGBUILD index e4d2a125cc..e1484213df 100644 --- a/BioArchLinux/r-isobayes/PKGBUILD +++ b/BioArchLinux/r-isobayes/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.0.1 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc="IsoBayes: Single Isoform protein inference Method via Bayesian Analyses" +pkgdesc="Single Isoform protein inference Method via Bayesian Analyses" arch=(x86_64) url="https://bioconductor.org/packages/$_pkgname" license=(GPL3) diff --git a/BioArchLinux/r-isobayes/lilac.yaml b/BioArchLinux/r-isobayes/lilac.yaml index 5f3f6bc38c..1a9be009a2 100644 --- a/BioArchLinux/r-isobayes/lilac.yaml +++ b/BioArchLinux/r-isobayes/lilac.yaml @@ -23,3 +23,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-mariner/PKGBUILD b/BioArchLinux/r-mariner/PKGBUILD index 58fcc3893d..6248145d06 100644 --- a/BioArchLinux/r-mariner/PKGBUILD +++ b/BioArchLinux/r-mariner/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.2.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc="Mariner: Explore the Hi-Cs" +pkgdesc="Explore the Hi-Cs" arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(GPL3) diff --git a/BioArchLinux/r-mariner/lilac.yaml b/BioArchLinux/r-mariner/lilac.yaml index acf93758af..110f9ece6b 100644 --- a/BioArchLinux/r-mariner/lilac.yaml +++ b/BioArchLinux/r-mariner/lilac.yaml @@ -38,3 +38,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-mbqtl/PKGBUILD b/BioArchLinux/r-mbqtl/PKGBUILD index 5ed5aa6abb..b86a970640 100644 --- a/BioArchLinux/r-mbqtl/PKGBUILD +++ b/BioArchLinux/r-mbqtl/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.2.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc="mbQTL: A package for SNP-Taxa mGWAS analysis" +pkgdesc="A package for SNP-Taxa mGWAS analysis" arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(MIT) diff --git a/BioArchLinux/r-mbqtl/lilac.yaml b/BioArchLinux/r-mbqtl/lilac.yaml index 46bd101a4b..a62dac28bf 100644 --- a/BioArchLinux/r-mbqtl/lilac.yaml +++ b/BioArchLinux/r-mbqtl/lilac.yaml @@ -18,3 +18,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-micsqtl/PKGBUILD b/BioArchLinux/r-micsqtl/PKGBUILD index a5a5919364..d77fb27413 100644 --- a/BioArchLinux/r-micsqtl/PKGBUILD +++ b/BioArchLinux/r-micsqtl/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.0.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc="MICSQTL (Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait Loci)" +pkgdesc="Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait Loci" arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(GPL3) diff --git a/BioArchLinux/r-micsqtl/lilac.py b/BioArchLinux/r-micsqtl/lilac.py index b5cdb057c5..378566db8f 100644 --- a/BioArchLinux/r-micsqtl/lilac.py +++ b/BioArchLinux/r-micsqtl/lilac.py @@ -7,7 +7,10 @@ sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) from lilac_r_utils import r_pre_build def pre_build(): - r_pre_build(_G) + r_pre_build( + _G, + expect_title = "MICSQTL (Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait Loci)", + ) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-micsqtl/lilac.yaml b/BioArchLinux/r-micsqtl/lilac.yaml index 5d103d23b1..e77d6c17b3 100644 --- a/BioArchLinux/r-micsqtl/lilac.yaml +++ b/BioArchLinux/r-micsqtl/lilac.yaml @@ -24,3 +24,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-msquality/PKGBUILD b/BioArchLinux/r-msquality/PKGBUILD index 0cc7b1ad4e..61cdddc0f6 100644 --- a/BioArchLinux/r-msquality/PKGBUILD +++ b/BioArchLinux/r-msquality/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.2.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc="MsQuality - Quality metric calculation from Spectra and MsExperiment objects" +pkgdesc="Quality metric calculation from Spectra and MsExperiment objects" arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(GPL3) diff --git a/BioArchLinux/r-msquality/lilac.yaml b/BioArchLinux/r-msquality/lilac.yaml index f2bae225dc..d3b2a7613a 100644 --- a/BioArchLinux/r-msquality/lilac.yaml +++ b/BioArchLinux/r-msquality/lilac.yaml @@ -27,3 +27,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-multiwgcna/PKGBUILD b/BioArchLinux/r-multiwgcna/PKGBUILD index d485e09b86..c9f4eb9589 100644 --- a/BioArchLinux/r-multiwgcna/PKGBUILD +++ b/BioArchLinux/r-multiwgcna/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.0.