Bug#933828: ncbi-tools6/6.1.20170106+dfsg1-0+deb{9,10}u1

To: Debian Bug Tracking System <submit@bugs.debian.org>
Subject: Bug#933828: ncbi-tools6/6.1.20170106+dfsg1-0+deb{9,10}u1
From: "Aaron M. Ucko" <ucko@debian.org>
Date: Sat, 03 Aug 2019 23:27:41 -0400
Message-id: <[🔎] 156488926146.12854.3957197078087548532.reportbug@his-pc.internal.ucko.debian.net>
Reply-to: "Aaron M. Ucko" <ucko@debian.org>, 933828@bugs.debian.org

Package: release.debian.org
Severity: normal
Tags: stretch buster
User: release.debian.org@packages.debian.org
Usertags: pu

Thorsten Alteholz from the FTP Master team recently pointed out a
couple of long-standing copyright-related issues with ncbi-tools6:
some data files turned out to contain non-free portions, and
debian/copyright didn't mention some third-party code I'd previously
overlooked.  I've addressed these issues in unstable with ncbi-tools6
6.1.20170106+dfsg1-1.

Thorsten asked me to upload fixes to (old)stable as well, so I've
drafted uploads targeting both releases per
https://salsa.debian.org/med-team/ncbi-tools6/tree/stretch
https://salsa.debian.org/med-team/ncbi-tools6/tree/buster
and the attached debdiffs.

NB: I left stretch at source format 1.0 for now to keep changes to a
minimum, which means it will need an .orig.tar.gz rather than the
identically numbered .orig.tar.xz we have in unstable.  If that
discrepancy is a problem, I can cherry-pick more changes; please let
me know.

Could you please take a look?

Thanks!

Binary files /tmp/user/7286/_0/49j3fHIAMn/ncbi-tools6-6.1.20170106/data/UniVec.nhr and /tmp/user/7286/_0/EJkaUzF4ix/ncbi-tools6-6.1.20170106+dfsg1/data/UniVec.nhr differ
Binary files /tmp/user/7286/_0/49j3fHIAMn/ncbi-tools6-6.1.20170106/data/UniVec.nin and /tmp/user/7286/_0/EJkaUzF4ix/ncbi-tools6-6.1.20170106+dfsg1/data/UniVec.nin differ
Binary files /tmp/user/7286/_0/49j3fHIAMn/ncbi-tools6-6.1.20170106/data/UniVec.nsq and /tmp/user/7286/_0/EJkaUzF4ix/ncbi-tools6-6.1.20170106+dfsg1/data/UniVec.nsq differ
diff -Nru ncbi-tools6-6.1.20170106/debian/changelog ncbi-tools6-6.1.20170106+dfsg1/debian/changelog
--- ncbi-tools6-6.1.20170106/debian/changelog	2019-08-03 22:46:14.000000000 -0400
+++ ncbi-tools6-6.1.20170106+dfsg1/debian/changelog	2019-08-03 22:46:18.000000000 -0400
@@ -1,3 +1,19 @@
+ncbi-tools6 (6.1.20170106+dfsg1-0+deb9u1) stretch; urgency=medium
+
+  * Belatedly repackage without data/UniVec.*, some portions of which
+    turned out to be non-free (with copyright held by Invitrogen
+    Corporation, which requires a license for commercial use thereof).
+  * debian/copyright:
+    - Cover previously overlooked third-party code (all DFSG-free).
+    - Update authors and dates for debian/*.
+    - Set Files-Excluded to reflect repackaging.
+  * debian/rules: Introduce NCBI_VERSION_SHLIB, with +dfsg1 stripped off.
+  * debian/watch: Reflect usage of +dfsg1.
+  * make/makeshlb.unx: NCBI_VERSION -> NCBI_VERSION_SHLIB.
+  * Temporarily revert ncbi-cn3d splitout to expedite the above fixes.
+
+ -- Aaron M. Ucko <ucko@debian.org>  Sat, 03 Aug 2019 22:12:51 -0400
+
 ncbi-tools6 (6.1.20170106-2) unstable; urgency=medium
 
   * debian/control: Correctly version ncbi-tools-bin's Breaks/Replaces
diff -Nru ncbi-tools6-6.1.20170106/debian/copyright ncbi-tools6-6.1.20170106+dfsg1/debian/copyright
--- ncbi-tools6-6.1.20170106/debian/copyright	2019-08-03 22:46:14.000000000 -0400
+++ ncbi-tools6-6.1.20170106+dfsg1/debian/copyright	2019-08-03 22:46:18.000000000 -0400
@@ -2,15 +2,62 @@
 Upstream-Contact: toolbox@ncbi.nlm.nih.gov
 Upstream-Name: ncbi
 Source: http://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/
+Files-Excluded: ncbi/data/UniVec.*
 
 Files: *
 Copyright: 1996-2017 NCBI
 License: public_domain
 
+Files: algo/blast/core/boost_erf.c
+Copyright: 2006 John Maddock
+License: BSL-1.0
+
+Files: connect/mitsock/*
+Copyright: 1998-1999 The Massachusetts Institute of Technology
+License: MIT
+
+Files: connect/mitsock/OTErrno.c connect/mitsock/OTnetdb.c
+ connect/mitsock/sock_ext.h
+Copyright: ???? National Center for Supercomputing Applications
+License: NCSA
+
+Files: connect/mitsock/a_inet.h:
+Copyright: 1983 Regents of the University of California
+License: BSD-3-Clause
+
+Files: connect/mitsock/carbon_netdb.h:
+Copyright: 1980, 1983, 1988 Regents of the University of California
+License: BSD-3-Clause
+
+Files: connect/mitsock/neterrno.h:
+Copyright: 1982, 1986, 1989 Regents of the University of California
+License: BSD-3-Clause
+
+Files: connect/mitsock/neti_in.h:
+Copyright: 1982, 1986, 1990 Regents of the University of California
+License: BSD-3-Clause
+
+Files: connect/mitsock/s_types.h:
+Copyright: 1982 Regents of the University of California
+License: BSD-3-Clause
+
+Files: connect/parson.?
+Copyright: 2012-2016 Krzysztof Gabis
+License: Expat
+
+Files: corelib/regex.c
+Copyright: 1993 Free Software Foundation, Inc.
+License: GPL-2+
+
+Files: corelib/regex.h
+Copyright: 1985, 1989, 1990, 1991, 1992, 1993 Free Software Foundation, Inc.
+License: GPL-2+
+
 Files: debian/*
 Copyright: 1998-1999 Stephane Bortzmeyer <bortzmeyer@pasteur.fr>
            2001      Dr. Guenter Bechly <gbechly@debian.org>
-           2001-2017 Aaron M. Ucko <ucko@debian.org>
+           2001-2019 Aaron M. Ucko <ucko@debian.org>
+           2012-2017 Andreas Tille <tille@debian.org>
 License: public_domain
 
