49 pkgs can't be installed because they are in official jammy/universe for R-4.1 but not in r2u
Closed this issue · 17 comments
The r-bioc-affxparser package is not included in your r2u packages probably because no CRAN package depends on it.
However it is part of the ubuntu jammy universe repository https://packages.ubuntu.com/jammy/r-bioc-affxparser
And since ubuntu jammy ships with R-4.1, the package is not installable on an R-4.2 system:
$ sudo apt install r-bioc-affxparser
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
r-bioc-affxparser : Depends: r-api-bioc-3.14
E: Unable to correct problems, you have held broken packages.
Could you extend your r2u inclusion criteria to all those bioconductor packages already in ubuntu jammy? I took the 99 "r-bioc-" packages from https://packages.ubuntu.com/search?suite=jammy&arch=amd64&searchon=names&keywords=r-bioc- and with a rudimentary script I filtered out those already in r2u. If I am not mistaken, I would be asking you to include 49 additional packages in r2u that since they are already in ubuntu jammy they are not installable on my system via apt:
r-bioc-affxparser
r-bioc-altcdfenvs
r-bioc-arrayexpress
r-bioc-ballgown
r-bioc-basilisk.utils
r-bioc-bioccheck
r-bioc-biocviews
r-bioc-bitseq
r-bioc-bladderbatch
r-bioc-cner
r-bioc-ctc
r-bioc-cummerbund
r-bioc-dada2
r-bioc-degnorm
r-bioc-degreport
r-bioc-demixt
r-bioc-deseq
r-bioc-destiny
r-bioc-dexseq
r-bioc-dir.expiry
r-bioc-dirichletmultinomial
r-bioc-drimseq
r-bioc-dropletutils
r-bioc-dupradar
r-bioc-ebseq
r-bioc-edaseq
r-bioc-eir
r-bioc-experimenthub
r-bioc-fishpond
r-bioc-genelendatabase
r-bioc-genomeinfodbdata
r-bioc-genomicfiles
r-bioc-ggbio
r-bioc-glmgampoi
r-bioc-goseq
r-bioc-grohmm
r-bioc-hilbertvis
r-bioc-hsmmsinglecell
r-bioc-htsfilter
r-bioc-hypergraph
r-bioc-ihw
r-bioc-ioniser
r-bioc-isoformswitchanalyzer
r-bioc-lpsymphony
r-bioc-makecdfenv
I'll get those packages straight from Bioconductor if I need them, but I feel it would make sense to cover those and they are not that many (I'm assuming the build process is mostly automated)
Thanks
Correct, r-bioc-affxparser is not yet in the set.
Could you extend your r2u inclusion criteria to all those bioconductor packages already in ubuntu jammy?
It is actually manual labor (no prebuilds to lean on ...) and my personal focus in CRAN/ I see what I can do but this is a slight feature-creep.
OTOH we do have a fair number. You could use my RcppAPT package on CRAN to search your apt index programmatically from R if you want.
r-bioc-a4core_1.44.0-1.ca2204.1_all.deb
r-bioc-affy_1.74.0-1.ca2204.1_amd64.deb
r-bioc-affyio_1.66.0-1.ca2204.1_amd64.deb
r-bioc-aims_1.28.0-1.ca2204.1_all.deb
r-bioc-all_1.38.0-1.ca2204.1_all.deb
r-bioc-annotate_1.74.0-1.ca2204.1_all.deb
r-bioc-annotationdbi_1.58.0-1.ca2204.1_all.deb
r-bioc-annotationfilter_1.20.0-1.ca2204.1_all.deb
r-bioc-annotationforge_1.38.0-1.ca2204.1_all.deb
r-bioc-annotationhub_3.4.0-1.ca2204.1_amd64.deb
r-bioc-apeglm_1.18.0-1.ca2204.1_amd64.deb
r-bioc-aroma.light_3.26.0-1.ca2204.1_all.deb
r-bioc-bamsignals_1.28.0-1.ca2204.1_amd64.deb
