Package: release.debian.org Severity: normal Tags: buster User: release.debian....@packages.debian.org Usertags: pu
As Adam noted in #934311 (and Paul Gevers reported in #935424), the removal of UniVec.* in my previous stable update introduced an autopkgtest regression, for which I hereby apologize. I've prepared a proposed update that addresses this regression and gives ncbi-data a NEWS.Debian.gz file explaining the removal, which clearly turned out to have a bigger impact than anticipated. Could you please let this fixup through? Thanks!
diff -Nru ncbi-tools6-6.1.20170106+dfsg1/debian/changelog ncbi-tools6-6.1.20170106+dfsg1/debian/changelog --- ncbi-tools6-6.1.20170106+dfsg1/debian/changelog 2019-08-11 22:11:03.000000000 -0400 +++ ncbi-tools6-6.1.20170106+dfsg1/debian/changelog 2019-08-25 21:15:12.000000000 -0400 @@ -1,3 +1,12 @@ +ncbi-tools6 (6.1.20170106+dfsg1-0+deb10u2) buster; urgency=medium + + * debian/ncbi-data.NEWS: Note UniVec removal, which turned out to have a + bigger impact than anticipated. + * debian/tests/run-unit-test: Explicitly point vecscreen at UniVec_Core. + (See #935424.) + + -- Aaron M. Ucko <u...@debian.org> Sun, 25 Aug 2019 21:15:12 -0400 + ncbi-tools6 (6.1.20170106+dfsg1-0+deb10u1) buster; urgency=medium * Belatedly repackage without data/UniVec.*, some portions of which diff -Nru ncbi-tools6-6.1.20170106+dfsg1/debian/ncbi-data.NEWS ncbi-tools6-6.1.20170106+dfsg1/debian/ncbi-data.NEWS --- ncbi-tools6-6.1.20170106+dfsg1/debian/ncbi-data.NEWS 1969-12-31 19:00:00.000000000 -0500 +++ ncbi-tools6-6.1.20170106+dfsg1/debian/ncbi-data.NEWS 2019-08-25 21:15:12.000000000 -0400 @@ -0,0 +1,17 @@ +ncbi-tools6 (6.1.20170106+dfsg1-0+deb10u2) buster; urgency=medium + + As of version 6.1.20170106+dfsg1-1 (and corresponding -0+deb* stable + updates), Debian no longer distributes the full UniVec database + because it contains some non-free sequences. (Invitrogen Corporation + holds copyright on them and requires a license for commercial use.) + + The UniVec_Core database remains available for explicit use, for + instance by passing -d /usr/share/ncbi/data/UniVec_Core to vecscreen. + + Also, any user for whom this legal restriction isn't a concern can + download and use a copy of the UniVec database from + https://ftp.ncbi.nlm.nih.gov/entrez/misc/data/. + + Apologies for any resulting inconvenience. + + -- Aaron M. Ucko <u...@debian.org> Sun, 25 Aug 2019 21:15:11 -0400 diff -Nru ncbi-tools6-6.1.20170106+dfsg1/debian/tests/run-unit-test ncbi-tools6-6.1.20170106+dfsg1/debian/tests/run-unit-test --- ncbi-tools6-6.1.20170106+dfsg1/debian/tests/run-unit-test 2019-08-11 22:11:03.000000000 -0400 +++ ncbi-tools6-6.1.20170106+dfsg1/debian/tests/run-unit-test 2019-08-25 21:15:12.000000000 -0400 @@ -139,7 +139,7 @@ ################################################################## echo '---vecscreen test---' ################################################################## -/usr/bin/vecscreen -f 3 < nc0225.fna > vecscreen.output +/usr/bin/vecscreen -f 3 -d UniVec_Core < nc0225.fna > vecscreen.output [ -s vecscreen.output ] last_in="$(grep ">" nc0225.fna | tail -1 | sed 's/>//' | sed 's/ .*//')" last_out="$(grep ">" vecscreen.output | tail -1 | sed 's/>Vector //' | sed 's/ .*//')"
