Hi I am trying to install biomart and rtracklayer packages to my R. But I got an error. It is a pretty easy thing to install but I couldnt manage.
> BiocManager::install(c("biomaRt", "rtracklayer"))
I am writing that command to my Rstudio to install both biomart and rtracklayer in the same time. But it gives me warnings as in below.
Warning messages:
1: In .inet_warning(msg) :
unable to access index for repository https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1:
cannot open URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
2: In .inet_warning(msg) :
unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1:
cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
3: In .inet_warning(msg) :
unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1:
cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
4: In .inet_warning(msg) :
unable to access index for repository https://bioconductor.org/packages/3.14/workflows/bin/macosx/big-sur-arm64/contrib/4.1:
cannot open URL 'https://bioconductor.org/packages/3.14/workflows/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
5: In .inet_warning(msg) :
unable to access index for repository https://bioconductor.org/packages/3.14/books/bin/macosx/big-sur-arm64/contrib/4.1:
cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
6: In .inet_warning(msg) :
installation of package ‘Biobase’ had non-zero exit status
7: In .inet_warning(msg) :
installation of package ‘BiocParallel’ had non-zero exit status
8: In .inet_warning(msg) :
installation of package ‘BiocFileCache’ had non-zero exit status
9: In .inet_warning(msg) :
installation of package ‘S4Vectors’ had non-zero exit status
10: In .inet_warning(msg) :
installation of package ‘zlibbioc’ had non-zero exit status
11: In .inet_warning(msg) :
installation of package ‘Rhtslib’ had non-zero exit status
12: In .inet_warning(msg) :
installation of package ‘IRanges’ had non-zero exit status
13: In .inet_warning(msg) :
installation of package ‘BiocIO’ had non-zero exit status
14: In .inet_warning(msg) :
installation of package ‘DelayedArray’ had non-zero exit status
15: In .inet_warning(msg) :
installation of package ‘XVector’ had non-zero exit status
16: In .inet_warning(msg) :
installation of package ‘GenomeInfoDb’ had non-zero exit status
17: In .inet_warning(msg) :
installation of package ‘GenomicRanges’ had non-zero exit status
18: In .inet_warning(msg) :
installation of package ‘Biostrings’ had non-zero exit status
19: In .inet_warning(msg) :
installation of package ‘KEGGREST’ had non-zero exit status
20: In .inet_warning(msg) :
installation of package ‘SummarizedExperiment’ had non-zero exit status
21: In .inet_warning(msg) :
installation of package ‘Rsamtools’ had non-zero exit status
22: In .inet_warning(msg) :
installation of package ‘AnnotationDbi’ had non-zero exit status
23: In .inet_warning(msg) :
installation of package ‘GenomicAlignments’ had non-zero exit status
24: In .inet_warning(msg) :
installation of package ‘biomaRt’ had non-zero exit status
25: In .inet_warning(msg) :
installation of package ‘rtracklayer’ had non-zero exit status
So what should I do? Thanks
can you also paste output of
sessionInfo()
?