Control: tags -1 upstream
Control: tags -1 help
Control: forwarded -1 Antonio Colaprico <axc1...@med.miami.edu>, Tiago
Chedraoui Silva <tiagoc...@usp.br>
Hi Antonio and Tiago,
the Debian packaged version of TCGAbiolinks received a bug report about
a failure in its test suite. I have the impression that the SSL
certificate of a site where data are downloaded from is not correct.
Could you please verify the test suite and let me know whether you
might also get
── 1. Error: Preparing HT_HG-U133A as SE works (@test-prepare-download.R#193)
─
failed to get URL after 3 tries:
error: SSL certificate problem: unable to get local issuer certificate
Kind regards
Andreas.
On Tue, Oct 13, 2020 at 08:36:21AM +0200, Graham Inggs wrote:
> Source: r-bioc-tcgabiolinks
> Version: 2.16.4+dfsg-1
> Severity: serious
> Tags: sid bullseye
> X-Debbugs-CC: debian...@lists.debian.org
> User: debian...@lists.debian.org
> Usertags: regression
>
> Hi Maintainer
>
> Since 2020-10-08, the autopkgtest of r-bioc-tcgabiolinks has been failing [1].
>
> I've copied what I hope is the relevant part of the log below.
>
> Does this autopkgtest download data? If so, please add the
> 'needs-internet' [2] restriction to debian/tests/control, or even skip
> that particular test.
>
> Regards
> Graham
>
>
> [1] https://ci.debian.net/packages/r/r-bioc-tcgabiolinks/testing/amd64/
> [2]
> https://salsa.debian.org/ci-team/autopkgtest/raw/master/doc/README.package-tests.rst
>
>
> ── 1. Error: Preparing HT_HG-U133A as SE works (@test-prepare-download.R#193)
> ─
> failed to get URL after 3 tries:
> error: SSL certificate problem: unable to get local issuer certificate
> Backtrace:
> 1. TCGAbiolinks::GDCprepare(query, summarizedExperiment = TRUE)
> 2. TCGAbiolinks:::readGeneExpressionQuantification(...)
> 3. TCGAbiolinks:::makeSEfromGeneExpressionQuantification(...)
> 4. TCGAbiolinks::get.GRCh.bioMart(genome)
>
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