Aaron M. Ucko · Aaron M. Ucko · Aaron M. Ucko · Aaron M. Ucko · Aaron M. Ucko · Aaron M. Ucko
--- a/data/UniVec.nhr
+++ b/data/UniVec.nhr
--- a/data/UniVec.nin
+++ b/data/UniVec.nin
--- a/data/UniVec.nsq
+++ b/data/UniVec.nsq
--- a/debian/.gitignore
+++ b/debian/.gitignore
@@ -7,7 +7,6 @@ libncbi6
 libvibrant6b
 lib*-dbg
 lib*-dev
-ncbi-cn3d
 ncbi-data
 ncbi-rrna-data
 ncbi-tools-bin

--- a/debian/changelog
+++ b/debian/changelog
+ncbi-tools6 (6.1.20170106+dfsg1-1) unstable; urgency=medium
+
+  [Andreas Tille]
+  * debian/upstream/metadata: Fix DOI syntax (shouldn't be a full URL).
+
+  [Aaron M. Ucko]
+  * 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>  Mon, 29 Jul 2019 22:12:41 -0400
+
 ncbi-tools6 (6.1.20170106-7) unstable; urgency=medium

  [ Steffen Möller ]

--- a/debian/control
+++ b/debian/control
@@ -82,7 +82,6 @@ Depends: libncbi6 (<< ${source:Upstream-Version}.1),
         ${shlibs:Depends}
 Suggests: libvibrant6b,
          ncbi-blast+,
-          ncbi-cn3d,
          ncbi-tools-x11
 Breaks: blast2 (<< 1:2.2.26.20160908)
 Replaces: blast2 (<< 1:2.2.26.20160908)
@@ -102,33 +101,14 @@ Depends: libncbi6 (<< ${source:Upstream-Version}.1),
         libncbi6 (>= ${source:Upstream-Version}),
         libvibrant6b (<< ${source:Upstream-Version}.1),
         libvibrant6b (>= ${source:Upstream-Version}),
-         ncbi-cn3d,
         ${misc:Depends},
         ${shlibs:Depends}
 Suggests: ncbi-tools-bin
 Description: NCBI libraries for biology applications (X-based utilities)
 This package includes some X-based utilities distributed with the
- NCBI C SDK: Network Entrez, Sequin, ddv, and udv.  These programs
- are not part of ncbi-tools-bin because they depend on several
- additional library packages.
-
-Package: ncbi-cn3d
-Architecture: any
-Multi-Arch: foreign
-Section: science
-Depends: libncbi6 (<< ${source:Upstream-Version}.1),
-         libncbi6 (>= ${source:Upstream-Version}),
-         libvibrant6b (<< ${source:Upstream-Version}.1),
-         libvibrant6b (>= ${source:Upstream-Version}),
-         ${misc:Depends},
-         ${shlibs:Depends}
-Suggests: ncbi-tools-bin,
-           ncbi-tools-x11
-Breaks: ncbi-tools-x11 (<< 6.1.20170106-7~)
-Replaces: ncbi-tools-x11 (<< 6.1.20170106-7~)
-Description: 3-dimensional viewer for biological molecules
- Cn3D is a helper application for your web browser that allows you to
- view 3-dimensional structures from NCBI's Entrez retrieval service.
+ NCBI C SDK: Cn3D, Network Entrez, Sequin, ddv, and udv.  These
+ programs are not part of ncbi-tools-bin because they depend on
+ several additional library packages.

