Hi Andreas, 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.
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. Best regards, Tiago Chedraoui Silva On Tue, Oct 13, 2020 at 6:04 AM Andreas Tille <ti...@debian.org> wrote: > 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) > > > > _______________________________________________ > > R-pkg-team mailing list > > r-pkg-t...@alioth-lists.debian.net > > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/r-pkg-team > > -- > http://fam-tille.de >