 License: public_domain
@@ -35,3 +82,122 @@
  purpose.
  .
  Please cite the author in any work or product based on this material.
+
+License: BSL-1.0
+ Permission is hereby granted, free of charge, to any person or organization
+ obtaining a copy of the software and accompanying documentation covered by
+ this license (the "Software") to use, reproduce, display, distribute,
+ execute, and transmit the Software, and to prepare derivative works of the
+ Software, and to permit third-parties to whom the Software is furnished to
+ do so, all subject to the following:
+ .
+ The copyright notices in the Software and this entire statement, including
+ the above license grant, this restriction and the following disclaimer,
+ must be included in all copies of the Software, in whole or in part, and
+ all derivative works of the Software, unless such copies or derivative
+ works are solely in the form of machine-executable object code generated by
+ a source language processor.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
+ SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
+ FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
+ ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ DEALINGS IN THE SOFTWARE.
+
+License: Expat
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to
+ deal in the Software without restriction, including without limitation the
+ rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+ sell copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
+ IN THE SOFTWARE.
+
+License: MIT
+ Permission to use, copy, modify, and distribute this software and its
+ documentation for any purpose and without fee is hereby granted,
+ provided that the above copyright notice appear in all copies and that
+ both that copyright notice and this permission notice appear in
+ supporting documentation, and that the name of M.I.T. not be used in
+ advertising or publicity pertaining to distribution of the software
+ without specific, written prior permission.  Furthermore if you modify
+ this software you must label your software as modified software and not
+ distribute it in such a fashion that it might be confused with the
+ original MIT software. M.I.T. makes no representations about the
+ suitability of this software for any purpose.  It is provided "as is"
+ without express or implied warranty.
+ . 
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR IMPLIED
+ WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
+ MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+ .
+ Individual source code files are copyright MIT, Cygnus Support,
+ OpenVision, Oracle, Sun Soft, FundsXpress, and others.
+ .
+ Project Athena, Athena, Athena MUSE, Discuss, Hesiod, Kerberos, Moira,
+ and Zephyr are trademarks of the Massachusetts Institute of Technology
+ (MIT).  No commercial use of these trademarks may be made without prior
+ written permission of MIT.
+ .
+ "Commercial use" means use of a name in a product or other for-profit
+ manner.  It does NOT prevent a commercial firm from referring to the MIT
+ trademarks in order to convey information (although in doing so,
+ recognition of their trademark status should be given).
+
+License: NCSA
+ This source file is placed in the public domian.
+ Any resemblance to NCSA Telnet, living or dead, is purely coincidental.
+ .
+      National Center for Supercomputing Applications
+      152 Computing Applications Building
+      605 E. Springfield Ave.
+      Champaign, IL  61820
+
+License: BSD-3-Clause
+ Redistribution and use in source and binary forms are permitted
+ provided that: (1) source distributions retain this entire copyright
+ notice and comment, and (2) distributions including binaries display
+ the following acknowledgement:  ``This product includes software
+ developed by the University of California, Berkeley and its contributors''
+ in the documentation or other materials provided with the distribution
+ and in all advertising materials mentioning features or use of this
+ software. Neither the name of the University nor the names of its
+ contributors may be used to endorse or promote products derived
+ from this software without specific prior written permission.
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR
+ IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+
+License: GPL-2+
+ This program is free software; you can redistribute it
+ and/or modify it under the terms of the GNU General Public
+ License as published by the Free Software Foundation; either
+ version 2 of the License, or (at your option) any later
+ version.
+ .
+ This program is distributed in the hope that it will be
+ useful, but WITHOUT ANY WARRANTY; without even the implied
+ warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE.  See the GNU General Public License for more
+ details.
+ .
+ You should have received a copy of the GNU General Public
+ License along with this package; if not, write to the Free
+ Software Foundation, Inc., 51 Franklin St, Fifth Floor,
+ Boston, MA  02110-1301 USA
+ .
+ On Debian systems, the full text of the GNU General Public
+ License version 2 can be found in the file
+ `/usr/share/common-licenses/GPL-2'.
diff -Nru ncbi-tools6-6.1.20170106/debian/rules ncbi-tools6-6.1.20170106+dfsg1/debian/rules
--- ncbi-tools6-6.1.20170106/debian/rules	2019-08-03 22:46:14.000000000 -0400
+++ ncbi-tools6-6.1.20170106+dfsg1/debian/rules	2019-08-03 22:46:18.000000000 -0400
@@ -6,6 +6,7 @@
 export NCBI_VERSION_MINOR=$(NCBI_VERSION:$(NCBI_VERSION_MAJOR).%=%)
 export NCBI_VERSION_DATE =$(word 3, $(subst ., ,$(NCBI_VERSION)))
 export NCBI_VERSION_DEBREL=$(word 2, $(subst -, ,$(NCBI_VERSION_FULL)))
+export NCBI_VERSION_SHLIB=$(NCBI_VERSION:%+dfsg1=%)
 