 Package: libvibrant6b
 Architecture: any

--- a/debian/copyright
+++ b/debian/copyright
@@ -2,15 +2,63 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 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 @@ License: public_domain
 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'.
--- a/debian/ncbi-cn3d.install
+++ b/debian/ncbi-cn3d.install
-usr/bin/Cn3D-3.0
--- a/debian/ncbi-tools-x11.install
+++ b/debian/ncbi-tools-x11.install
+usr/bin/Cn3D-3.0
 usr/bin/Psequin
 usr/bin/ddv
 usr/bin/entrez2

--- a/debian/ncbi-cn3d.mime
+++ b/debian/ncbi-cn3d.mime
--- a/debian/ncbi-cn3d.postinst
+++ b/debian/ncbi-cn3d.postinst
--- a/debian/ncbi-cn3d.prerm
+++ b/debian/ncbi-cn3d.prerm
--- a/debian/patches/debian-changes
+++ b/debian/patches/debian-changes
 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 @@ Combined patches from git.
 +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 @@ Combined patches from git.
 }
 
 #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 @@ Combined patches from git.
        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 @@ Combined patches from git.
 
     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 @@ Combined patches from git.
             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 @@ Combined patches from git.
 #    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 @@ Combined patches from git.
   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 @@ Combined patches from git.
 
   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 @@ Combined patches from git.
   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 @@ Combined patches from git.
   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 @@ Combined patches from git.
   } 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 @@ Combined patches from git.
 	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 @@ Combined patches from git.
   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 @@ Combined patches from git.
   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 @@ Combined patches from git.
   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 @@ Combined patches from git.
     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 @@ Combined patches from git.
     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 @@ Combined patches from git.
         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 @@ Combined patches from git.
     <!-- 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 @@ Combined patches from git.
 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 @@ Combined patches from git.
 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 @@ Combined patches from git.
 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 @@ Combined patches from git.
 +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 @@ Combined patches from git.
 	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 @@ Combined patches from git.
 
 # 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 @@ Combined patches from git.
 
 # 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 @@ Combined patches from git.
 	$(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 $@ \
@@ -848,8 +848,8 @@ Combined patches from git.
 +libvibnet.$(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 @@ Combined patches from git.
 
     /* 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 @@ Combined patches from git.
         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 @@ Combined patches from git.
         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 @@ Combined patches from git.
 #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 ();

--- a/debian/rules
+++ b/debian/rules
@@ -6,6 +6,7 @@ export NCBI_VERSION_MAJOR=$(word 1, $(subst ., ,$(NCBI_VERSION)))
 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 @@ hi = debian/ncbi-data/usr/share/icons/hicolor

 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
@@ -186,7 +187,6 @@ override_dh_installchangelogs:

 override_dh_installmenu-arch:
 	chmod +x debian/makemenu
-	debian/makemenu debian/ncbi-cn3d.install
 	debian/makemenu debian/ncbi-tools-x11.install
 #	debian/makemenu -v debian/ncbi-tools-bin.install
 	dh_installmenu
@@ -206,7 +206,6 @@ override_dh_installman:
 	dh_link # otherwise runs too late to influence debian/installman
 	chmod +x debian/installman
 ifneq "" "$(filter ncbi-tools-bin, $(shell dh_listpackages))"
-	debian/installman ncbi-cn3d
 	debian/installman ncbi-tools-bin
 	debian/installman ncbi-tools-x11
 endif

--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -13,14 +13,14 @@ Reference:
   PMID: 10838572
   URL: https://linkinghub.elsevier.com/retrieve/pii/S0968-0004(00)01561-9
   DOI: 10.1016/S0968-0004(00)01561-9
-   Debian-package: ncbi-cn3d
+   Debian-package: ncbi-tools-x11
 Registry:
 - Name: OMICtools
   Entry:  OMICS_05052
-   Debian-package: ncbi-cn3d
+   Debian-package: ncbi-tools-x11
 - Name: bio.tools
   Entry: cn3d
-   Debian-package: ncbi-cn3d
+   Debian-package: ncbi-tools-x11
 - Name: SciCrunch
   Entry: SCR_004861
-   Debian-package: ncbi-cn3d
+   Debian-package: ncbi-tools-x11
--- a/debian/watch
+++ b/debian/watch
 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
--- a/make/makeshlb.unx
+++ b/make/makeshlb.unx
@@ -20,7 +20,7 @@ SH2 = `lorder *.o | tsort` $(NCBI_OTHERLIBS)
 	$(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 $@ \