Install using BiocManager::install() doesn't work in docker container
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@Khai-Chuong-24452
Last seen 28 days ago
United States

Hi Bioconductor Community,

I am new to Bioconductor. I would like to make a R docker container that has a specific version of R (3.6.x). I got the image to spin up and tried to install some Bioconductor packages using BiocManager::install() but it is failing. Please see the output below. I tried looking for other threads and on stackoverflow but there weren't any solutions that seemed relevant to mine. Can anyone provide some help? Greatly appreciate it. Thanks.

BiocManager::install("CytoML")
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.3 (2020-02-29)
Installing package(s) 'BiocVersion', 'CytoML'
Warning: unable to access index for repository https://bioconductor.org/packages/3.10/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.10/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.10/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.10/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.10/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.10/workflows/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.10/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:
  cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.10/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.10/data/annotation/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.10/data/annotation/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.10/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.10/data/experiment/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.10/workflows/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.10/workflows/src/contrib/PACKAGES'
Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:
  cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES'
Warning message:
packages ‘BiocVersion’, ‘CytoML’ are not available (for R version 3.6.3)


BiocManager::version()
[1] ‘3.10’
Warning message:
In file(con, "r") :
  URL 'https://bioconductor.org/config.yaml': status was 'SSL peer certificate or SSH remote key was not OK'



R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_3.6.3
Bioconductor docker Install • 274 views
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Entering edit mode
@martin-morgan-1513
Last seen 4 days ago
United States

These messages suggest that you are behind a 'proxy' or 'firewall', and that you need to follow the instructions in "setting proxies" section of ?download.file

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