 testversions:
 	env | fgrep NCBI_VERSION
@@ -120,23 +121,23 @@
 
 override_dh_auto_install-arch:
 	install -d $(destlibdir)
-	install -m 644 lib/* shlib/*.so.$(NCBI_VERSION) $(destlibdir)
+	install -m 644 lib/* shlib/*.so.$(NCBI_VERSION_SHLIB) $(destlibdir)
 	for x in ncbiacc ncbiCacc netentr; do \
-	    rm -f $(destlibdir)/lib$$x.so.$(NCBI_VERSION) && \
+	    rm -f $(destlibdir)/lib$$x.so.$(NCBI_VERSION_SHLIB) && \
 	    ln -s libncbiNacc.so.$(NCBI_VERSION_MAJOR) \
 	        $(destlibdir)/lib$$x.so.$(NCBI_VERSION_MAJOR) && \
 	    ln -s libncbiNacc.so $(destlibdir)/lib$$x.so; \
 	done
 	for x in ncbicn3d vibrant; do \
-	    rm -f $(destlibdir)/lib$$x.so.$(NCBI_VERSION) && \
+	    rm -f $(destlibdir)/lib$$x.so.$(NCBI_VERSION_SHLIB) && \
 	    ln -s lib$${x}OGL.so.$(NCBI_VERSION_MAJOR) \
 	        $(destlibdir)/lib$$x.so.$(NCBI_VERSION_MAJOR) && \
 	    ln -s lib$${x}OGL.so $(destlibdir)/lib$$x.so; \
 	done
 	rm -f $(destlibdir)/libregexp.*
 	cd $(destlibdir) && \
-	for f in *.so.$(NCBI_VERSION); do \
-	    base=`basename $$f .so.$(NCBI_VERSION)` && \
+	for f in *.so.$(NCBI_VERSION_SHLIB); do \
+	    base=`basename $$f .so.$(NCBI_VERSION_SHLIB)` && \
 	    ln -s $$f $$base.so.$(NCBI_VERSION_MAJOR) && \
 	    ln -s $$f $$base.so; \
 	done
diff -Nru ncbi-tools6-6.1.20170106/debian/watch ncbi-tools6-6.1.20170106+dfsg1/debian/watch
--- ncbi-tools6-6.1.20170106/debian/watch	2019-08-03 22:46:14.000000000 -0400
+++ ncbi-tools6-6.1.20170106+dfsg1/debian/watch	2019-08-03 22:46:18.000000000 -0400
@@ -1,3 +1,3 @@
 version=4
-opts="passive,uversionmangle=s|^|6.1.|,downloadurlmangle=s/$/ncbi.tar.gz/" \
+opts="passive,uversionmangle=s|^|6.1.|,downloadurlmangle=s/$/ncbi.tar.gz/,dversionmangle=s/\+dfsg1//,repacksuffix=+dfsg1" \
 http://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/ (\d{8}[a-z]*)/
\ No newline at end of file
diff -Nru ncbi-tools6-6.1.20170106/make/makeshlb.unx ncbi-tools6-6.1.20170106+dfsg1/make/makeshlb.unx
--- ncbi-tools6-6.1.20170106/make/makeshlb.unx	2019-08-03 22:46:14.000000000 -0400
+++ ncbi-tools6-6.1.20170106+dfsg1/make/makeshlb.unx	2019-08-03 22:46:18.000000000 -0400
@@ -20,7 +20,7 @@
 	$(SH1) $@ $(SH2)
 	rm -f *.o __*
 
-so=so.$(NCBI_VERSION_MAJOR).$(NCBI_VERSION_MINOR)
+so=so.$(NCBI_VERSION_SHLIB)
 
 %.$(so): %.a
 	$(CC) -shared -Wl,-soname=$*.so.$(NCBI_VERSION_MAJOR) -o $@ \

Binary files /tmp/user/7286/_0/mQVugLytdB/ncbi-tools6-6.1.20170106/data/UniVec.nhr and /tmp/user/7286/_0/SRBkRZ_JRj/ncbi-tools6-6.1.20170106+dfsg1/data/UniVec.nhr differ
Binary files /tmp/user/7286/_0/mQVugLytdB/ncbi-tools6-6.1.20170106/data/UniVec.nin and /tmp/user/7286/_0/SRBkRZ_JRj/ncbi-tools6-6.1.20170106+dfsg1/data/UniVec.nin differ
Binary files /tmp/user/7286/_0/mQVugLytdB/ncbi-tools6-6.1.20170106/data/UniVec.nsq and /tmp/user/7286/_0/SRBkRZ_JRj/ncbi-tools6-6.1.20170106+dfsg1/data/UniVec.nsq differ
diff -Nru ncbi-tools6-6.1.20170106/debian/changelog ncbi-tools6-6.1.20170106+dfsg1/debian/changelog
--- ncbi-tools6-6.1.20170106/debian/changelog	2018-12-27 22:39:09.000000000 -0500
+++ ncbi-tools6-6.1.20170106+dfsg1/debian/changelog	2019-08-03 22:04:16.000000000 -0400
@@ -1,3 +1,19 @@
+ncbi-tools6 (6.1.20170106+dfsg1-0+deb10u1) buster; urgency=medium
+
+  * Belatedly repackage without data/UniVec.*, some portions of which
+    turned out to be non-free (with copyright held by Invitrogen
+    Corporation, which requires a license for commercial use thereof).
+  * debian/copyright:
+    - Cover previously overlooked third-party code (all DFSG-free).
+    - Update authors and dates for debian/*.
+    - Set Files-Excluded to reflect repackaging.
+  * debian/rules: Introduce NCBI_VERSION_SHLIB, with +dfsg1 stripped off.
+  * debian/watch: Reflect usage of +dfsg1.
+  * make/makeshlb.unx: NCBI_VERSION -> NCBI_VERSION_SHLIB.
+  * Temporarily revert ncbi-cn3d splitout to expedite the above fixes.
+
+ -- Aaron M. Ucko <ucko@debian.org>  Sat, 03 Aug 2019 22:04:16 -0400
+
 ncbi-tools6 (6.1.20170106-6) unstable; urgency=medium
 
