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'
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 likepackageDescription("BiocInstaller")can show where the package is installed.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.