r-bioc-bayseq_2.30.0-1.ca2204.1_all.deb
r-bioc-beachmat_2.12.0-1.ca2204.1_amd64.deb
r-bioc-beadarray_2.46.0-1.ca2204.1_amd64.deb
r-bioc-beaddatapackr_1.48.0-1.ca2204.1_amd64.deb
r-bioc-bicare_1.54.0-1.ca2204.1_amd64.deb
r-bioc-biobase_2.56.0-1.ca2204.1_amd64.deb
r-bioc-biocfilecache_2.4.0-1.ca2204.1_all.deb
r-bioc-biocgenerics_0.42.0-1.ca2204.1_all.deb
r-bioc-biocio_1.6.0-1.ca2204.1_all.deb
r-bioc-biocneighbors_1.14.0-1.ca2204.1_amd64.deb
r-bioc-biocparallel_1.30.0-1.ca2204.1_amd64.deb
r-bioc-biocsingular_1.12.0-1.ca2204.1_amd64.deb
r-bioc-biocstyle_2.24.0-1.ca2204.1_all.deb
r-bioc-biocversion_3.15.2-1.ca2204.1_all.deb
r-bioc-biomart_2.52.0-1.ca2204.1_all.deb
r-bioc-biomformat_1.24.0-1.ca2204.1_all.deb
r-bioc-biostrings_2.64.0-1.ca2204.1_amd64.deb
r-bioc-biovizbase_1.44.0-1.ca2204.1_amd64.deb
r-bioc-birewire_3.28.0-1.ca2204.1_amd64.deb
r-bioc-bluster_1.6.0-1.ca2204.1_amd64.deb
r-bioc-bsgenome_1.64.0-1.ca2204.1_all.deb
r-bioc-bsgenome.hsapiens.ucsc.hg19_1.4.3-1.ca2204.1_all.deb
r-bioc-bsgenome.hsapiens.ucsc.hg38_1.4.4-1.ca2204.1_all.deb
r-bioc-bsgenome.mmusculus.ucsc.mm10_1.4.3-1.ca2204.1_all.deb
r-bioc-bsgenome.mmusculus.ucsc.mm9_1.4.0-1.ca2204.1_all.deb
r-bioc-bumphunter_1.38.0-1.ca2204.1_all.deb
r-bioc-bumpymatrix_1.4.0-1.ca2204.1_all.deb
r-bioc-category_2.62.0-1.ca2204.1_all.deb
r-bioc-cellnoptr_1.42.0-1.ca2204.1_amd64.deb
r-bioc-cghbase_1.56.0-1.ca2204.1_all.deb
r-bioc-chemminer_3.48.0-1.ca2204.1_amd64.deb
r-bioc-chipseeker_1.32.0-1.ca2204.1_all.deb
r-bioc-chopsticks_1.62.0-1.ca2204.1_amd64.deb
r-bioc-cliquems_1.10.0-1.ca2204.1_amd64.deb
r-bioc-clusterprofiler_4.4.1-1.ca2204.1_all.deb
r-bioc-cnorode_1.38.0-1.ca2204.1_amd64.deb
r-bioc-complexheatmap_2.12.0-1.ca2204.1_all.deb
r-bioc-consensusclusterplus_1.60.0-1.ca2204.1_all.deb
r-bioc-copynumber_1.36.0-1.ca2204.1_all.deb
r-bioc-cordon_1.14.0-1.ca2204.1_all.deb
r-bioc-coregx_2.0.0-1.ca2204.1_all.deb
r-bioc-correp_1.62.0-1.ca2204.1_all.deb
r-bioc-cqn_1.42.0-1.ca2204.1_all.deb
r-bioc-decipher_2.24.0-1.ca2204.1_amd64.deb
r-bioc-delayedarray_0.22.0-1.ca2204.1_amd64.deb
r-bioc-delayedmatrixstats_1.18.0-1.ca2204.1_all.deb
r-bioc-deseq2_1.36.0-1.ca2204.1_amd64.deb
r-bioc-diffbind_3.6.0-1.ca2204.1_amd64.deb
r-bioc-diffcoexp_1.16.0-1.ca2204.1_all.deb
r-bioc-dnacopy_1.70.0-1.ca2204.1_amd64.deb
r-bioc-do.db_2.9-1.ca2204.1_all.deb
r-bioc-dose_3.22.0-1.ca2204.1_all.deb
r-bioc-dyndoc_1.74.0-1.ca2204.1_all.deb
r-bioc-ebimage_4.38.0-1.ca2204.1_amd64.deb
r-bioc-edger_3.38.1-1.ca2204.1_amd64.deb
r-bioc-empiricalbrownsmethod_1.24.0-1.ca2204.1_all.deb
r-bioc-enrichplot_1.16.0-1.ca2204.1_all.deb
r-bioc-ensembldb_2.20.1-1.ca2204.1_all.deb
r-bioc-fabia_2.42.0-1.ca2204.1_amd64.deb
r-bioc-fgsea_1.22.0-1.ca2204.1_amd64.deb
r-bioc-fmcsr_1.38.0-1.ca2204.1_amd64.deb
r-bioc-gage_2.46.0-1.ca2204.1_all.deb
r-bioc-gdsfmt_1.32.0-1.ca2204.1_amd64.deb
r-bioc-genbankr_1.24.0-1.ca2204.1_all.deb
r-bioc-genefilter_1.78.0-1.ca2204.1_amd64.deb
r-bioc-genefu_2.28.0-1.ca2204.1_all.deb
r-bioc-geneplotter_1.74.0-1.ca2204.1_all.deb
r-bioc-geneticsped_1.58.0-1.ca2204.1_amd64.deb
r-bioc-genie3_1.18.0-1.ca2204.1_amd64.deb