   * debian/rules: Find indirectly needed libraries via -rpath-link rather
diff -Nru ncbi-tools6-6.1.20170106/debian/copyright ncbi-tools6-6.1.20170106+dfsg1/debian/copyright
--- ncbi-tools6-6.1.20170106/debian/copyright	2018-12-27 22:39:09.000000000 -0500
+++ ncbi-tools6-6.1.20170106+dfsg1/debian/copyright	2019-08-03 22:04:16.000000000 -0400
@@ -2,15 +2,63 @@
 Upstream-Contact: toolbox@ncbi.nlm.nih.gov
 Upstream-Name: ncbi
 Source: http://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/
+Files-Excluded: ncbi/data/UniVec.*
 
 Files: *
 Copyright: 1996-2017 NCBI
 License: public_domain
 
+Files: algo/blast/core/boost_erf.c
+Copyright: 2006 John Maddock
+License: BSL-1.0
+
+Files: connect/mitsock/*
+Copyright: 1998-1999 The Massachusetts Institute of Technology
+License: MIT
+
+Files: connect/mitsock/OTErrno.c connect/mitsock/OTnetdb.c
+ connect/mitsock/sock_ext.h
+Copyright: ???? National Center for Supercomputing Applications
+License: NCSA
+
+Files: connect/mitsock/a_inet.h:
+Copyright: 1983 Regents of the University of California
+License: BSD-3-Clause
+
+Files: connect/mitsock/carbon_netdb.h:
+Copyright: 1980, 1983, 1988 Regents of the University of California
+License: BSD-3-Clause
+
+Files: connect/mitsock/neterrno.h:
+Copyright: 1982, 1986, 1989 Regents of the University of California
+License: BSD-3-Clause
+
+Files: connect/mitsock/neti_in.h:
+Copyright: 1982, 1986, 1990 Regents of the University of California
+License: BSD-3-Clause
+
+Files: connect/mitsock/s_types.h:
+Copyright: 1982 Regents of the University of California
+License: BSD-3-Clause
+
+Files: connect/parson.?
+Copyright: 2012-2016 Krzysztof Gabis
+License: Expat
+
+Files: corelib/regex.c
+Copyright: 1993 Free Software Foundation, Inc.
+License: GPL-2+
+
+Files: corelib/regex.h
+Copyright: 1985, 1989, 1990, 1991, 1992, 1993 Free Software Foundation, Inc.
+License: GPL-2+
+
 Files: debian/*
 Copyright: 1998-1999 Stephane Bortzmeyer <bortzmeyer@pasteur.fr>
            2001      Dr. Guenter Bechly <gbechly@debian.org>
-           2001-2018 Aaron M. Ucko <ucko@debian.org>
+           2001-2019 Aaron M. Ucko <ucko@debian.org>
+	   2012-2019 Andreas Tille <tille@debian.org
+	   2019      Steffen Möller <moeller@debian.org>
 License: public_domain
 
 Files: debian/tests/test-data/* (except for trnascan-se_sample.output)
@@ -62,3 +110,122 @@
  purpose.
  .
  Please cite the author in any work or product based on this material.
+
+License: BSL-1.0
+ Permission is hereby granted, free of charge, to any person or organization
+ obtaining a copy of the software and accompanying documentation covered by
+ this license (the "Software") to use, reproduce, display, distribute,
+ execute, and transmit the Software, and to prepare derivative works of the
+ Software, and to permit third-parties to whom the Software is furnished to
+ do so, all subject to the following:
+ .
+ The copyright notices in the Software and this entire statement, including
+ the above license grant, this restriction and the following disclaimer,
+ must be included in all copies of the Software, in whole or in part, and
+ all derivative works of the Software, unless such copies or derivative
+ works are solely in the form of machine-executable object code generated by
+ a source language processor.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
+ SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
+ FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
+ ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ DEALINGS IN THE SOFTWARE.
+
+License: Expat
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to
+ deal in the Software without restriction, including without limitation the
+ rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+ sell copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
+ IN THE SOFTWARE.
+
+License: MIT
+ Permission to use, copy, modify, and distribute this software and its
+ documentation for any purpose and without fee is hereby granted,
+ provided that the above copyright notice appear in all copies and that
+ both that copyright notice and this permission notice appear in
+ supporting documentation, and that the name of M.I.T. not be used in
+ advertising or publicity pertaining to distribution of the software
+ without specific, written prior permission.  Furthermore if you modify
+ this software you must label your software as modified software and not
+ distribute it in such a fashion that it might be confused with the
+ original MIT software. M.I.T. makes no representations about the
+ suitability of this software for any purpose.  It is provided "as is"
+ without express or implied warranty.
+ . 
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR IMPLIED
+ WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
+ MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+ .
+ Individual source code files are copyright MIT, Cygnus Support,
+ OpenVision, Oracle, Sun Soft, FundsXpress, and others.
+ .
+ Project Athena, Athena, Athena MUSE, Discuss, Hesiod, Kerberos, Moira,
+ and Zephyr are trademarks of the Massachusetts Institute of Technology
+ (MIT).  No commercial use of these trademarks may be made without prior
+ written permission of MIT.
+ .
+ "Commercial use" means use of a name in a product or other for-profit
+ manner.  It does NOT prevent a commercial firm from referring to the MIT
+ trademarks in order to convey information (although in doing so,
+ recognition of their trademark status should be given).
+
+License: NCSA
+ This source file is placed in the public domian.
+ Any resemblance to NCSA Telnet, living or dead, is purely coincidental.
+ .
+      National Center for Supercomputing Applications
+      152 Computing Applications Building
+      605 E. Springfield Ave.
+      Champaign, IL  61820
+
+License: BSD-3-Clause
+ Redistribution and use in source and binary forms are permitted
+ provided that: (1) source distributions retain this entire copyright
+ notice and comment, and (2) distributions including binaries display
+ the following acknowledgement:  ``This product includes software
+ developed by the University of California, Berkeley and its contributors''
+ in the documentation or other materials provided with the distribution
+ and in all advertising materials mentioning features or use of this
+ software. Neither the name of the University nor the names of its
+ contributors may be used to endorse or promote products derived
+ from this software without specific prior written permission.
+ THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR
+ IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+
+License: GPL-2+
+ This program is free software; you can redistribute it
+ and/or modify it under the terms of the GNU General Public
+ License as published by the Free Software Foundation; either
+ version 2 of the License, or (at your option) any later
+ version.
+ .
+ This program is distributed in the hope that it will be
+ useful, but WITHOUT ANY WARRANTY; without even the implied
+ warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE.  See the GNU General Public License for more
+ details.
+ .
+ You should have received a copy of the GNU General Public
+ License along with this package; if not, write to the Free
+ Software Foundation, Inc., 51 Franklin St, Fifth Floor,
+ Boston, MA  02110-1301 USA
+ .
+ On Debian systems, the full text of the GNU General Public
+ License version 2 can be found in the file
+ `/usr/share/common-licenses/GPL-2'.
diff -Nru ncbi-tools6-6.1.20170106/debian/patches/debian-changes ncbi-tools6-6.1.20170106+dfsg1/debian/patches/debian-changes
--- ncbi-tools6-6.1.20170106/debian/patches/debian-changes	2018-12-27 22:39:09.000000000 -0500
+++ ncbi-tools6-6.1.20170106+dfsg1/debian/patches/debian-changes	2019-08-03 22:04:16.000000000 -0400
@@ -1,6 +1,6 @@
 Combined patches from git.
 --- /dev/null
-+++ ncbi-tools6-6.1.20170106/.gitignore
++++ ncbi-tools6-6.1.20170106+dfsg1/.gitignore
 @@ -0,0 +1,6 @@
 +bin
 +build
@@ -8,8 +8,8 @@
 +lib
 +shlib
 +*-stamp
---- ncbi-tools6-6.1.20170106.orig/access/ent2api.c
-+++ ncbi-tools6-6.1.20170106/access/ent2api.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/access/ent2api.c
++++ ncbi-tools6-6.1.20170106+dfsg1/access/ent2api.c
 @@ -1273,7 +1273,7 @@ NLM_EXTERN CONN EntrezOpenConnection (
      *arg = '\0';
  
