Your message dated Sat, 07 Sep 2019 14:34:49 +0100
with message-id
<f49e2985d8466065c49c03185c24465a32228fb5.ca...@adam-barratt.org.uk>
and subject line Closing bugs for fixes including in 10.1 point release
has caused the Debian Bug report #935770,
regarding buster-pu: package ncbi-tools6/6.1.20170106+dfsg1-0+deb10u2
to be marked as done.
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If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
935770: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=935770
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: release.debian.org
Severity: normal
Tags: buster
User: [email protected]
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 <[email protected]> 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 <[email protected]> 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/
.*//')"
--- End Message ---
--- Begin Message ---
Version: 10.1
Hi,
The fixes referenced by each of these bugs were included in today's
buster point release.
Regards,
Adam
--- End Message ---