r-bioc-genomeinfodb_1.32.2-1.ca2204.1_all.deb
r-bioc-genomicalignments_1.32.0-1.ca2204.1_amd64.deb
r-bioc-genomicfeatures_1.48.0-1.ca2204.1_all.deb
r-bioc-genomicinteractions_1.30.0-1.ca2204.1_all.deb
r-bioc-genomicranges_1.48.0-1.ca2204.1_amd64.deb
r-bioc-geometadb_1.58.0-1.ca2204.1_all.deb
r-bioc-geoquery_2.64.0-1.ca2204.1_all.deb
r-bioc-ggmsa_1.2.0-1.ca2204.1_all.deb
r-bioc-ggtree_3.4.0-1.ca2204.1_all.deb
r-bioc-globalancova_4.14.0-1.ca2204.1_amd64.deb
r-bioc-globaltest_5.50.0-1.ca2204.1_all.deb
r-bioc-go.db_3.15.0-1.ca2204.1_all.deb
r-bioc-gosemsim_2.22.0-1.ca2204.1_amd64.deb
r-bioc-gosim_1.34.0-1.ca2204.1_amd64.deb
r-bioc-gostats_2.62.0-1.ca2204.1_all.deb
r-bioc-gpls_1.68.0-1.ca2204.1_all.deb
r-bioc-graph_1.74.0-1.ca2204.1_amd64.deb
r-bioc-graphite_1.42.0-1.ca2204.1_all.deb
r-bioc-greylistchip_1.28.0-1.ca2204.1_all.deb
r-bioc-gseabase_1.58.0-1.ca2204.1_all.deb
r-bioc-gsva_1.44.0-1.ca2204.1_amd64.deb
r-bioc-gsvadata_1.32.0-1.ca2204.1_all.deb
r-bioc-gviz_1.40.1-1.ca2204.1_all.deb
r-bioc-hdf5array_1.24.0-1.ca2204.1_amd64.deb
r-bioc-heatplus_3.4.0-1.ca2204.1_all.deb
r-bioc-hgu95a.db_3.13.0-1.ca2204.1_all.deb
r-bioc-hibag_1.32.0-1.ca2204.1_amd64.deb
r-bioc-hopach_2.56.0-1.ca2204.1_amd64.deb
r-bioc-ibbig_1.40.0-1.ca2204.1_amd64.deb
r-bioc-icens_1.68.0-1.ca2204.1_all.deb
r-bioc-illuminaio_0.38.0-1.ca2204.1_amd64.deb
r-bioc-impute_1.70.0-1.ca2204.1_amd64.deb
r-bioc-interactionset_1.24.0-1.ca2204.1_amd64.deb
r-bioc-interactivedisplaybase_1.34.0-1.ca2204.1_all.deb
r-bioc-iranges_2.30.0-1.ca2204.1_amd64.deb
r-bioc-kegggraph_1.56.0-1.ca2204.1_all.deb
r-bioc-keggrest_1.36.0-1.ca2204.1_all.deb
r-bioc-lbe_1.64.0-1.ca2204.1_all.deb
r-bioc-lfa_1.26.0-1.ca2204.1_amd64.deb
r-bioc-limma_3.52.1-1.ca2204.1_amd64.deb
r-bioc-m3c_1.18.0-1.ca2204.1_all.deb
r-bioc-maanova_1.66.0-1.ca2204.1_amd64.deb
r-bioc-maftools_2.12.0-1.ca2204.1_amd64.deb
r-bioc-marray_1.74.0-1.ca2204.1_all.deb
r-bioc-massspecwavelet_1.62.0-1.ca2204.1_all.deb
r-bioc-mast_1.22.0-1.ca2204.1_all.deb
r-bioc-matrixgenerics_1.8.0-1.ca2204.1_all.deb
r-bioc-meigor_1.29.0-1.ca2204.1_all.deb
r-bioc-metagenomeseq_1.38.0-1.ca2204.1_all.deb
r-bioc-metapod_1.4.0-1.ca2204.1_amd64.deb
r-bioc-mfuzz_2.56.0-1.ca2204.1_all.deb
r-bioc-minet_3.54.0-1.ca2204.1_amd64.deb
r-bioc-minfi_1.42.0-1.ca2204.1_all.deb
r-bioc-mixomics_6.20.0-1.ca2204.1_all.deb
r-bioc-mlinterfaces_1.76.0-1.ca2204.1_all.deb
r-bioc-mscoreutils_1.8.0-1.ca2204.1_amd64.deb
r-bioc-msfeatures_1.4.0-1.ca2204.1_all.deb
r-bioc-msnbase_2.22.0-1.ca2204.1_amd64.deb
r-bioc-multiassayexperiment_1.22.0-1.ca2204.1_all.deb
r-bioc-multidataset_1.24.0-1.ca2204.1_all.deb
r-bioc-multtest_2.52.0-1.ca2204.1_amd64.deb
r-bioc-muscle_3.38.0-1.ca2204.1_amd64.deb
r-bioc-mzid_1.34.0-1.ca2204.1_all.deb
r-bioc-mzr_2.30.0-1.ca2204.1_amd64.deb
r-bioc-opossom_2.14.0-1.ca2204.1_amd64.deb
r-bioc-org.hs.eg.db_3.15.0-1.ca2204.1_all.deb
r-bioc-org.mm.eg.db_3.15.0-1.ca2204.1_all.deb
r-bioc-pathview_1.36.0-1.ca2204.1_all.deb
r-bioc-pcamethods_1.88.0-1.ca2204.1_amd64.deb
r-bioc-pharmacogx_3.0.0-1.ca2204.1_amd64.deb
r-bioc-phyloseq_1.40.0-1.ca2204.1_all.deb
r-bioc-piano_2.12.0-1.ca2204.1_all.deb
