<div dir="ltr">Hi Andreas,<div><br></div><div>The software access an external database to retrieve the genome information. The database has experienced problems in the last days and it has not been fixed yet.</div><div><br></div><div>I am trying to save the genome information inside the package so it does not depends on the database anymore. I'll let you know when I fix it. </div><div><br></div><div>Best regards,</div><div><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div></div>Tiago Chedraoui Silva<br></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Oct 13, 2020 at 6:04 AM Andreas Tille <<a href="mailto:tille@debian.org">tille@debian.org</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Control: tags -1 upstream<br>
Control: tags -1 help<br>
Control: forwarded -1 Antonio Colaprico <<a href="mailto:axc1833@med.miami.edu" target="_blank">axc1833@med.miami.edu</a>>, Tiago Chedraoui Silva <<a href="mailto:tiagochst@usp.br" target="_blank">tiagochst@usp.br</a>><br>
<br>
<br>
Hi Antonio and Tiago,<br>
<br>
the Debian packaged version of TCGAbiolinks received a bug report about<br>
a failure in its test suite. I have the impression that the SSL<br>
certificate of a site where data are downloaded from is not correct.<br>
Could you please verify the test suite and let me know whether you<br>
might also get<br>
<br>
── 1. Error: Preparing HT_HG-U133A as SE works (@test-prepare-download.R#193) ─ <br>
failed to get URL after 3 tries: <br>
error: SSL certificate problem: unable to get local issuer certificate <br>
<br>
Kind regards<br>
<br>
Andreas.<br>
<br>
On Tue, Oct 13, 2020 at 08:36:21AM +0200, Graham Inggs wrote:<br>
> Source: r-bioc-tcgabiolinks<br>
> Version: 2.16.4+dfsg-1<br>
> Severity: serious<br>
> Tags: sid bullseye<br>
> X-Debbugs-CC: <a href="mailto:debian-ci@lists.debian.org" target="_blank">debian-ci@lists.debian.org</a><br>
> User: <a href="mailto:debian-ci@lists.debian.org" target="_blank">debian-ci@lists.debian.org</a><br>
> Usertags: regression<br>
> <br>
> Hi Maintainer<br>
> <br>
> Since 2020-10-08, the autopkgtest of r-bioc-tcgabiolinks has been failing [1].<br>
> <br>
> I've copied what I hope is the relevant part of the log below.<br>
> <br>
> Does this autopkgtest download data? If so, please add the<br>
> 'needs-internet' [2] restriction to debian/tests/control, or even skip<br>
> that particular test.<br>
> <br>
> Regards<br>
> Graham<br>
> <br>
> <br>
> [1] <a href="https://ci.debian.net/packages/r/r-bioc-tcgabiolinks/testing/amd64/" rel="noreferrer" target="_blank">https://ci.debian.net/packages/r/r-bioc-tcgabiolinks/testing/amd64/</a><br>
> [2] <a href="https://salsa.debian.org/ci-team/autopkgtest/raw/master/doc/README.package-tests.rst" rel="noreferrer" target="_blank">https://salsa.debian.org/ci-team/autopkgtest/raw/master/doc/README.package-tests.rst</a><br>
> <br>
> <br>
> ── 1. Error: Preparing HT_HG-U133A as SE works (@test-prepare-download.R#193) ─<br>
> failed to get URL after 3 tries:<br>
> error: SSL certificate problem: unable to get local issuer certificate<br>
> Backtrace:<br>
> 1. TCGAbiolinks::GDCprepare(query, summarizedExperiment = TRUE)<br>
> 2. TCGAbiolinks:::readGeneExpressionQuantification(...)<br>
> 3. TCGAbiolinks:::makeSEfromGeneExpressionQuantification(...)<br>
> 4. TCGAbiolinks::get.GRCh.bioMart(genome)<br>
> <br>
> _______________________________________________<br>
> R-pkg-team mailing list<br>
> <a href="mailto:R-pkg-team@alioth-lists.debian.net" target="_blank">R-pkg-team@alioth-lists.debian.net</a><br>
> <a href="https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/r-pkg-team" rel="noreferrer" target="_blank">https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/r-pkg-team</a><br>
<br>
-- <br>
<a href="http://fam-tille.de" rel="noreferrer" target="_blank">http://fam-tille.de</a><br>
</blockquote></div>