$ ./pre-inst-env guix refresh -t bioconductor -u # NOT DONE r-bamsignals: consider removing this input: zlib # NOT DONE r-rsamtools: consider removing this input: zlib r-rsamtools: consider adding this propagated input: r-zlibbioc # NOT DONE r-methylkit: consider removing this input: zlib # NOT DONE r-variantannotation: consider removing this input: zlib r-variantannotation: consider adding this propagated input: r-matrixgenerics # NOt DONE r-rhdf5: consider removing this input: zlib r-rhdf5: consider adding this propagated input: r-rhdf5filters # NOT DONE r-gdsfmt: consider removing this input: lz4 r-gdsfmt: consider removing this input: xz r-gdsfmt: consider removing this input: zlib # NOT DONE r-rbowtie2: consider removing this input: zlib # NOT DONE r-seqbias: consider removing this input: zlib # NOT DONE r-cytolib: consider removing this input: zlib r-cytolib: consider adding this native input: pkg-config # NOT DONE r-ncdfflow: consider removing this input: zlib r-hdf5array: consider removing this input: zlib # DEP but added (my bad) r-annaffy: consider adding this propagated input: r-kegg-db # DEP r-flowworkspace: consider adding this propagated input: r-aws-s3 r-flowworkspace: consider adding this propagated input: r-aws-signature r-flowworkspace: consider removing this propagated input: r-stringr # DEP r-scater: consider adding this propagated input: r-gridextra r-scater: consider adding this propagated input: r-scuttle r-scater: consider removing this propagated input: r-beachmat r-scater: consider removing this propagated input: r-rcpp # DEP r-biocset: consider adding this propagated input: r-biocio r-biocset: consider adding this propagated input: r-ontologyindex r-biocset: consider adding this propagated input: r-s4vectors r-biocset: consider adding this propagated input: r-tidyr r-biocset: consider removing this propagated input: r-rtracklayer # DEP r-scran: consider adding this propagated input: r-bluster r-scran: consider adding this propagated input: r-scuttle r-scran: consider removing this propagated input: r-iranges r-scran: consider removing this propagated input: r-scater # DEP r-xcms: consider adding this propagated input: r-mscoreutils # DEP r-webbioc: consider adding this input: unix # DEP r-biocpkgtools: consider adding this input: mailsend-go # DEP r-enrichplot: consider adding this propagated input: r-shadowtext r-enrichplot: consider removing this propagated input: r-annotationdbi r-enrichplot: consider removing this propagated input: r-europepmc r-enrichplot: consider removing this propagated input: r-ggplotify r-enrichplot: consider removing this propagated input: r-ggridges r-enrichplot: consider removing this propagated input: r-gridextra # DEP r-delayedarray: consider adding this propagated input: r-matrixgenerics r-delayedarray: consider removing this propagated input: r-matrixstats # DEP r-genomicfiles: consider adding this propagated input: r-matrixgenerics # DEP r-diffbind: consider removing this input: zlib r-diffbind: consider adding this propagated input: r-apeglm r-diffbind: consider adding this propagated input: r-ashr r-diffbind: consider adding this propagated input: r-greylistchip r-diffbind: consider removing this propagated input: r-edger # DEP r-delayedmatrixstats: consider adding this propagated input: r-matrixgenerics r-delayedmatrixstats: consider adding this propagated input: r-sparsematrixstats # NOT DONE r-complexheatmap: consider adding this propagated input: r-cairo r-complexheatmap: consider adding this propagated input: r-digest r-complexheatmap: consider adding this propagated input: r-iranges r-complexheatmap: consider adding this propagated input: r-matrixstats r-complexheatmap: consider adding this propagated input: r-s4vectors # NOT DONE r-gwascat: consider adding this propagated input: r-biocfilecache r-gwascat: consider adding this propagated input: r-readr r-gwascat: consider adding this propagated input: r-snpstats r-gwascat: consider adding this propagated input: r-variantannotation r-gwascat: consider removing this propagated input: r-biocgenerics r-gwascat: consider removing this propagated input: r-ggplot2 r-gwascat: consider removing this propagated input: r-rsamtools r-gwascat: consider removing this propagated input: r-rtracklayer # NOT DONE r-rcas: consider adding this input: pandoc r-rcas: consider adding this propagated input: r-knitr r-rcas: consider removing this propagated input: pandoc # NOT DONE r-mutationalpatterns: consider adding this native input: r-knitr r-mutationalpatterns: consider adding this propagated input: r-bsgenome r-mutationalpatterns: consider adding this propagated input: r-dplyr r-mutationalpatterns: consider adding this propagated input: r-ggalluvial r-mutationalpatterns: consider adding this propagated input: r-magrittr r-mutationalpatterns: consider adding this propagated input: r-purrr r-mutationalpatterns: consider adding this propagated input: r-stringr r-mutationalpatterns: consider adding this propagated input: r-tibble