r-bioc-preprocesscore_1.58.0-1.ca2204.1_amd64.deb
r-bioc-protgenerics_1.28.0-1.ca2204.1_all.deb
r-bioc-pvca_1.36.0-1.ca2204.1_all.deb
r-bioc-qpgraph_2.30.0-1.ca2204.1_amd64.deb
r-bioc-qusage_2.30.0-1.ca2204.1_all.deb
r-bioc-qvalue_2.28.0-1.ca2204.1_all.deb
r-bioc-r4rna_1.24.0-1.ca2204.1_all.deb
r-bioc-rankprod_3.22.0-1.ca2204.1_all.deb
r-bioc-rbgl_1.72.0-1.ca2204.1_amd64.deb
r-bioc-rcy3_2.16.0-1.ca2204.1_all.deb
r-bioc-rdisop_1.56.0-1.ca2204.1_amd64.deb
r-bioc-reactome.db_1.79.0-1.ca2204.1_all.deb
r-bioc-reder_2.0.0-1.ca2204.1_all.deb
r-bioc-rgraphviz_2.40.0-1.ca2204.1_amd64.deb
r-bioc-rhdf5_2.40.0-1.ca2204.1_amd64.deb
r-bioc-rhdf5filters_1.8.0-1.ca2204.1_amd64.deb
r-bioc-rhdf5lib_1.18.0-1.ca2204.1_amd64.deb
r-bioc-rhtslib_1.28.0-1.ca2204.1_amd64.deb
r-bioc-rlmm_1.58.0-1.ca2204.1_all.deb
r-bioc-roc_1.72.0-1.ca2204.1_amd64.deb
r-bioc-ropls_1.28.0-1.ca2204.1_all.deb
r-bioc-rsamtools_2.12.0-1.ca2204.1_amd64.deb
r-bioc-rtracklayer_1.56.0-1.ca2204.1_amd64.deb
r-bioc-rwikipathways_1.16.0-1.ca2204.1_all.deb
r-bioc-s4vectors_0.34.0-1.ca2204.1_amd64.deb
r-bioc-safe_3.36.0-1.ca2204.1_all.deb
r-bioc-scaledmatrix_1.4.0-1.ca2204.1_all.deb
r-bioc-scater_1.24.0-1.ca2204.1_all.deb
r-bioc-scran_1.24.0-1.ca2204.1_amd64.deb
r-bioc-scuttle_1.6.0-1.ca2204.1_amd64.deb
r-bioc-seqarray_1.36.0-1.ca2204.1_amd64.deb
r-bioc-seqvartools_1.34.0-1.ca2204.1_all.deb
r-bioc-shortread_1.54.0-1.ca2204.1_amd64.deb
r-bioc-siggenes_1.70.0-1.ca2204.1_all.deb
r-bioc-singlecellexperiment_1.18.0-1.ca2204.1_all.deb
r-bioc-singscore_1.16.0-1.ca2204.1_all.deb
r-bioc-snprelate_1.30.1-1.ca2204.1_amd64.deb
r-bioc-snpstats_1.46.0-1.ca2204.1_amd64.deb
r-bioc-sparsematrixstats_1.8.0-1.ca2204.1_amd64.deb
r-bioc-splatter_1.20.0-1.ca2204.1_all.deb
r-bioc-stringdb_2.8.0-1.ca2204.1_all.deb
r-bioc-summarizedexperiment_1.26.1-1.ca2204.1_all.deb
r-bioc-suprahex_1.34.0-1.ca2204.1_all.deb
r-bioc-survcomp_1.46.0-1.ca2204.1_amd64.deb
r-bioc-sva_3.44.0-1.ca2204.1_amd64.deb
r-bioc-systempiper_2.2.2-1.ca2204.1_all.deb
r-bioc-tcc_1.36.0-1.ca2204.1_all.deb
r-bioc-tkwidgets_1.74.0-1.ca2204.1_all.deb
r-bioc-topgo_2.48.0-1.ca2204.1_all.deb
r-bioc-toxicogx_2.0.0-1.ca2204.1_all.deb
r-bioc-trajectoryutils_1.4.0-1.ca2204.1_all.deb
r-bioc-treeio_1.20.0-1.ca2204.1_all.deb
r-bioc-trio_3.34.0-1.ca2204.1_all.deb
r-bioc-tscan_1.34.0-1.ca2204.1_all.deb
r-bioc-tweedeseq_1.42.0-1.ca2204.1_amd64.deb
r-bioc-txdb.hsapiens.ucsc.hg19.knowngene_3.2.2-1.ca2204.1_all.deb
r-bioc-txdb.hsapiens.ucsc.hg38.knowngene_3.15.0-1.ca2204.1_all.deb
r-bioc-txdb.mmusculus.ucsc.mm10.knowngene_3.10.0-1.ca2204.1_all.deb
r-bioc-variantannotation_1.42.0-1.ca2204.1_amd64.deb
r-bioc-vbmp_1.64.0-1.ca2204.1_all.deb
r-bioc-vsn_3.64.0-1.ca2204.1_amd64.deb
r-bioc-widgettools_1.74.0-1.ca2204.1_all.deb
r-bioc-wrench_1.14.0-1.ca2204.1_all.deb
r-bioc-xcms_3.18.0-1.ca2204.1_amd64.deb
r-bioc-xvector_0.36.0-1.ca2204.1_amd64.deb
r-bioc-zinbwave_1.18.0-1.ca2204.1_all.deb
r-bioc-zlibbioc_1.42.0-1.ca2204.1_amd64.deb
I just added r-bioc-affxparser for both focal and jammy, see if this works now. The best way forward is probably to do this on a as-needed basis.