@@ -19,8 +19,8 @@
  }
  
  #ifdef OS_MAC
---- ncbi-tools6-6.1.20170106.orig/api/sqnutil3.c
-+++ ncbi-tools6-6.1.20170106/api/sqnutil3.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/api/sqnutil3.c
++++ ncbi-tools6-6.1.20170106+dfsg1/api/sqnutil3.c
 @@ -33198,7 +33198,7 @@ ClickableItemPtr LIBCALL ClickableGlobal
         cip->clickable_item_type = item_type;
         cip->description 
@@ -30,8 +30,8 @@
         return cip;
    }
    return NULL;
---- ncbi-tools6-6.1.20170106.orig/connect/ncbi_gnutls.c
-+++ ncbi-tools6-6.1.20170106/connect/ncbi_gnutls.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/connect/ncbi_gnutls.c
++++ ncbi-tools6-6.1.20170106+dfsg1/connect/ncbi_gnutls.c
 @@ -585,6 +585,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull
  
      assert(!s_GnuTlsCredAnon);
@@ -48,8 +48,8 @@
  
      val = ConnNetInfo_GetValue(0, "GNUTLS_LOGLEVEL", buf, sizeof(buf), 0);
      CORE_LOCK_READ;
---- ncbi-tools6-6.1.20170106.orig/connect/ncbi_http_connector.c
-+++ ncbi-tools6-6.1.20170106/connect/ncbi_http_connector.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/connect/ncbi_http_connector.c
++++ ncbi-tools6-6.1.20170106+dfsg1/connect/ncbi_http_connector.c
 @@ -240,8 +240,14 @@ static int/*bool*/ x_UnsafeRedirectOK(SH
      if (uuu->unsafe_redir == eDefault) {
          if (!(uuu->flags & fHTTP_UnsafeRedirects)) {
@@ -66,8 +66,8 @@
              uuu->unsafe_redir = ConnNetInfo_Boolean(val) ? eOn : eOff;
          } else
              uuu->unsafe_redir = eOn;
---- ncbi-tools6-6.1.20170106.orig/connect/ncbi_util.c
-+++ ncbi-tools6-6.1.20170106/connect/ncbi_util.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/connect/ncbi_util.c
++++ ncbi-tools6-6.1.20170106+dfsg1/connect/ncbi_util.c
 @@ -49,7 +49,9 @@
  #  ifndef NCBI_OS_SOLARIS
  #    include <limits.h>
@@ -79,8 +79,8 @@
  #    include <sys/user.h>
  #  endif /*NCBI_OS_LINUX*/
  #  include <pwd.h>
---- ncbi-tools6-6.1.20170106.orig/connect/urlquery.c
-+++ ncbi-tools6-6.1.20170106/connect/urlquery.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/connect/urlquery.c
++++ ncbi-tools6-6.1.20170106+dfsg1/connect/urlquery.c
 @@ -128,7 +128,10 @@ NLM_EXTERN CONN QUERY_OpenUrlQuery (
    }
    if ( host_port ) {
@@ -92,8 +92,8 @@
    StringNCpy_0 (net_info->path, host_path, sizeof (net_info->path));
    if (StringDoesHaveText (arguments)) {
      StringNCpy_0 (net_info->args, arguments, sizeof (net_info->args));
---- ncbi-tools6-6.1.20170106.orig/corelib/ncbimain.c
-+++ ncbi-tools6-6.1.20170106/corelib/ncbimain.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/corelib/ncbimain.c
++++ ncbi-tools6-6.1.20170106+dfsg1/corelib/ncbimain.c
 @@ -67,6 +67,7 @@
  #pragma segment NlmSegA
  #endif
@@ -116,8 +116,8 @@
  
    NlmThreadJoinAll();
  
