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Bug#935770: marked as done (buster-pu: package ncbi-tools6/6.1.20170106+dfsg1-0+deb10u2)

Your message dated Sat, 07 Sep 2019 14:34:49 +0100
with message-id <[🔎] f49e2985d8466065c49c03185c24465a32228fb5.camel@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.

This means that you claim that the problem has been dealt with.
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 owner@bugs.debian.org with problems
--- Begin Message --- 
Package: release.debian.org
Severity: normal
Tags: buster
User: release.debian.org@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 <ucko@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 <ucko@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/ .*//')"

--- 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 ---
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