Can you provide evidence of the claimed other 48 packages not installing (if and when you have pinning set up) ?
Also your initial post is wrong: the dependency issue is on the virtual BioC release tag the Debian maintainers add. No more, no less.
Correct,
r-bioc-affxparseris not yet in the set.Could you extend your r2u inclusion criteria to all those bioconductor packages already in ubuntu jammy?
It is actually manual labor (no prebuilds to lean on ...) and my personal focus in CRAN/ I see what I can do but this is a slight feature-creep.
Oh, if it implies manual labor please don't do this!
Can you provide evidence of the claimed other 48 packages not installing (if and when you have pinning set up) ?
Also your initial post is wrong: the dependency issue is on the virtual BioC release tag the Debian maintainers add. No more, no less.
I have set apt pinning:
Package: *
Pin: origin "dirk.eddelbuettel.com"
Pin-Priority: 700
The 49 packages (now 48) I mentioned are not in r2u. They come from the ubuntu universe package and therefore they have the r-api-bioc-3.14 virtual tag set and are not installable.
Reproducible example of the installation issue:
My concern is that those 48 packages on your r2u docker image may fail to be installed without giving any notice:
Here is a reproducible example of me trying to install the biocViews BioConductor package:
docker run \
--rm
docker.io/eddelbuettel/r2u:22.04 \
bash -c 'install.r BiocManager; R -e "BiocManager::install(\"biocViews\"); library(biocViews)"'With the corresponding output:
The install.r BiocManager` part works:
Install system packages as root...
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Get:1 http://security.ubuntu.com/ubuntu jammy-security InRelease [110 kB]
Hit http://archive.ubuntu.com/ubuntu jammy InRelease
Get:2 http://archive.ubuntu.com/ubuntu jammy-updates InRelease [109 kB]
Get:3 https://ppa.launchpadcontent.net/marutter/rrutter4.0/ubuntu jammy InRelease [17.5 kB]
Get:4 http://archive.ubuntu.com/ubuntu jammy-backports InRelease [99.8 kB]
Ign https://dirk.eddelbuettel.com/cranapt jammy InRelease
Get:5 http://security.ubuntu.com/ubuntu jammy-security/universe amd64 Packages [89.8 kB]
Get:6 http://security.ubuntu.com/ubuntu jammy-security/restricted amd64 Packages [212 kB]
Get:7 https://dirk.eddelbuettel.com/cranapt jammy Release [5713 B]
Get:8 http://security.ubuntu.com/ubuntu jammy-security/main amd64 Packages [229 kB]
Get:9 http://security.ubuntu.com/ubuntu jammy-security/multiverse amd64 Packages [4648 B]
Get:10 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 Packages [380 kB]
Get:11 https://dirk.eddelbuettel.com/cranapt jammy Release.gpg [793 B]
Get:12 https://ppa.launchpadcontent.net/marutter/rrutter4.0/ubuntu jammy/main Sources [8932 B]
Get:13 http://archive.ubuntu.com/ubuntu jammy-updates/universe amd64 Packages [153 kB]
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Get:15 http://archive.ubuntu.com/ubuntu jammy-updates/multiverse amd64 Packages [4648 B]
Get:16 http://archive.ubuntu.com/ubuntu jammy-backports/universe amd64 Packages [2016 B]
Get:17 https://ppa.launchpadcontent.net/marutter/rrutter4.0/ubuntu jammy/main amd64 Packages [7564 B]
Get:18 https://dirk.eddelbuettel.com/cranapt jammy/main amd64 Packages [2062 kB]
Get:19 https://dirk.eddelbuettel.com/cranapt jammy/main all Packages [6382 kB]
Fetched 10.1 MB in 6s (931 kB/s)
Reading package lists... Done
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Get:1 https://dirk.eddelbuettel.com/cranapt jammy/main all r-cran-biocmanager all 1.30.18-1.ca2204.1 [338 kB]
Fetched 338 kB in 6s (17.2 kB/s)
Selecting previously unselected package r-cran-biocmanager.