---- ncbi-tools6-6.1.20170106.orig/corelib/ncbitime.c
-+++ ncbi-tools6-6.1.20170106/corelib/ncbitime.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/corelib/ncbitime.c
++++ ncbi-tools6-6.1.20170106+dfsg1/corelib/ncbitime.c
 @@ -77,6 +77,7 @@
  #include <ncbi.h>
  #include <ncbithr.h>
@@ -161,8 +161,8 @@
    if ((dt = localtime (&ltime)) != NULL)
   	{
          Nlm_MemCopy ((Nlm_VoidPtr) dtp, (Nlm_VoidPtr) dt, sizeof (struct tm));
---- ncbi-tools6-6.1.20170106.orig/demo/asndisc.c
-+++ ncbi-tools6-6.1.20170106/demo/asndisc.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/demo/asndisc.c
++++ ncbi-tools6-6.1.20170106+dfsg1/demo/asndisc.c
 @@ -65,6 +65,7 @@
  #include <objmacro.h>
  #include <macroapi.h>
@@ -180,8 +180,8 @@
    if (! AllObjLoad ()) {
      Message (MSG_FATAL, "AllObjLoad failed");
      return 1;
---- ncbi-tools6-6.1.20170106.orig/demo/entrez2.c
-+++ ncbi-tools6-6.1.20170106/demo/entrez2.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/demo/entrez2.c
++++ ncbi-tools6-6.1.20170106+dfsg1/demo/entrez2.c
 @@ -61,6 +61,8 @@
  
  #include <entrez2.h>
@@ -209,8 +209,8 @@
    } else if (useTestServ) {
      EntrezSetService ("Entrez2Test");
    } else if (useURL) {
---- ncbi-tools6-6.1.20170106.orig/demo/findspl.c
-+++ ncbi-tools6-6.1.20170106/demo/findspl.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/demo/findspl.c
++++ ncbi-tools6-6.1.20170106+dfsg1/demo/findspl.c
 @@ -62,6 +62,8 @@
  #include <accentr.h>
  #include <sequtil.h>
@@ -229,8 +229,8 @@
  	if ( !GetArgs("findspl", NUMARGS, myargs) ) return 1;
  
  	gi = myargs[0].intvalue;
---- ncbi-tools6-6.1.20170106.orig/demo/gbseqget.c
-+++ ncbi-tools6-6.1.20170106/demo/gbseqget.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/demo/gbseqget.c
++++ ncbi-tools6-6.1.20170106+dfsg1/demo/gbseqget.c
 @@ -54,6 +54,8 @@
  #include <pmfapi.h>
  #include <asn2gnbp.h>
@@ -249,8 +249,8 @@
    if (! AllObjLoad ()) {
      Message (MSG_FATAL, "AllObjLoad failed");
      return 1;
---- ncbi-tools6-6.1.20170106.orig/demo/insdseqget.c
-+++ ncbi-tools6-6.1.20170106/demo/insdseqget.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/demo/insdseqget.c
++++ ncbi-tools6-6.1.20170106+dfsg1/demo/insdseqget.c
 @@ -55,6 +55,8 @@
  #include <pmfapi.h>
  #include <asn2gnbp.h>
@@ -269,8 +269,8 @@
    if (! AllObjLoad ()) {
      Message (MSG_FATAL, "AllObjLoad failed");
      return 1;
---- ncbi-tools6-6.1.20170106.orig/demo/nps2gps.c
-+++ ncbi-tools6-6.1.20170106/demo/nps2gps.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/demo/nps2gps.c
++++ ncbi-tools6-6.1.20170106+dfsg1/demo/nps2gps.c
 @@ -50,6 +50,8 @@
  #include <toasn3.h>
  #include <pmfapi.h>
@@ -289,8 +289,8 @@
    if (! AllObjLoad ()) {
      Message (MSG_FATAL, "AllObjLoad failed");
      return 1;
---- ncbi-tools6-6.1.20170106.orig/demo/taxblast_main.c
-+++ ncbi-tools6-6.1.20170106/demo/taxblast_main.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/demo/taxblast_main.c
++++ ncbi-tools6-6.1.20170106+dfsg1/demo/taxblast_main.c
 @@ -41,6 +41,8 @@ static char const rcsid[] = "$Id: taxbla
  #include <objgen.h>
  #include <taxblast.h>
@@ -309,8 +309,8 @@
      if (!GetArgs("txblast", NUMARG, myargs)) {
          return 1;
      }
---- ncbi-tools6-6.1.20170106.orig/demo/tbl2asn.c
-+++ ncbi-tools6-6.1.20170106/demo/tbl2asn.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/demo/tbl2asn.c
++++ ncbi-tools6-6.1.20170106+dfsg1/demo/tbl2asn.c
 @@ -8911,10 +8911,12 @@ Int2 Main (void)
      return 1;
    }
@@ -334,8 +334,8 @@
      return 1;
    }
  
