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Question: Bioconductor installation problem (MacOSX El-Capitan)
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gravatar for zhanxw
5 months ago by
zhanxw0
zhanxw0 wrote:

After I upgraded to R 3.4.0, I cannot upgrade or install Bioconductor packages. Bottom are the error messages.

I tried to remove installer ( remove.packages("BiocInstaller")), but that did not help either.

Does BioConductor host packages for MacOSX El-Capitan? 

How should I fix this problem and be able to upgrade Bioconductor packages?

 

> R --vanilla

R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocInstaller::biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.4.0 (2017-04-21).
Old packages: 'Biobase', 'flowClust', 'flowWorkspace', 'graph', 'IRanges',
  'ncdfFlow', 'openCyto', 'RBGL', 'Rgraphviz', 'AnnotationHub', 'flowCore',
  'GenomicAlignments', 'GenomicRanges', 'limma', 'Rsamtools', 'rtracklayer',
  'S4Vectors', 'VariantAnnotation', 'XVector'
Update all/some/none? [a/s/n]: a
Warning: unable to access index for repository https://bioconductor.org/packages/3.4/bioc/bin/macosx/el-capitan/contrib/3.4:
  cannot open URL 'https://bioconductor.org/packages/3.4/bioc/bin/macosx/el-capitan/contrib/3.4/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.4/data/annotation/bin/macosx/el-capitan/contrib/3.4:
  cannot open URL 'https://bioconductor.org/packages/3.4/data/annotation/bin/macosx/el-capitan/contrib/3.4/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.4/data/experiment/bin/macosx/el-capitan/contrib/3.4:
  cannot open URL 'https://bioconductor.org/packages/3.4/data/experiment/bin/macosx/el-capitan/contrib/3.4/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.4/extra/bin/macosx/el-capitan/contrib/3.4:
  cannot open URL 'https://bioconductor.org/packages/3.4/extra/bin/macosx/el-capitan/contrib/3.4/PACKAGES'

ADD COMMENTlink modified 5 months ago • written 5 months ago by zhanxw0
0
gravatar for zhanxw
5 months ago by
zhanxw0
zhanxw0 wrote:

Solved: I deleted all Bioconductor packages, removed R program completed. Then I reinstall R and Bioconductor,

In this fresh installation, Bioconductor 3.5 (instead of 3.4) was used and worked fine for me.

ADD COMMENTlink modified 5 months ago • written 5 months ago by zhanxw0

Sounds like overkill; the BiocInstaller::biocLite() command shows that you're getting version 3.4, so somehow you failed to remove the previous version of BiocInstaller. It could be that there are two (or more!) versions of BiocInstaller. Also, you might not have permission to remove it (e.g., installed under an admin account). Something like packageDescription("BiocInstaller") can show where the package is installed.

ADD REPLYlink written 5 months ago by Martin Morgan ♦♦ 20k

You're probably right that I may have multiple versions of BiocInstaller. However, `BiocInstaller` may not be the only source of error, as I did try to run `remove.packages("BiocInstaller")` multiple times.

ADD REPLYlink written 5 months ago by zhanxw0
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