(Reading database ... 21839 files and directories currently installed.)
Preparing to unpack .../r-cran-biocmanager_1.30.18-1.ca2204.1_all.deb ...
Unpacking r-cran-biocmanager (1.30.18-1.ca2204.1) ...
Setting up r-cran-biocmanager (1.30.18-1.ca2204.1) ...
The R -e "BiocManager::install(\"biocViews\"); library(biocViews)"'does not succeed:
This is the `BiocManager::install("biocViews") output, which does not show any relevant error but also it does not show any installation of the biocViews package:
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details
replacement repositories:
CRAN: https://cloud.r-project.org
Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.0 (2022-04-22)
Installing package(s) 'BiocVersion', 'biocViews'
Install system packages as root...
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Get:1 https://dirk.eddelbuettel.com/cranapt jammy/main all r-bioc-biocversion all 3.15.2-1.ca2204.1 [6976 B]
Fetched 6976 B in 0s (0 B/s)
Selecting previously unselected package r-bioc-biocversion.
(Reading database ... 21873 files and directories currently installed.)
Preparing to unpack .../r-bioc-biocversion_3.15.2-1.ca2204.1_all.deb ...
Unpacking r-bioc-biocversion (3.15.2-1.ca2204.1) ...
Setting up r-bioc-biocversion (3.15.2-1.ca2204.1) ...
Old packages: 'nlme'
And indeed we can verify it is not installed:
Error in library(biocViews) : there is no package called ‘biocViews’
Since the virtual BioC release tag is there, the packages are not installable and bspm fails to install them.
Maybe this should be reported to bspm instead?
Ah, now we're talking. Your "error", if any, is to use BiocManager.
And just like using the RStudio Package manager, or renv, or .... [insert any other mechanism not using install.packages()] fails. There is nothing we can do here.
If I do a quick check (in the r2u container) of install.r S4Vectors it installs and is loadable (and of course pulls in BiocGenerics too).
With install.r I face the same issue, as long as the package I try to install is one of the 48 packages I mentioned (S4Vectors is not in the list I compiled because it is found in r2u already):
docker run \
--rm \
docker.io/eddelbuettel/r2u:22.04 \
bash -c 'install.r biocViews; Rscript -e "library(biocViews)"'
Gives me:
Install system packages as root...
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Hit http://archive.ubuntu.com/ubuntu jammy InRelease
Get:1 http://archive.ubuntu.com/ubuntu jammy-updates InRelease [109 kB]
Get:2 http://security.ubuntu.com/ubuntu jammy-security InRelease [110 kB]
Get:3 https://ppa.launchpadcontent.net/marutter/rrutter4.0/ubuntu jammy InRelease [17.5 kB]
Ign https://dirk.eddelbuettel.com/cranapt jammy InRelease
Get:4 https://dirk.eddelbuettel.com/cranapt jammy Release [5713 B]
Get:5 http://archive.ubuntu.com/ubuntu jammy-backports InRelease [99.8 kB]
Get:6 https://dirk.eddelbuettel.com/cranapt jammy Release.gpg [793 B]
Get:7 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 Packages [380 kB]
Get:8 https://ppa.launchpadcontent.net/marutter/rrutter4.0/ubuntu jammy/main Sources [8932 B]
Get:9 http://security.ubuntu.com/ubuntu jammy-security/universe amd64 Packages [89.8 kB]
Get:10 http://archive.ubuntu.com/ubuntu jammy-updates/multiverse amd64 Packages [4648 B]
Get:11 http://archive.ubuntu.com/ubuntu jammy-updates/restricted amd64 Packages [236 kB]
Get:12 http://archive.ubuntu.com/ubuntu jammy-updates/universe amd64 Packages [153 kB]
Get:13 http://archive.ubuntu.com/ubuntu jammy-backports/universe amd64 Packages [2016 B]
Get:14 http://security.ubuntu.com/ubuntu jammy-security/multiverse amd64 Packages [4648 B]
Get:15 http://security.ubuntu.com/ubuntu jammy-security/restricted amd64 Packages [212 kB]
Get:16 https://dirk.eddelbuettel.com/cranapt jammy/main amd64 Packages [2062 kB]
Get:17 https://ppa.launchpadcontent.net/marutter/rrutter4.0/ubuntu jammy/main amd64 Packages [7564 B]
Get:18 http://security.ubuntu.com/ubuntu jammy-security/main amd64 Packages [229 kB]
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Reading package lists... Done
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Error in library(biocViews) : there is no package called ‘biocViews’
Execution halted
This problem happens with packages found in the ubuntu 22.04 universe repository and not found in r2u.
Of course. The 'Depends: r-bioc-3.14' makes it so.
Eg try the more explicit apt command:
root@7bf6236df37e:/# sudo apt install r-bioc-biocViews
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
E: Unable to locate package r-bioc-biocViews
root@7bf6236df37e:/# sudo apt install r-bioc-biocviews
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
r-bioc-biocviews : Depends: r-api-bioc-3.14
E: Unable to correct problems, you have held broken packages.
root@7bf6236df37e:/#
bspm may just hide the error.