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc="multiWGCNA" +pkgdesc="An R package for deeping mining gene co-expression networks in multi-trait expression data" arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(GPL3) diff --git a/BioArchLinux/r-multiwgcna/lilac.py b/BioArchLinux/r-multiwgcna/lilac.py index b5cdb057c5..f412c30e38 100644 --- a/BioArchLinux/r-multiwgcna/lilac.py +++ b/BioArchLinux/r-multiwgcna/lilac.py @@ -7,7 +7,10 @@ sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) from lilac_r_utils import r_pre_build def pre_build(): - r_pre_build(_G) + r_pre_build( + _G, + expect_title = "multiWGCNA", + ) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-multiwgcna/lilac.yaml b/BioArchLinux/r-multiwgcna/lilac.yaml index 74d177f3e9..1186c9df7b 100644 --- a/BioArchLinux/r-multiwgcna/lilac.yaml +++ b/BioArchLinux/r-multiwgcna/lilac.yaml @@ -28,3 +28,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-regionereloaded/PKGBUILD b/BioArchLinux/r-regionereloaded/PKGBUILD index 45ababc002..bf5910e22e 100644 --- a/BioArchLinux/r-regionereloaded/PKGBUILD +++ b/BioArchLinux/r-regionereloaded/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.4.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc="RegioneReloaded: Multiple Association for Genomic Region Sets" +pkgdesc="Multiple Association for Genomic Region Sets" arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(Artistic2.0) diff --git a/BioArchLinux/r-regionereloaded/lilac.yaml b/BioArchLinux/r-regionereloaded/lilac.yaml index f9d4f215d1..bb40579c15 100644 --- a/BioArchLinux/r-regionereloaded/lilac.yaml +++ b/BioArchLinux/r-regionereloaded/lilac.yaml @@ -19,3 +19,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-resolve/PKGBUILD b/BioArchLinux/r-resolve/PKGBUILD index dd706abaf8..2401d06c81 100644 --- a/BioArchLinux/r-resolve/PKGBUILD +++ b/BioArchLinux/r-resolve/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.4.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc="RESOLVE: An R package for the efficient analysis of mutational signatures from cancer genomes" +pkgdesc="An R package for the efficient analysis of mutational signatures from cancer genomes" arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(Apache) diff --git a/BioArchLinux/r-resolve/lilac.yaml b/BioArchLinux/r-resolve/lilac.yaml index 27f6413a34..c5edb0b4d5 100644 --- a/BioArchLinux/r-resolve/lilac.yaml +++ b/BioArchLinux/r-resolve/lilac.yaml @@ -26,3 +26,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-retrofit/PKGBUILD b/BioArchLinux/r-retrofit/PKGBUILD index d70d3e66c4..efe531c409 100644 --- a/BioArchLinux/r-retrofit/PKGBUILD +++ b/BioArchLinux/r-retrofit/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.2.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc="RETROFIT: Reference-free deconvolution of cell mixtures in spatial transcriptomics" +pkgdesc="Reference-free deconvolution of cell mixtures in spatial transcriptomics" arch=(x86_64) url="https://bioconductor.org/packages/$_pkgname" license=(GPL3) diff --git a/BioArchLinux/r-retrofit/lilac.yaml b/BioArchLinux/r-retrofit/lilac.yaml index 4823d96020..a71499b486 100644 --- a/BioArchLinux/r-retrofit/lilac.yaml +++ b/BioArchLinux/r-retrofit/lilac.yaml @@ -12,3 +12,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-rolde/PKGBUILD b/BioArchLinux/r-rolde/PKGBUILD index 760d1e8df1..f6fdab677b 100644 --- a/BioArchLinux/r-rolde/PKGBUILD +++ b/BioArchLinux/r-rolde/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.6.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc="RolDE: Robust longitudinal Differential Expression" +pkgdesc="Robust longitudinal Differential Expression" arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(GPL3) diff --git a/BioArchLinux/r-rolde/lilac.yaml b/BioArchLinux/r-rolde/lilac.yaml index ea8566dd23..331280e5e4 100644 --- a/BioArchLinux/r-rolde/lilac.yaml +++ b/BioArchLinux/r-rolde/lilac.yaml @@ -17,3 +17,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-scfeatures/PKGBUILD b/BioArchLinux/r-scfeatures/PKGBUILD index a0bcc4bfa8..8ec7e5d6bb 100644 --- a/BioArchLinux/r-scfeatures/PKGBUILD +++ b/BioArchLinux/r-scfeatures/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.2.