---- ncbi-tools6-6.1.20170106.orig/desktop/bspview.c
-+++ ncbi-tools6-6.1.20170106/desktop/bspview.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/desktop/bspview.c
++++ ncbi-tools6-6.1.20170106+dfsg1/desktop/bspview.c
 @@ -2549,13 +2549,13 @@ NLM_EXTERN void Nlm_LaunchWebPage (Char
      }
  #endif
@@ -353,8 +353,8 @@
          exit(-1);
      }
    }
---- ncbi-tools6-6.1.20170106.orig/doc/dispatcher.html
-+++ ncbi-tools6-6.1.20170106/doc/dispatcher.html
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/doc/dispatcher.html
++++ ncbi-tools6-6.1.20170106+dfsg1/doc/dispatcher.html
 @@ -9,15 +9,15 @@
  -->
    <META NAME="keywords" CONTENT="dispatcher toolkit">
@@ -392,8 +392,8 @@
      <!-- right content column  --> 
      <td width="460"> 
        <p>&nbsp;</p>
---- ncbi-tools6-6.1.20170106.orig/doc/firewall.html
-+++ ncbi-tools6-6.1.20170106/doc/firewall.html
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/doc/firewall.html
++++ ncbi-tools6-6.1.20170106+dfsg1/doc/firewall.html
 @@ -9,15 +9,15 @@
   <META NAME="keywords" CONTENT="insert your keywords for the search engine">
   <META NAME="description" CONTENT="insert the description to be displayed by the search engine.  Also searched by the search engine.">
@@ -455,8 +455,8 @@
  the preset ports, and it is kept in-sync with currently
  configured open ports (so remember to refresh your download
  prior to actual use).
---- ncbi-tools6-6.1.20170106.orig/doc/fwd_check.sh
-+++ ncbi-tools6-6.1.20170106/doc/fwd_check.sh
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/doc/fwd_check.sh
++++ ncbi-tools6-6.1.20170106+dfsg1/doc/fwd_check.sh
 @@ -8,7 +8,7 @@
  delay_sec="$1"
  delay_sec=${delay_sec:="10"}
@@ -466,8 +466,8 @@
  helper="./fwd_failure_helper.exe"
  test -z "$netcat"  &&  netcat="`whereis nc | sed 's/^[^:]*://;s/ //g'`"
  test -z "$HTTP_NCBI_EXTERNAL"  &&  HTTP_CAF_EXTERNAL="$HTTP_NCBI_EXTERNAL"
---- ncbi-tools6-6.1.20170106.orig/doc/man/cleanasn.1
-+++ ncbi-tools6-6.1.20170106/doc/man/cleanasn.1
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/doc/man/cleanasn.1
++++ ncbi-tools6-6.1.20170106+dfsg1/doc/man/cleanasn.1
 @@ -1,4 +1,4 @@
 -.TH CLEANASN 1 2016-09-01 NCBI "NCBI Tools User's Manual"
 +.TH CLEANASN 1 2017-01-09 NCBI "NCBI Tools User's Manual"
@@ -495,7 +495,7 @@
  Virtual gaps inside segmented sequence
  .IP s
 --- /dev/null
-+++ ncbi-tools6-6.1.20170106/doc/man/taxblast.1
++++ ncbi-tools6-6.1.20170106+dfsg1/doc/man/taxblast.1
 @@ -0,0 +1,31 @@
 +.TH TAXBLAST 1 2016-12-05 NCBI "NCBI Tools User's Manual"
 +.SH NAME
@@ -528,8 +528,8 @@
 +Sequence is DNA
 +.SH AUTHOR
 +The National Center for Biotechnology Information.
---- ncbi-tools6-6.1.20170106.orig/make/makeall.unx
-+++ ncbi-tools6-6.1.20170106/make/makeall.unx
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/make/makeall.unx
++++ ncbi-tools6-6.1.20170106+dfsg1/make/makeall.unx
 @@ -1,4 +1,4 @@
 -#	makefile for asntool and ncbi core routines,
 +#	-*- makefile -*- for asntool and ncbi core routines,
@@ -597,8 +597,8 @@
  	cp -fp ../algo/blast/composition_adjustment/*.h \
  		../include/algo/blast/composition_adjustment
  	- mkdir -p ../include/algo/blast/api
---- ncbi-tools6-6.1.20170106.orig/make/makedemo.unx
-+++ ncbi-tools6-6.1.20170106/make/makedemo.unx
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/make/makedemo.unx
++++ ncbi-tools6-6.1.20170106+dfsg1/make/makedemo.unx
 @@ -1,4 +1,4 @@
 -#	makefile for demo programs
 +#	-*- makefile -*- for demo programs
@@ -615,8 +615,8 @@
  
  # errhdr
  
---- ncbi-tools6-6.1.20170106.orig/make/makenet.unx
-+++ ncbi-tools6-6.1.20170106/make/makenet.unx
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/make/makenet.unx
++++ ncbi-tools6-6.1.20170106+dfsg1/make/makenet.unx
 @@ -1,4 +1,4 @@
 -#   makefile for network demo programs and network entrez
 +#   -*- makefile -*- for network demo programs and network entrez
@@ -723,8 +723,8 @@
  
  # test client for the suggest network service
  suggcli: suggcli.c $(BNETCLILIB) $(BLIB24)
---- ncbi-tools6-6.1.20170106.orig/make/makeshlb.unx
-+++ ncbi-tools6-6.1.20170106/make/makeshlb.unx
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/make/makeshlb.unx
++++ ncbi-tools6-6.1.20170106+dfsg1/make/makeshlb.unx
 @@ -1,4 +1,4 @@
 -#
 +# -*- makefile -*-
@@ -744,7 +744,7 @@
  	$(SH1) $@ $(SH2)
  	rm -f *.o __*
 +
-+so=so.$(NCBI_VERSION_MAJOR).$(NCBI_VERSION_MINOR)
++so=so.$(NCBI_VERSION_SHLIB)
 +
 +%.$(so): %.a
 +	$(CC) -shared -Wl,-soname=$*.so.$(NCBI_VERSION_MAJOR) -o $@ \
@@ -848,8 +848,8 @@
 +libvibnet.$(so):      $(libvibnet_deps)
 +# libvibrant.$(so):   $(libvibrant_deps)
 +libvibrantOGL.$(so):  $(libvibrantOGL_deps)
---- ncbi-tools6-6.1.20170106.orig/tools/readdb.c
-+++ ncbi-tools6-6.1.20170106/tools/readdb.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/tools/readdb.c
++++ ncbi-tools6-6.1.20170106+dfsg1/tools/readdb.c
 @@ -10167,7 +10167,10 @@ static    Int2    FDBFinish (FormatDBPtr
              return 1;
      
@@ -862,8 +862,8 @@
  
      /* write db_title and date-time stamp eigth bytes aligned */
      tmp = title_len + StringLen(dateTime);
---- ncbi-tools6-6.1.20170106.orig/vibrant/netscape.c
-+++ ncbi-tools6-6.1.20170106/vibrant/netscape.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/vibrant/netscape.c
++++ ncbi-tools6-6.1.20170106+dfsg1/vibrant/netscape.c
 @@ -548,9 +548,8 @@ static Boolean NS_LoadNetscape(const cha
      }
  