If you want to look hard into pinning I believe there is a way to set an exclusion too so maybe you can try that (I haven't ...)
Alternatively, you could create an (almost empty, near-virtual) package providing r-api-bioc-3.14 to satisfy the constraint imposed by the fellow Debian maintainers who think we need r-api-bioc-* packages (I take a different view....)
Ok, to prove that point I just created a dummy 'empty' package, currently called 'fake-bioc' which has a Provides: r-api-bioc-3.14 and with that can work:
root@cffc07a66985:/deb# dpkg -i fake-bioc_0.0.1_all.deb
Selecting previously unselected package fake-bioc.
(Reading database ... 21839 files and directories currently installed.)
Preparing to unpack fake-bioc_0.0.1_all.deb ...
Unpacking fake-bioc (0.0.1) ...
Setting up fake-bioc (0.0.1) ...
root@cffc07a66985:/deb# install.r BiocViews
Install system packages as root...
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Ign https://dirk.eddelbuettel.com/cranapt jammy InRelease
Get:1 https://dirk.eddelbuettel.com/cranapt jammy Release [5713 B]
Get:2 https://dirk.eddelbuettel.com/cranapt jammy Release.gpg [793 B]
Get:3 http://security.ubuntu.com/ubuntu jammy-security InRelease [110 kB]
Hit http://archive.ubuntu.com/ubuntu jammy InRelease
Get:4 https://dirk.eddelbuettel.com/cranapt jammy/main amd64 Packages [2062 kB]
Get:5 http://archive.ubuntu.com/ubuntu jammy-updates InRelease [109 kB]
Get:6 https://ppa.launchpadcontent.net/marutter/rrutter4.0/ubuntu jammy InRelease [17.5 kB]
Get:7 https://dirk.eddelbuettel.com/cranapt jammy/main all Packages [6382 kB]
Get:8 http://archive.ubuntu.com/ubuntu jammy-backports InRelease [99.8 kB]
Get:9 http://security.ubuntu.com/ubuntu jammy-security/restricted amd64 Packages [212 kB]
Get:10 http://archive.ubuntu.com/ubuntu jammy-updates/universe amd64 Packages [153 kB]
Get:11 http://security.ubuntu.com/ubuntu jammy-security/universe amd64 Packages [89.8 kB]
Get:12 http://security.ubuntu.com/ubuntu jammy-security/main amd64 Packages [229 kB]
Get:13 http://security.ubuntu.com/ubuntu jammy-security/multiverse amd64 Packages [4648 B]
Get:14 http://archive.ubuntu.com/ubuntu jammy-updates/restricted amd64 Packages [236 kB]
Get:15 https://ppa.launchpadcontent.net/marutter/rrutter4.0/ubuntu jammy/main Sources [8932 B]
Get:16 http://archive.ubuntu.com/ubuntu jammy-updates/multiverse amd64 Packages [4648 B]
Get:17 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 Packages [380 kB]
Get:18 http://archive.ubuntu.com/ubuntu jammy-backports/universe amd64 Packages [2016 B]
Get:19 https://ppa.launchpadcontent.net/marutter/rrutter4.0/ubuntu jammy/main amd64 Packages [7564 B]
Fetched 10.1 MB in 0s (0 B/s)
Reading package lists... Done
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Get:1 http://archive.ubuntu.com/ubuntu jammy/universe amd64 r-bioc-biocviews all 1.62.1-1 [655 kB]
Get:2 https://dirk.eddelbuettel.com/cranapt jammy/main all r-bioc-biocgenerics all 0.42.0-1.ca2204.1 [582 kB]
Get:3 https://dirk.eddelbuettel.com/cranapt jammy/main amd64 r-bioc-biobase amd64 2.56.0-1.ca2204.1 [2096 kB]
Get:4 https://dirk.eddelbuettel.com/cranapt jammy/main amd64 r-bioc-graph amd64 1.74.0-1.ca2204.1 [1237 kB]
Get:5 https://dirk.eddelbuettel.com/cranapt jammy/main all r-cran-bh all 1.78.0-0-1.ca2204.1 [8330 kB]
Get:6 https://dirk.eddelbuettel.com/cranapt jammy/main amd64 r-bioc-rbgl amd64 1.72.0-1.ca2204.1 [2583 kB]
Get:7 https://dirk.eddelbuettel.com/cranapt jammy/main amd64 r-cran-xml amd64 3.99-0.10-1.ca2204.1 [1696 kB]
Get:8 https://dirk.eddelbuettel.com/cranapt jammy/main amd64 r-cran-bitops amd64 1.0-7-1.ca2204.1 [25.5 kB]
Get:9 https://dirk.eddelbuettel.com/cranapt jammy/main amd64 r-cran-rcurl amd64 1.98-1.7-1.ca2204.1 [799 kB]
Get:10 https://dirk.eddelbuettel.com/cranapt jammy/main all r-cran-runit all 0.4.32-1.ca2204.1 [281 kB]
Get:11 https://dirk.eddelbuettel.com/cranapt jammy/main all r-cran-biocmanager all 1.30.18-1.ca2204.1 [338 kB]
Fetched 18.6 MB in 6s (0 B/s)
Selecting previously unselected package r-bioc-biocgenerics.