r-mutationalpatterns: consider adding this propagated input: r-tidyr r-mutationalpatterns: consider removing this propagated input: r-bsgenome-hsapiens-1000g r-mutationalpatterns: consider removing this propagated input: r-bsgenome-hsapiens-ucsc-hg19 r-mutationalpatterns: consider removing this propagated input: r-plyr r-mutationalpatterns: consider removing this propagated input: r-reshape2 r-mutationalpatterns: consider removing this propagated input: r-summarizedexperiment # NOT DONE r-msnid: consider adding this propagated input: r-annotationdbi r-msnid: consider adding this propagated input: r-annotationhub r-msnid: consider adding this propagated input: r-biocgenerics r-msnid: consider adding this propagated input: r-biocstyle r-msnid: consider adding this propagated input: r-biostrings r-msnid: consider adding this propagated input: r-ggplot2 r-msnid: consider adding this propagated input: r-msmstests r-msnid: consider adding this propagated input: r-purrr r-msnid: consider adding this propagated input: r-rlang r-msnid: consider adding this propagated input: r-runit r-msnid: consider adding this propagated input: r-stringr r-msnid: consider adding this propagated input: r-tibble r-msnid: consider adding this propagated input: r-xtable # NOT DONE r-rhtslib: consider removing this propagated input: curl # NOT DONE r-mzr: consider removing this input: boost # NOT DONE r-pcamethods: consider adding this input: rcpp # NOT DONE r-mzid: consider removing this propagated input: r-rcpp # NOT DONE r-edger: consider removing this propagated input: r-statmod # NOT DONE r-flowclust: consider removing this input: gsl # NOT DONE r-cytoml: consider adding this input: xml2 r-cytoml: consider removing this input: libxml2 # NOT DONE r-roc: consider adding this native input: r-knitr # NOT DONE r-rhdf5lib: consider removing this native input: hdf5-source r-rhdf5lib: consider removing this propagated input: hdf5 # MISSED what had be done r-abseqr: consider removing this input: pandoc-citeproc # MISSED what had be done r-rbowtie: consider removing this input: zlib # # DONE # r-shortread: consider adding this propagated input: r-rhtslib r-summarizedexperiment: consider adding this propagated input: r-matrixgenerics r-biomart: consider adding this propagated input: r-xml2 r-a4preproc: consider adding this native input: r-knitr r-a4preproc: consider adding this propagated input: r-biobase r-a4preproc: consider adding this propagated input: r-biocgenerics r-a4preproc: consider removing this propagated input: r-annotationdbi r-a4classif: consider adding this native input: r-knitr r-a4classif: consider adding this propagated input: r-biobase r-a4classif: consider removing this propagated input: r-mlinterfaces r-a4core: consider adding this native input: r-knitr r-a4base: consider removing this propagated input: r-annotationdbi r-destiny: consider removing this native input: r-nbconvertr r-destiny: consider removing this propagated input: r-nbconvertr r-yapsa: consider adding this propagated input: r-limsolve r-yapsa: consider removing this propagated input: r-lsei r-annotate: consider adding this propagated input: r-httr r-annotate: consider removing this propagated input: r-rcurl r-wavcluster: consider removing this propagated input: r-wmtsa r-depecher: consider adding this propagated input: r-gmodels r-mixomics: consider adding this propagated input: r-ggrepel r-motifstack: consider removing this propagated input: r-grimport2 r-motifstack: consider removing this propagated input: r-motiv r-motifstack: consider removing this propagated input: r-scales r-genomicscores: consider adding this propagated input: r-biocfilecache r-genomicscores: consider adding this propagated input: r-biocmanager r-a4reporting: consider adding this native input: r-knitr r-a4reporting: consider removing this propagated input: r-annaffy r-chippeakanno: consider adding this propagated input: r-ggplot2 r-chippeakanno: consider adding this propagated input: r-keggrest r-chippeakanno: consider removing this propagated input: r-biobase r-chippeakanno: consider removing this propagated input: r-biocmanager r-chippeakanno: consider removing this propagated input: r-bsgenome r-chippeakanno: consider removing this propagated input: r-delayedarray r-chippeakanno: consider removing this propagated input: r-go-db r-chippeakanno: consider removing this propagated input: r-idr r-chippeakanno: consider removing this propagated input: r-limma r-chippeakanno: consider removing this propagated input: r-seqinr r-edaseq: consider removing this propagated input: r-deseq r-glimma: consider adding this propagated input: r-deseq2 r-glimma: consider adding this propagated input: r-htmlwidgets r-glimma: consider adding this propagated input: r-limma r-glimma: consider adding this propagated input: r-summarizedexperiment r-seqlogo: consider adding this native input: r-knitr r-systempiper: consider adding this propagated input: r-iranges r-rtracklayer: consider adding this propagated input: r-zlibbioc