@@ -876,8 +876,8 @@
          exit(1);
      }
  
---- ncbi-tools6-6.1.20170106.orig/vibrant/shim3d.c
-+++ ncbi-tools6-6.1.20170106/vibrant/shim3d.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/vibrant/shim3d.c
++++ ncbi-tools6-6.1.20170106+dfsg1/vibrant/shim3d.c
 @@ -321,6 +321,7 @@
  
  #ifdef _PNG
@@ -918,8 +918,8 @@
          MemFree(fblock);
  }
 -
---- ncbi-tools6-6.1.20170106.orig/vibrant/vibmain.c
-+++ ncbi-tools6-6.1.20170106/vibrant/vibmain.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/vibrant/vibmain.c
++++ ncbi-tools6-6.1.20170106+dfsg1/vibrant/vibmain.c
 @@ -44,6 +44,21 @@
  
  
@@ -942,8 +942,8 @@
  #ifdef WIN_MAC
  #ifdef OS_UNIX_DARWIN
  int main (int argc, char *argv[]) 
---- ncbi-tools6-6.1.20170106.orig/vibrant/vibwndws.c
-+++ ncbi-tools6-6.1.20170106/vibrant/vibwndws.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/vibrant/vibwndws.c
++++ ncbi-tools6-6.1.20170106+dfsg1/vibrant/vibwndws.c
 @@ -6818,7 +6818,7 @@ extern void Nlm_VibMainPrelude (int argc
    Nlm_InitPrompt ();
    Nlm_InitSlate ();
diff -Nru ncbi-tools6-6.1.20170106/debian/rules ncbi-tools6-6.1.20170106+dfsg1/debian/rules
--- ncbi-tools6-6.1.20170106/debian/rules	2018-12-27 22:39:09.000000000 -0500
+++ ncbi-tools6-6.1.20170106+dfsg1/debian/rules	2019-08-03 22:04:16.000000000 -0400
@@ -6,6 +6,7 @@
 export NCBI_VERSION_MINOR=$(NCBI_VERSION:$(NCBI_VERSION_MAJOR).%=%)
 export NCBI_VERSION_DATE =$(word 3, $(subst ., ,$(NCBI_VERSION)))
 export NCBI_VERSION_DEBREL=$(word 2, $(subst -, ,$(NCBI_VERSION_FULL)))
+export NCBI_VERSION_SHLIB=$(NCBI_VERSION:%+dfsg1=%)
 
 testversions:
 	env | fgrep NCBI_VERSION
@@ -114,23 +115,23 @@
 
 override_dh_auto_install-arch:
 	install -d $(destlibdir)
-	install -m 644 lib/* shlib/*.so.$(NCBI_VERSION) $(destlibdir)
+	install -m 644 lib/* shlib/*.so.$(NCBI_VERSION_SHLIB) $(destlibdir)
 	for x in ncbiacc ncbiCacc netentr; do \
-	    rm -f $(destlibdir)/lib$$x.so.$(NCBI_VERSION) && \
+	    rm -f $(destlibdir)/lib$$x.so.$(NCBI_VERSION_SHLIB) && \
 	    ln -s libncbiNacc.so.$(NCBI_VERSION_MAJOR) \
 	        $(destlibdir)/lib$$x.so.$(NCBI_VERSION_MAJOR) && \
 	    ln -s libncbiNacc.so $(destlibdir)/lib$$x.so; \
 	done
 	for x in ncbicn3d vibrant; do \
-	    rm -f $(destlibdir)/lib$$x.so.$(NCBI_VERSION) && \
+	    rm -f $(destlibdir)/lib$$x.so.$(NCBI_VERSION_SHLIB) && \
 	    ln -s lib$${x}OGL.so.$(NCBI_VERSION_MAJOR) \
 	        $(destlibdir)/lib$$x.so.$(NCBI_VERSION_MAJOR) && \
 	    ln -s lib$${x}OGL.so $(destlibdir)/lib$$x.so; \
 	done
 	rm -f $(destlibdir)/libregexp.*
 	cd $(destlibdir) && \
-	for f in *.so.$(NCBI_VERSION); do \
-	    base=`basename $$f .so.$(NCBI_VERSION)` && \
+	for f in *.so.$(NCBI_VERSION_SHLIB); do \
+	    base=`basename $$f .so.$(NCBI_VERSION_SHLIB)` && \
 	    ln -s $$f $$base.so.$(NCBI_VERSION_MAJOR) && \
 	    ln -s $$f $$base.so; \
 	done
diff -Nru ncbi-tools6-6.1.20170106/debian/watch ncbi-tools6-6.1.20170106+dfsg1/debian/watch
--- ncbi-tools6-6.1.20170106/debian/watch	2018-12-27 22:39:09.000000000 -0500
+++ ncbi-tools6-6.1.20170106+dfsg1/debian/watch	2019-08-03 22:04:16.000000000 -0400
@@ -1,3 +1,3 @@
 version=4
-opts="passive,uversionmangle=s|^|6.1.|,downloadurlmangle=s/$/ncbi.tar.gz/" \
+opts="passive,uversionmangle=s|^|6.1.|,downloadurlmangle=s/$/ncbi.tar.gz/,dversionmangle=s/\+dfsg1//,repacksuffix=+dfsg1" \
 http://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/ (\d{8}[a-z]*)/
\ No newline at end of file

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  - From: "Adam D. Barratt" <adam@adam-barratt.org.uk>
- Processed: Re: Bug#933828: ncbi-tools6/6.1.20170106+dfsg1-0+deb10u1
  - From: "Debian Bug Tracking System" <owner@bugs.debian.org>
- Bug#933828: ncbi-tools6 6.1.20170106+dfsg1-0+deb9u1 flagged for acceptance
  - From: Adam D Barratt <adam@adam-barratt.org.uk>
- Bug#934311: ncbi-tools6 6.1.20170106+dfsg1-0+deb10u1 flagged for acceptance
  - From: Adam D Barratt <adam@adam-barratt.org.uk>

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