(Reading database ... 21841 files and directories currently installed.)
Preparing to unpack .../00-r-bioc-biocgenerics_0.42.0-1.ca2204.1_all.deb ...
Unpacking r-bioc-biocgenerics (0.42.0-1.ca2204.1) ...
Selecting previously unselected package r-bioc-biobase.
Preparing to unpack .../01-r-bioc-biobase_2.56.0-1.ca2204.1_amd64.deb ...
Unpacking r-bioc-biobase (2.56.0-1.ca2204.1) ...
Selecting previously unselected package r-bioc-graph.
Preparing to unpack .../02-r-bioc-graph_1.74.0-1.ca2204.1_amd64.deb ...
Unpacking r-bioc-graph (1.74.0-1.ca2204.1) ...
Selecting previously unselected package r-cran-bh.
Preparing to unpack .../03-r-cran-bh_1.78.0-0-1.ca2204.1_all.deb ...
Unpacking r-cran-bh (1.78.0-0-1.ca2204.1) ...
Selecting previously unselected package r-bioc-rbgl.
Preparing to unpack .../04-r-bioc-rbgl_1.72.0-1.ca2204.1_amd64.deb ...
Unpacking r-bioc-rbgl (1.72.0-1.ca2204.1) ...
Selecting previously unselected package r-cran-xml.
Preparing to unpack .../05-r-cran-xml_3.99-0.10-1.ca2204.1_amd64.deb ...
Unpacking r-cran-xml (3.99-0.10-1.ca2204.1) ...
Selecting previously unselected package r-cran-bitops.
Preparing to unpack .../06-r-cran-bitops_1.0-7-1.ca2204.1_amd64.deb ...
Unpacking r-cran-bitops (1.0-7-1.ca2204.1) ...
Selecting previously unselected package r-cran-rcurl.
Preparing to unpack .../07-r-cran-rcurl_1.98-1.7-1.ca2204.1_amd64.deb ...
Unpacking r-cran-rcurl (1.98-1.7-1.ca2204.1) ...
Selecting previously unselected package r-cran-runit.
Preparing to unpack .../08-r-cran-runit_0.4.32-1.ca2204.1_all.deb ...
Unpacking r-cran-runit (0.4.32-1.ca2204.1) ...
Selecting previously unselected package r-cran-biocmanager.
Preparing to unpack .../09-r-cran-biocmanager_1.30.18-1.ca2204.1_all.deb ...
Unpacking r-cran-biocmanager (1.30.18-1.ca2204.1) ...
Selecting previously unselected package r-bioc-biocviews.
Preparing to unpack .../10-r-bioc-biocviews_1.62.1-1_all.deb ...
Unpacking r-bioc-biocviews (1.62.1-1) ...
Setting up r-cran-bh (1.78.0-0-1.ca2204.1) ...
Setting up r-bioc-biocgenerics (0.42.0-1.ca2204.1) ...
Setting up r-cran-bitops (1.0-7-1.ca2204.1) ...
Setting up r-cran-biocmanager (1.30.18-1.ca2204.1) ...
Setting up r-bioc-biobase (2.56.0-1.ca2204.1) ...
Setting up r-cran-runit (0.4.32-1.ca2204.1) ...
Setting up r-cran-xml (3.99-0.10-1.ca2204.1) ...
Setting up r-cran-rcurl (1.98-1.7-1.ca2204.1) ...
Setting up r-bioc-graph (1.74.0-1.ca2204.1) ...
Setting up r-bioc-rbgl (1.72.0-1.ca2204.1) ...
Setting up r-bioc-biocviews (1.62.1-1) ...
root@cffc07a66985:/deb# See https://github.com/eddelbuettel/bioc-api-package for a version of that helper package (now slightly renamed).
@zeehio -- did you get a chance to test this?
The tests I did worked fine. I think it would be nice if the bspm package could report installation errors but that's beyond this repository and the r2u packaging. I may contact the rspm maintainer and try to provide a patch.
Beyond that we can close this issue if you like.
(Feel free to provide the almost virtual package in your r2u repository if you feel like it)
Thanks for your time and work. It helped me a lot to understand how all of this works
The 'almost virtual' package is now on github, I think I will just point to it from the r2u documentation. Maybe sticking it into r2u is the way to go too. Gotta think about that...
Repos and their mechanics are very very cool and powerful, but not that well documented. I learned some ropes as a Debian maintainer. There is a bit of a formal / bureaucratic hurdle to climb these days to join Debian but you can always experiment with local packages, or with Ubuntu via Launchpad. Bug me (or the r-sig-debian list) if you have questions -- we all want to see this used and made more robust so your inquiries do help and are appreciated. Keep it comin...
I added such a package to jammy (and focal, though it may matter less there) and updated the FAQ with a new entry. So I think this can now be closed for good.