Dear all
While installing packages from bioconductor using following command BiocManager: install("pheatmap") , we got the following error (sample of error log below). In the end, and despite the error gives no good clue for the real problem, the issue was that we are using Netskope for security and we had to temporally disable any influence from it to allow install the packages. As this is not a good security practice, could you please let us know what alterations shall we do in our Firewalls set up so that we can install the bioconductor packages without getting our selves exposed to attacks. Please be informed that the issue was from our end and not from bioconductor site. It is more a security setting that needed alteration to make these actions smoother and safer from our end.
Error log got:
Replacement repositories: CRAN: https://cran.rstudio.com/ Warning: unable to access index for repository https://bioconductor.org/packages/3.16/bioc/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/annotation/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/experiment/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.16/workflows/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.16/workflows/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.16/books/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.16/books/src/contrib/PACKAGES' Bioconductor version 3.16 (BiocManager 1.30.21), R 4.2.1 (2022-06-23 ucrt) Installing package(s) 'BiocVersion' Warning: unable to access index for repository https://bioconductor.org/packages/3.16/bioc/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/annotation/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.16/data/experiment/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.16/data/experiment/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.16/workflows/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.16/workflows/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.16/books/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.16/books/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2: cannot open URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/PACKAGES' Warning: unable to access index for repository
Thank You a lot,
Albert
I would assume there is something in the settings where you can add a trusted site/domain. I would look for that location and add bioconductor.org/*
Thanks @shepherl but we already whitelisted that and it was not enough, we finally had to disable completely Netskope from the pc. Can you provide some specific subdomains or similar than can be more accurate? thanks a lot!
Ah I see what could be the issue. You are using an older version of Bioconductor. We use OSN (used to use AWS S3 buckets) to store older versions of Bioconductor not hosted on cloudfront. You could try also adding https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/ and sub directories from there
many thanks!!! we will add these paths also. You mention that we use an old version of BC. Can we update to latest without any trouble on our pcs? thanks again!
To use Bioconductor 3.17 you would have to update your version of R to 4.3.