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Fix ssl problem in bioc_install command #9349

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roi-meir
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Problem

Currently, the tests fail at the first bioc_install command because of SSL error

For example:

package 'BiocManager' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
	C:\Users\appveyor\AppData\Local\Temp\1\RtmpSQSWPh\downloaded_packages
Error: Bioconductor version cannot be validated; no internet connection?  See
  #troubleshooting section in vignette
In addition: Warning messages:
1: In file(con, "r") :
  URL 'https://bioconductor.org/config.yaml': status was 'SSL connect error'
2: In file(con, "r") :
  URL 'https://bioconductor.org/config.yaml': status was 'SSL connect error'
Execution halted
Command exited with code 1
7z a failure.zip *.Rcheck\*
7-Zip 19.00 (x64) : Copyright (c) 1999-2018 Igor Pavlov : 2019-02-21

Fix

Set R_LIBCURL_SSL_REVOKE_BEST_EFFORT to TRUE (see https://stat.ethz.ch/R-manual/R-devel/library/utils/html/download.file.html for details)

@roi-meir roi-meir marked this pull request as draft September 30, 2024 08:26
@roi-meir
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It turns out that the variable CURL_SSL_BACKEND='openssl' is also needed

@roi-meir roi-meir marked this pull request as ready for review September 30, 2024 11:22
@rharao
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rharao commented Nov 19, 2024

Thanks for this. Because of the Appveyor error, this PR is the first to pass CI checks in more than a year. I hope the maintainers will merge this or pursue something like #7751.

@rharao
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rharao commented Dec 9, 2024

@roi-meir #9538 would cut out Appveyor altogether

@dcollins15
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@roi-meir I can't tell you how much I appreciate the effort you put into getting these checks back up and running 🙏

As @rharao pointed out, we are planning to move away from AppVeyor in favor of GitHub actions and #9538 drops the corresponding config files accordingly. On second thought, there's probably utility in having both sets of checks running concurrently for a little while to make sure nothing is sneaking through the new set that shouldn't be (in general the new checks should be stricter than the old but still).

Unless you've got any objections, I'll revert d669d9d and then squash-merge roi-meir:bugfix/fix_ssl_error_in_travis into satijalab:ci_revamp so that your fix is incorporated when #9538 is merged to develop.

@roi-meir
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Sound good for me.
Thank you for developing this amazing tool!

@dcollins15 dcollins15 mentioned this pull request Dec 11, 2024
@dcollins15
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Closing in favor of:

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3 participants