installation failure with BiocManager (URL status was 'Couldn't resolve proxy name')
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Entering edit mode
chen • 0
@chen-23685
Last seen 12 months ago
China/Xiamen

Hi, I was trying to install AnnotationHub package but got warning results and failures. I returned back to check the BiocManager codes, found that the whole connection with Bioconductor seemed to failed because URL status 'Couldn't resolve proxy name'. Below is my code and results.

This did work perfectly few days ago. I have downloaded version 3.11 Bioconductor with my R and I loaded other core packages. I have changed several CRAN repository Mirrors near my location. But it just didn't work...

I'd really appreciate it if anyone can help me with this problem.

Thanks and regards, Chen

This is when I tried to check and upgrade BiocManager (which worked well days ago):

BiocManager::install() Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/PACKAGES.rds': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/PACKAGES.gz': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/PACKAGES': status was 'Couldn't resolve proxy name'unable to access index for repository https://bioconductor.org/packages/3.11/bioc/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/PACKAGES'URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/PACKAGES.rds': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/PACKAGES.gz': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/PACKAGES': status was 'Couldn't resolve proxy name'unable to access index for repository https://bioconductor.org/packages/3.11/data/annotation/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/PACKAGES'URL 'https://bioconductor.org/packages/3.11/data/experiment/src/contrib/PACKAGES.rds': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/data/experiment/src/contrib/PACKAGES.gz': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/data/experiment/src/contrib/PACKAGES': status was 'Couldn't resolve proxy name'unable to access index for repository https://bioconductor.org/packages/3.11/data/experiment/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.11/data/experiment/src/contrib/PACKAGES'URL 'https://bioconductor.org/packages/3.11/workflows/src/contrib/PACKAGES.rds': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/workflows/src/contrib/PACKAGES.gz': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/workflows/src/contrib/PACKAGES': status was 'Couldn't resolve proxy name'unable to access index for repository https://bioconductor.org/packages/3.11/workflows/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.11/workflows/src/contrib/PACKAGES'URL 'https://mirrors.e-ducation.cn/CRAN/src/contrib/PACKAGES.rds': status was 'Couldn't resolve proxy name'URL 'https://mirrors.e-ducation.cn/CRAN/src/contrib/PACKAGES.gz': status was 'Couldn't resolve proxy name'URL 'https://mirrors.e-ducation.cn/CRAN/src/contrib/PACKAGES': status was 'Couldn't resolve proxy name'unable to access index for repository https://mirrors.e-ducation.cn/CRAN/src/contrib: cannot open URL 'https://mirrors.e-ducation.cn/CRAN/src/contrib/PACKAGES'Warning message: In download.file(mirrorscsvurl, destfile = mirrorscsv, quiet = TRUE) : URL 'https://cran.r-project.org/CRANmirrors.csv': status was 'Couldn't resolve proxy name'

This is when I tried to install AnnotationHub package:

BiocManager::install("AnnotationHub") Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.1 (2020-06-06) Installing package(s) 'AnnotationHub' URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/PACKAGES.rds': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/PACKAGES.gz': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/PACKAGES': status was 'Couldn't resolve proxy name'unable to access index for repository https://bioconductor.org/packages/3.11/bioc/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/PACKAGES'URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/PACKAGES.rds': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/PACKAGES.gz': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/PACKAGES': status was 'Couldn't resolve proxy name'unable to access index for repository https://bioconductor.org/packages/3.11/data/annotation/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/PACKAGES'URL 'https://bioconductor.org/packages/3.11/data/experiment/src/contrib/PACKAGES.rds': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/data/experiment/src/contrib/PACKAGES.gz': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/data/experiment/src/contrib/PACKAGES': status was 'Couldn't resolve proxy name'unable to access index for repository https://bioconductor.org/packages/3.11/data/experiment/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.11/data/experiment/src/contrib/PACKAGES'URL 'https://bioconductor.org/packages/3.11/workflows/src/contrib/PACKAGES.rds': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/workflows/src/contrib/PACKAGES.gz': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/workflows/src/contrib/PACKAGES': status was 'Couldn't resolve proxy name'unable to access index for repository https://bioconductor.org/packages/3.11/workflows/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.11/workflows/src/contrib/PACKAGES'URL 'https://mirrors.e-ducation.cn/CRAN/src/contrib/PACKAGES.rds': status was 'Couldn't resolve proxy name'URL 'https://mirrors.e-ducation.cn/CRAN/src/contrib/PACKAGES.gz': status was 'Couldn't resolve proxy name'URL 'https://mirrors.e-ducation.cn/CRAN/src/contrib/PACKAGES': status was 'Couldn't resolve proxy name'unable to access index for repository https://mirrors.e-ducation.cn/CRAN/src/contrib: cannot open URL 'https://mirrors.e-ducation.cn/CRAN/src/contrib/PACKAGES'package ‘AnnotationHub’ is not available (for R version 4.0.1)URL 'https://bioconductor.org/packages/3.11/bioc/bin/macosx/contrib/4.0/PACKAGES.rds': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/bioc/bin/macosx/contrib/4.0/PACKAGES.gz': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/bioc/bin/macosx/contrib/4.0/PACKAGES': status was 'Couldn't resolve proxy name'unable to access index for repository https://bioconductor.org/packages/3.11/bioc/bin/macosx/contrib/4.0: cannot open URL 'https://bioconductor.org/packages/3.11/bioc/bin/macosx/contrib/4.0/PACKAGES'URL 'https://bioconductor.org/packages/3.11/data/annotation/bin/macosx/contrib/4.0/PACKAGES.rds': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/data/annotation/bin/macosx/contrib/4.0/PACKAGES.gz': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/data/annotation/bin/macosx/contrib/4.0/PACKAGES': status was 'Couldn't resolve proxy name'unable to access index for repository https://bioconductor.org/packages/3.11/data/annotation/bin/macosx/contrib/4.0: cannot open URL 'https://bioconductor.org/packages/3.11/data/annotation/bin/macosx/contrib/4.0/PACKAGES'URL 'https://bioconductor.org/packages/3.11/data/experiment/bin/macosx/contrib/4.0/PACKAGES.rds': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/data/experiment/bin/macosx/contrib/4.0/PACKAGES.gz': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/data/experiment/bin/macosx/contrib/4.0/PACKAGES': status was 'Couldn't resolve proxy name'unable to access index for repository https://bioconductor.org/packages/3.11/data/experiment/bin/macosx/contrib/4.0: cannot open URL 'https://bioconductor.org/packages/3.11/data/experiment/bin/macosx/contrib/4.0/PACKAGES'URL 'https://bioconductor.org/packages/3.11/workflows/bin/macosx/contrib/4.0/PACKAGES.rds': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/workflows/bin/macosx/contrib/4.0/PACKAGES.gz': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/workflows/bin/macosx/contrib/4.0/PACKAGES': status was 'Couldn't resolve proxy name'unable to access index for repository https://bioconductor.org/packages/3.11/workflows/bin/macosx/contrib/4.0: cannot open URL 'https://bioconductor.org/packages/3.11/workflows/bin/macosx/contrib/4.0/PACKAGES'URL 'https://mirrors.e-ducation.cn/CRAN/bin/macosx/contrib/4.0/PACKAGES.rds': status was 'Couldn't resolve proxy name'URL 'https://mirrors.e-ducation.cn/CRAN/bin/macosx/contrib/4.0/PACKAGES.gz': status was 'Couldn't resolve proxy name'URL 'https://mirrors.e-ducation.cn/CRAN/bin/macosx/contrib/4.0/PACKAGES': status was 'Couldn't resolve proxy name'unable to access index for repository https://mirrors.e-ducation.cn/CRAN/bin/macosx/contrib/4.0: cannot open URL 'https://mirrors.e-ducation.cn/CRAN/bin/macosx/contrib/4.0/PACKAGES'URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/PACKAGES.rds': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/PACKAGES.gz': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/PACKAGES': status was 'Couldn't resolve proxy name'unable to access index for repository https://bioconductor.org/packages/3.11/bioc/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/PACKAGES'URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/PACKAGES.rds': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/PACKAGES.gz': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/PACKAGES': status was 'Couldn't resolve proxy name'unable to access index for repository https://bioconductor.org/packages/3.11/data/annotation/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/PACKAGES'URL 'https://bioconductor.org/packages/3.11/data/experiment/src/contrib/PACKAGES.rds': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/data/experiment/src/contrib/PACKAGES.gz': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/data/experiment/src/contrib/PACKAGES': status was 'Couldn't resolve proxy name'unable to access index for repository https://bioconductor.org/packages/3.11/data/experiment/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.11/data/experiment/src/contrib/PACKAGES'URL 'https://bioconductor.org/packages/3.11/workflows/src/contrib/PACKAGES.rds': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/workflows/src/contrib/PACKAGES.gz': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/workflows/src/contrib/PACKAGES': status was 'Couldn't resolve proxy name'unable to access index for repository https://bioconductor.org/packages/3.11/workflows/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.11/workflows/src/contrib/PACKAGES'URL 'https://mirrors.e-ducation.cn/CRAN/src/contrib/PACKAGES.rds': status was 'Couldn't resolve proxy name'URL 'https://mirrors.e-ducation.cn/CRAN/src/contrib/PACKAGES.gz': status was 'Couldn't resolve proxy name'URL 'https://mirrors.e-ducation.cn/CRAN/src/contrib/PACKAGES': status was 'Couldn't resolve proxy name'unable to access index for repository https://mirrors.e-ducation.cn/CRAN/src/contrib: cannot open URL 'https://mirrors.e-ducation.cn/CRAN/src/contrib/PACKAGES'

Below is my session info:

sessionInfo() R version 4.0.1 (2020-06-06) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Mojave 10.14.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale: [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8

attached base packages: [1] stats4 parallel stats graphics grDevices [6] utils datasets methods base

other attached packages: [1] IRanges2.22.2 S4Vectors0.26.1
[3] BiocGenerics_0.34.0

loaded via a namespace (and not attached): [1] BiocManager1.30.10 compiler4.0.1
[3] tools4.0.1 yaml2.2.1
[5] knitr1.28 xfun0.14

bioconductor installation proxy BiocManager • 610 views
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Entering edit mode
@martin-morgan-1513
Last seen 9 weeks ago
United States

This is likely because you are in an environment (maybe your institution?) that has a 'proxy' established. See ?download.file and 'proxy' on that page.

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Thank you, Martin! I checked the page suggested and solved the problem.

By the way, I used this method answered by Geek On Acid on the stackoverflow to set the proxy for R on Mac OS, just in case anyone needs it

https://stackoverflow.com/questions/6467277/proxy-setting-for-r

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Entering edit mode

Thank you, Martin! I checked the page suggested and solved the problem.

By the way, I used this method answered by Geek On Acid on the stackoverflow to set the proxy for R on Mac OS, just in case anyone needs it

https://stackoverflow.com/questions/6467277/proxy-setting-for-r

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