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samtools sourceforge download fails from open-uri: 'redirection forbidden' #67
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Hi, |
URI-redirection issues happen across multiple versions of bio-samtools >2.3 that I tested. As shown in the text above, the version of bio-samtools i was installing at the time was 2.3.0, but I've encountered the issue in 2.3.2, 2.4, and 2.5.1. When you are testing, do you have open_uri_redirections installed or are you running on a fresh gemset every time? v2.5.1 avoids the Config vs RbConfig syntax issue(#68), but it still doesn't avoid 2 types of URI redirection issues:
Second, v2.5.1 is still subject to htslib compilation issues (#66) |
I usually check that the gem is passing the tests in travis-ci: |
That's fine, I was able to eventually install the gem when I got the combination right. I'll try to provide some more reproducible gem version/ruby version combos. I am actually very surprised you haven't historically observed any of the uri-redirection issues from sourceforge. In travis.ci, I'm not seeing any reference to the sourceforge download.... can anyone explain this? Also, why do you need the accessory commands instead of |
Thanks for the feedback. We did see the problems with the uri redirection, and it should have been fixed when we updated the code to work with samtools 1.x... I'll need to investigate further, I wonder if my fork is not properly in sync with the master here. |
Error building with ruby 2.1.10 due to open-uri. The mkrf_conf.rb and Rakefile both contain http sourceforge urls. These fail to download properly thanks to open-uri. I am surprised this wasn't tested. Running on Arch linux, ruby 2.1.10 with rvm. More information available on request.
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