[med-svn] [Git][med-team/ncbi-tools6][master] 9 commits: Remove data/UniVec.* over DFSG-nonfree Invitrogen vectors.
Aaron M. Ucko
gitlab at salsa.debian.org
Tue Jul 30 03:18:51 BST 2019
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-tools6
Commits:
eef0ddc9 by Aaron M. Ucko at 2019-07-29T01:01:39Z
Remove data/UniVec.* over DFSG-nonfree Invitrogen vectors.
Per UniVec.nhr, Invitrogen Corporation holds copyright over some
portions of UniVec and requires a license for commercial use thereof.
Other files (even UniVec_Core.*) have no such restrictions.
- - - - -
7a4f8652 by Aaron M. Ucko at 2019-07-30T02:10:33Z
Merge tag 'upstream/6.1.20170106+dfsg1'.
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.)
- - - - -
2db6abd5 by Aaron M. Ucko at 2019-07-30T02:10:39Z
Note Andreas's d/u/metadata DOI syntax fix in changelog.
- - - - -
4349eba1 by Aaron M. Ucko at 2019-07-30T02:10:51Z
d/copyright: Cover previously overlooked third-party code (all DFSG-free).
- - - - -
1077452c by Aaron M. Ucko at 2019-07-30T02:11:12Z
debian/copyright: Update authors and dates for debian/*.
- - - - -
4af64252 by Aaron M. Ucko at 2019-07-30T02:11:15Z
Temporarily revert ncbi-cn3d splitout to expedite the above fixes.
This reverts commit e1fc91b7bac38a1fb3ff6e5e141589beb09d5691
("Split Cn3D(-3.0) out into a new ncbi-cn3d binary package.")
- - - - -
6729ff2e by Aaron M. Ucko at 2019-07-30T02:11:15Z
debian/{copyright,watch}: Formally update to reflect repackaging.
* debian/copyright: Set Files-Excluded.
* debian/watch: Reflect usage of +dfsg1.
- - - - -
bd6ad3ab by Aaron M. Ucko at 2019-07-30T02:11:15Z
Omit +dfsg1 suffix from library SONAMEs.
* debian/rules: Introduce NCBI_VERSION_SHLIB, with +dfsg1 stripped off.
* make/makeshlb.unx: NCBI_VERSION -> NCBI_VERSION_SHLIB.
- - - - -
1977de0b by Aaron M. Ucko at 2019-07-30T02:12:42Z
Finalize ncbi-tools6 6.1.20170106+dfsg1-1 for upload to unstable.
- - - - -
17 changed files:
- − data/UniVec.nhr
- − data/UniVec.nin
- − data/UniVec.nsq
- debian/.gitignore
- debian/changelog
- debian/control
- debian/copyright
- − debian/ncbi-cn3d.install
- debian/ncbi-tools-x11.install
- debian/ncbi-cn3d.mime → debian/ncbi-tools-x11.mime
- debian/ncbi-cn3d.postinst → debian/ncbi-tools-x11.postinst
- debian/ncbi-cn3d.prerm → debian/ncbi-tools-x11.prerm
- debian/patches/debian-changes
- debian/rules
- debian/upstream/metadata
- debian/watch
- make/makeshlb.unx
Changes:
=====================================
data/UniVec.nhr deleted
=====================================
Binary files a/data/UniVec.nhr and /dev/null differ
=====================================
data/UniVec.nin deleted
=====================================
Binary files a/data/UniVec.nin and /dev/null differ
=====================================
data/UniVec.nsq deleted
=====================================
Binary files a/data/UniVec.nsq and /dev/null differ
=====================================
debian/.gitignore
=====================================
@@ -7,7 +7,6 @@ libncbi6
libvibrant6b
lib*-dbg
lib*-dev
-ncbi-cn3d
ncbi-data
ncbi-rrna-data
ncbi-tools-bin
=====================================
debian/changelog
=====================================
@@ -1,3 +1,23 @@
+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 at debian.org> Mon, 29 Jul 2019 22:12:41 -0400
+
ncbi-tools6 (6.1.20170106-7) unstable; urgency=medium
[ Steffen Möller ]
=====================================
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
=====================================
debian/copyright
=====================================
@@ -2,15 +2,63 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Contact: toolbox at 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 at pasteur.fr>
2001 Dr. Guenter Bechly <gbechly at debian.org>
- 2001-2018 Aaron M. Ucko <ucko at debian.org>
+ 2001-2019 Aaron M. Ucko <ucko at debian.org>
+ 2012-2019 Andreas Tille <tille at debian.org
+ 2019 Steffen Möller <moeller at 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'.