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc="scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction" +pkgdesc="Multi-view representations of single-cell and spatial data for disease outcome prediction" arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(GPL3) diff --git a/BioArchLinux/r-scfeatures/lilac.yaml b/BioArchLinux/r-scfeatures/lilac.yaml index d587e572e3..e40324cc85 100644 --- a/BioArchLinux/r-scfeatures/lilac.yaml +++ b/BioArchLinux/r-scfeatures/lilac.yaml @@ -35,3 +35,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-scifer/PKGBUILD b/BioArchLinux/r-scifer/PKGBUILD index 34251d6c0b..408b2a98cc 100644 --- a/BioArchLinux/r-scifer/PKGBUILD +++ b/BioArchLinux/r-scifer/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.4.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc="Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences" +pkgdesc="Single-Cell Immunoglobulin Filtering of Sanger Sequences" arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(MIT) diff --git a/BioArchLinux/r-scifer/lilac.yaml b/BioArchLinux/r-scifer/lilac.yaml index ff1e8e60fb..f322d7cb62 100644 --- a/BioArchLinux/r-scifer/lilac.yaml +++ b/BioArchLinux/r-scifer/lilac.yaml @@ -27,3 +27,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-sgcp/PKGBUILD b/BioArchLinux/r-sgcp/PKGBUILD index 8b989dc596..c34ee647a1 100644 --- a/BioArchLinux/r-sgcp/PKGBUILD +++ b/BioArchLinux/r-sgcp/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.2.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc="SGCP: A semi-supervised pipeline for gene clustering using self-training approach in gene co-expression networks" +pkgdesc="A semi-supervised pipeline for gene clustering using self-training approach in gene co-expression networks" arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(GPL3) diff --git a/BioArchLinux/r-sgcp/lilac.yaml b/BioArchLinux/r-sgcp/lilac.yaml index 91cad3d50f..e63660262a 100644 --- a/BioArchLinux/r-sgcp/lilac.yaml +++ b/BioArchLinux/r-sgcp/lilac.yaml @@ -29,3 +29,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-spatialheatmap/PKGBUILD b/BioArchLinux/r-spatialheatmap/PKGBUILD index 50532efced..263efba7ba 100644 --- a/BioArchLinux/r-spatialheatmap/PKGBUILD +++ b/BioArchLinux/r-spatialheatmap/PKGBUILD @@ -6,7 +6,7 @@ _pkgver=2.8.2 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc="spatialHeatmap" +pkgdesc="Creating spatial heatmaps from R and Shiny" arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(Artistic2.0) diff --git a/BioArchLinux/r-spatialheatmap/lilac.py b/BioArchLinux/r-spatialheatmap/lilac.py index b5cdb057c5..7b54c62405 100644 --- a/BioArchLinux/r-spatialheatmap/lilac.py +++ b/BioArchLinux/r-spatialheatmap/lilac.py @@ -7,7 +7,10 @@ sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) from lilac_r_utils import r_pre_build def pre_build(): - r_pre_build(_G) + r_pre_build( + _G, + expect_title = "spatialHeatmap", + ) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-spatialheatmap/lilac.yaml b/BioArchLinux/r-spatialheatmap/lilac.yaml index eb8657385a..0ab0eb3198 100644 --- a/BioArchLinux/r-spatialheatmap/lilac.yaml +++ b/BioArchLinux/r-spatialheatmap/lilac.yaml @@ -40,3 +40,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-spatiallibd/PKGBUILD b/BioArchLinux/r-spatiallibd/PKGBUILD index 8cd6056cce..b3eab975d8 100644 --- a/BioArchLinux/r-spatiallibd/PKGBUILD +++ b/BioArchLinux/r-spatiallibd/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.14.1 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc="spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data" +pkgdesc="an R/Bioconductor package to visualize spatially-resolved transcriptomics data" arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(Artistic2.0) diff --git a/BioArchLinux/r-spatiallibd/lilac.yaml b/BioArchLinux/r-spatiallibd/lilac.yaml index 46048d4430..27f33a77aa 100644 --- a/BioArchLinux/r-spatiallibd/lilac.yaml +++ b/BioArchLinux/r-spatiallibd/lilac.yaml @@ -44,3 +44,5 @@ update_on: repo: bioc-data-experiment md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-stjoincount/PKGBUILD b/BioArchLinux/r-stjoincount/PKGBUILD index 63280e2be5..7d71daa7f3 100644 --- a/BioArchLinux/r-stjoincount/PKGBUILD +++ b/BioArchLinux/r-stjoincount/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.4.