biomart and rtracklayer

Question

[biology_inform]

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

[Chirag Parsania]

can you also paste output of sessionInfo()?

Answer 1

[Mike Smith]

This looks like you're using the M1 version of R, and unfortunately Bioconductor does not yet provide binary packages for that architecture.

An alternative is to use the Mac version of R for Intel CPUs and run it with Rosetta. Bioconductor build binary packages for this platform and you should be able to install whatever package you like without requiring any additional software. From what I've read there's no discernible speed difference between using the Arm and Intel versions of R on a M1 processor, so buy picking the Intel version you gain compatibility without really sacrificing anything.

[biology_inform]

yes I installed intel verison and then everything worked, thank you so much! :)