=====================================
debian/ncbi-cn3d.install deleted
=====================================
@@ -1 +0,0 @@
-usr/bin/Cn3D-3.0
=====================================
debian/ncbi-tools-x11.install
=====================================
@@ -1,3 +1,4 @@
+usr/bin/Cn3D-3.0
usr/bin/Psequin
usr/bin/ddv
usr/bin/entrez2
=====================================
debian/ncbi-cn3d.mime → debian/ncbi-tools-x11.mime
=====================================
=====================================
debian/ncbi-cn3d.postinst → debian/ncbi-tools-x11.postinst
=====================================
=====================================
debian/ncbi-cn3d.prerm → debian/ncbi-tools-x11.prerm
=====================================
=====================================
debian/patches/debian-changes
=====================================
@@ -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 @@ 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 (<ime)) != 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> </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): $(libvibrantOGL_deps)
---- ncbi-tools6-6.1.20170106.orig/tools/readdb.c
-+++ ncbi-tools6-6.1.20170106/tools/readdb.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/tools/readdb.c
++++ ncbi-tools6-6.1.20170106+dfsg1/tools/readdb.c
@@ -10167,7 +10167,10 @@ static Int2 FDBFinish (FormatDBPtr
return 1;
@@ -862,8 +862,8 @@ Combined patches from git.
/* write db_title and date-time stamp eigth bytes aligned */
tmp = title_len + StringLen(dateTime);
---- ncbi-tools6-6.1.20170106.orig/vibrant/netscape.c
-+++ ncbi-tools6-6.1.20170106/vibrant/netscape.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/vibrant/netscape.c
++++ ncbi-tools6-6.1.20170106+dfsg1/vibrant/netscape.c
@@ -548,9 +548,8 @@ static Boolean NS_LoadNetscape(const cha
}
@@ -876,8 +876,8 @@ Combined patches from git.
exit(1);
}
---- ncbi-tools6-6.1.20170106.orig/vibrant/shim3d.c
-+++ ncbi-tools6-6.1.20170106/vibrant/shim3d.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/vibrant/shim3d.c
++++ ncbi-tools6-6.1.20170106+dfsg1/vibrant/shim3d.c
@@ -321,6 +321,7 @@
#ifdef _PNG
@@ -918,8 +918,8 @@ Combined patches from git.
MemFree(fblock);
}
-
---- ncbi-tools6-6.1.20170106.orig/vibrant/vibmain.c
-+++ ncbi-tools6-6.1.20170106/vibrant/vibmain.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/vibrant/vibmain.c
++++ ncbi-tools6-6.1.20170106+dfsg1/vibrant/vibmain.c
@@ -44,6 +44,21 @@
@@ -942,8 +942,8 @@ Combined patches from git.
#ifdef WIN_MAC
#ifdef OS_UNIX_DARWIN
int main (int argc, char *argv[])
---- ncbi-tools6-6.1.20170106.orig/vibrant/vibwndws.c
-+++ ncbi-tools6-6.1.20170106/vibrant/vibwndws.c
+--- ncbi-tools6-6.1.20170106+dfsg1.orig/vibrant/vibwndws.c
++++ ncbi-tools6-6.1.20170106+dfsg1/vibrant/vibwndws.c
@@ -6818,7 +6818,7 @@ extern void Nlm_VibMainPrelude (int argc
Nlm_InitPrompt ();
Nlm_InitSlate ();
=====================================
debian/rules
=====================================
@@ -6,6 +6,7 @@ export NCBI_VERSION_MAJOR=$(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, $(shell dh_listpackages))"
- debian/installman ncbi-cn3d
debian/installman ncbi-tools-bin
debian/installman ncbi-tools-x11
endif
=====================================
debian/upstream/metadata
=====================================
@@ -13,14 +13,14 @@ Reference:
PMID: 10838572
URL: https://linkinghub.elsevier.com/retrieve/pii/S0968-0004(00)01561-9
DOI: 10.1016/S0968-0004(00)01561-9
- Debian-package: ncbi-cn3d
+ Debian-package: ncbi-tools-x11
Registry:
- Name: OMICtools
Entry: OMICS_05052
- Debian-package: ncbi-cn3d
+ Debian-package: ncbi-tools-x11
- Name: bio.tools
Entry: cn3d
- Debian-package: ncbi-cn3d
+ Debian-package: ncbi-tools-x11
- Name: SciCrunch
Entry: SCR_004861
- Debian-package: ncbi-cn3d
+ Debian-package: ncbi-tools-x11
=====================================
debian/watch
=====================================
@@ -1,3 +1,3 @@
version=4
-opts="passive,uversionmangle=s|^|6.1.|,downloadurlmangle=s/$/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
=====================================
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 $@ \
View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/compare/b5e93c7baad2c2695f069cd86bfaf1545f1d954c...1977de0be3b269d1a2996d7c8b2d7f527616c826
--
View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/compare/b5e93c7baad2c2695f069cd86bfaf1545f1d954c...1977de0be3b269d1a2996d7c8b2d7f527616c826
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