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc="stJoincount - Join count statistic for quantifying spatial correlation between clusters" +pkgdesc="Join count statistic for quantifying spatial correlation between clusters" arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(MIT) diff --git a/BioArchLinux/r-stjoincount/lilac.yaml b/BioArchLinux/r-stjoincount/lilac.yaml index 90f5293963..5745f1c284 100644 --- a/BioArchLinux/r-stjoincount/lilac.yaml +++ b/BioArchLinux/r-stjoincount/lilac.yaml @@ -21,3 +21,5 @@ update_on: repo: bioc md5: true - alias: r +- source: manual + manual: 1 diff --git a/BioArchLinux/r-tximportdata/PKGBUILD b/BioArchLinux/r-tximportdata/PKGBUILD index e119d868aa..883daee069 100644 --- a/BioArchLinux/r-tximportdata/PKGBUILD +++ b/BioArchLinux/r-tximportdata/PKGBUILD @@ -5,7 +5,7 @@ _pkgver=1.30.0 pkgname=r-${_pkgname,,} pkgver=${_pkgver//-/.} pkgrel=2 -pkgdesc="tximportData" +pkgdesc="provides the output of running various transcript abundance quantifiers on a set of 6 RNA-seq samples from the GEUVADIS project" arch=(any) url="https://bioconductor.org/packages/$_pkgname" license=(GPL) diff --git a/BioArchLinux/r-tximportdata/lilac.py b/BioArchLinux/r-tximportdata/lilac.py index b5cdb057c5..c92feab350 100644 --- a/BioArchLinux/r-tximportdata/lilac.py +++ b/BioArchLinux/r-tximportdata/lilac.py @@ -7,7 +7,10 @@ sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) from lilac_r_utils import r_pre_build def pre_build(): - r_pre_build(_G) + r_pre_build( + _G, + expect_title = "tximportData", + ) def post_build(): git_pkgbuild_commit() diff --git a/BioArchLinux/r-tximportdata/lilac.yaml b/BioArchLinux/r-tximportdata/lilac.yaml index ae4db5e5ca..95008767b8 100644 --- a/BioArchLinux/r-tximportdata/lilac.yaml +++ b/BioArchLinux/r-tximportdata/lilac.yaml @@ -8,3 +8,5 @@ update_on: repo: bioc-data-experiment md5: true - alias: r +- source: manual + manual: 1 diff --git a/lilac-extensions/lilac_r_utils.py b/lilac-extensions/lilac_r_utils.py index a5755c9d76..1b87151a30 100644 --- a/lilac-extensions/lilac_r_utils.py +++ b/lilac-extensions/lilac_r_utils.py @@ -230,11 +230,13 @@ class CheckConfig: expect_license: str = None, expect_needscompilation: bool = None, expect_systemrequirements: str = None, + expect_title: str = None, ignore_fortran_files: bool = False, ): self.expect_license = expect_license self.expect_needscompilation = expect_needscompilation self.expect_systemrequirements = expect_systemrequirements + self.expect_title = expect_title self.ignore_fortran_files = ignore_fortran_files def check_default_pkgs(pkg: Pkgbuild, desc: Description, cfg: CheckConfig): @@ -338,8 +340,23 @@ def check_license(pkg: Pkgbuild, desc: Description, cfg: CheckConfig): raise CheckFailed(f"Unknown license: {desc.license}. Consider setting CheckConfig.expect_license") def check_pkgdesc(pkg: Pkgbuild, desc: Description, cfg: CheckConfig): - if pkg.pkgdesc != desc.title: - raise CheckFailed(f"Wrong pkgdesc, expected '{desc.title}'") + title = desc.title + title_lower = title.lower() + name_lower = pkg._pkgname.lower() + # detect and remove package name from the title + for sep in [",", ":", " -"]: + prefix = f"{name_lower}{sep} " + if title_lower.startswith(prefix): + title = title[len(prefix):] + break + + if cfg.expect_title is not None: + if pkg.pkgdesc == title: + raise CheckFailed("Unnecessary expect_title") + elif cfg.expect_title != desc.title: + raise CheckFailed(f"Title has changed: {desc.title}") + elif pkg.pkgdesc != title: + raise CheckFailed(f"Wrong pkgdesc, expected '{title}'") def check_arch(pkg: Pkgbuild, desc: Description, cfg: CheckConfig): if cfg.expect_needscompilation is not None: