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tdhock / data.table-revdeps

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DESeq2 not available for checking Anaconda #10

Closed tdhock closed 8 months ago

tdhock commented 8 months ago 
> install.time <- system.time({
+   install.packages(rev.dep, dep=TRUE)
+ })
Installing package into '/tmp/th798/7296946/R-4.3.2/29/library'
(as 'lib' is unspecified)
Warning: dependency 'DESeq2' is not available
also installing the dependencies 'ape', 'pheatmap', 'lookup', 'rafalib'
tdhock commented 8 months ago

this is a bioc package https://bioconductor.org/packages/release/bioc/html/DESeq2.html so need to add that repo

tdhock commented 8 months ago

should be fixed by https://github.com/tdhock/data.table-revdeps/commit/cd1234263772b12100307601a69211fef9f64833

tdhock commented 8 months ago

same for rhdf5

tdhock commented 8 months ago

actually this is still not solved, but may be solved by using BiocManager::install as in https://github.com/tdhock/data.table-revdeps/issues/9#issuecomment-1904511126

tdhock commented 8 months ago

problem: RCurl is in popular_deps, which were installed after bioc. RCurl is required for GenomeInfoDb though (which is required for GO.db etc). Now trying to install GO.db after popular_deps, https://github.com/tdhock/data.table-revdeps/commit/4a00fd20513083bdc9510dac7558bb6dddad188c

tdhock commented 8 months ago

GO.db is installed but how do we get others? https://carpentries-incubator.github.io/bioc-project/03-installing-bioconductor.html says BiocManager::install takes pkg from bioc first, then cran after.

tdhock commented 8 months ago

for example RVA is a CRAN package that depends on a few bioc packages (igraph included). ICAMS too (not igraph), BSgenome.Hsapiens.UCSC.hg38 is suggested, and in versioned bioc repo. install.packages("ICAMS",dep=TRUE) says not avail. What about BiocManager::install()? we could just fix options to https://bioconductor.org/packages/devel/data/annotation/ etc,

 > BiocManager::repositories()
                                                 BioCsoft
            "https://bioconductor.org/packages/3.19/bioc"
                                                  BioCann
 "https://bioconductor.org/packages/3.19/data/annotation"
                                                  BioCexp
 "https://bioconductor.org/packages/3.19/data/experiment"
                                            BioCworkflows
       "https://bioconductor.org/packages/3.19/workflows"
                                                BioCbooks
           "https://bioconductor.org/packages/3.19/books"

      "http://www.bioconductor.org/packages/release/bioc"
tdhock commented 8 months ago

looks like this works,

!> install.packages("ICAMS",dep=TRUE,repos=c(BiocManager::repositories(),"http:/\
 /cloud.r-project.org"))
 also installing the dependencies 'BSgenome.Hsapiens.1000genomes.hs37d5', 'BSgen\
 ome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm10'

 trying URL 'https://bioconductor.org/packages/3.19/data/annotation/src/contrib/\
 BSgenome.Hsapiens.1000genomes.hs37d5_0.99.1.tar.gz'
 Content type 'application/x-gzip' length 687514862 bytes (655.7 MB)
tdhock commented 8 months ago

should be fixed by https://github.com/tdhock/data.table-revdeps/commit/9c1bafb0eae07f6bca7765045fe7a5b8b3ec8985