[med-svn] [Git][med-team/ncbi-tools6][master] 2 commits: debian/source: Populate to accommodate binary test data.
Aaron Ucko
gitlab at salsa.debian.org
Mon Mar 26 01:49:17 UTC 2018
Aaron Ucko pushed to branch master at Debian Med / ncbi-tools6
Commits:
2a33cd2a by Aaron M. Ucko at 2018-03-25T21:24:05-04:00
debian/source: Populate to accommodate binary test data.
* debian/source/format: Set to 3.0 (quilt).
* debian/source/include-binaries: List debian/tests/test-data/nc0305.aso.gz.
* debian/source/options: single-debian-patch (tracking changes purely
with git for now).
* debian/source/patch-header: "Combined patches from git."
- - - - -
48f368cb by Aaron M. Ucko at 2018-03-25T21:24:59-04:00
Commit Debian 3.0 (quilt) metadata
[dgit (4.3) quilt-fixup]
- - - - -
7 changed files:
- debian/changelog
- + debian/patches/debian-changes
- + debian/patches/series
- + debian/source/format
- + debian/source/include-binaries
- + debian/source/options
- + debian/source/patch-header
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,9 +1,17 @@
ncbi-tools6 (6.1.20170106-3) UNRELEASED; urgency=medium
+ [ Liubov Chuprikova ]
* Team upload.
* Added autopkgtest for part of ncbi-tools-bin.
- -- Liubov Chuprikova <chuprikovalv at gmail.com> Fri, 23 Mar 2018 22:20:21 +0000
+ [ Aaron M. Ucko ]
+ * debian/source/format: Set to 3.0 (quilt) to accommodate binary test data.
+ * debian/source/include-binaries: List debian/tests/test-data/nc0305.aso.gz.
+ * debian/source/options: single-debian-patch (tracking changes purely
+ with git for now).
+ * debian/source/patch-header: "Combined patches from git."
+
+ -- Aaron M. Ucko <ucko at debian.org> Sun, 25 Mar 2018 20:59:34 -0400
ncbi-tools6 (6.1.20170106-2) unstable; urgency=medium
=====================================
debian/patches/debian-changes
=====================================
--- /dev/null
+++ b/debian/patches/debian-changes
@@ -0,0 +1,823 @@
+Combined patches from git.
+--- /dev/null
++++ ncbi-tools6-6.1.20170106/.gitignore
+@@ -0,0 +1,6 @@
++bin
++build
++include
++lib
++shlib
++*-stamp
+--- ncbi-tools6-6.1.20170106.orig/access/ent2api.c
++++ ncbi-tools6-6.1.20170106/access/ent2api.c
+@@ -1273,7 +1273,7 @@ NLM_EXTERN CONN EntrezOpenConnection (
+ *arg = '\0';
+
+ return QUERY_OpenServiceQueryEx
+- (StringHasNoText (e2_service) ? "Entrez2" : e2_service, NULL, 30, arg);
++ (StringHasNoText (e2_service) ? "Entrez2s" : e2_service, NULL, 30, arg);
+ }
+
+ #ifdef OS_MAC
+--- ncbi-tools6-6.1.20170106.orig/api/sqnutil3.c
++++ ncbi-tools6-6.1.20170106/api/sqnutil3.c
+@@ -33198,7 +33198,7 @@ ClickableItemPtr LIBCALL ClickableGlobal
+ cip->clickable_item_type = item_type;
+ cip->description
+ = (CharPtr) MemNew ( sizeof (Char) * (StringLen (fmt) + 15));
+- sprintf (cip->description, fmt);
++ strcpy (cip->description, fmt);
+ return cip;
+ }
+ return NULL;
+--- ncbi-tools6-6.1.20170106.orig/connect/ncbi_gnutls.c
++++ ncbi-tools6-6.1.20170106/connect/ncbi_gnutls.c
+@@ -585,6 +585,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull
+
+ assert(!s_GnuTlsCredAnon);
+
++#if 0
+ version = gnutls_check_version(0);
+ if (strcasecmp(GNUTLS_VERSION, version) != 0) {
+ CORE_LOGF(eLOG_Critical,
+@@ -592,6 +593,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull
+ GNUTLS_VERSION, version));
+ assert(0);
+ }
++#endif
+
+ 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
+@@ -240,8 +240,14 @@ static int/*bool*/ x_UnsafeRedirectOK(SH
+ if (uuu->unsafe_redir == eDefault) {
+ if (!(uuu->flags & fHTTP_UnsafeRedirects)) {
+ char val[32];
++ const char* dflt = NULL;
++ if (uuu->net_info->scheme == eURL_Https
++ && (strspn(uuu->net_info->host, "0123456789.")
++ == strlen(uuu->net_info->host))) {
++ dflt = "TRUE";
++ }
+ ConnNetInfo_GetValue(0, "HTTP_UNSAFE_REDIRECTS",
+- val, sizeof(val), 0);
++ val, sizeof(val), dflt);
+ 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
+@@ -49,7 +49,9 @@
+ # ifndef NCBI_OS_SOLARIS
+ # include <limits.h>
+ # endif /*!NCBI_OS_SOLARIS*/
+-# ifdef NCBI_OS_LINUX
++# ifdef __MACH__
++# include <mach/vm_param.h>
++# elif defined(NCBI_OS_LINUX)
+ # 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
+@@ -128,7 +128,10 @@ NLM_EXTERN CONN QUERY_OpenUrlQuery (
+ }
+ if ( host_port ) {
+ net_info->port = host_port;
++ } else {
++ net_info->scheme = eURL_Https;
+ }
++
+ 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
+@@ -67,6 +67,7 @@
+ #pragma segment NlmSegA
+ #endif
+
++extern Nlm_Int2 Nlm_Main(void) __attribute__((weak));
+
+ /*****************************************************************************
+ *
+@@ -95,7 +96,12 @@ main(int argc, char *argv[])
+ /* Initialize connection library's logger, registry and lock */
+ CONNECT_Init(0);
+
+- retval = Nlm_Main();
++ if (Nlm_Main) {
++ retval = Nlm_Main();
++ } else {
++ ErrPost(0, 0, "Neither main nor Nlm_Main defined by program.");
++ retval = -1;
++ }
+
+ NlmThreadJoinAll();
+
+--- ncbi-tools6-6.1.20170106.orig/corelib/ncbitime.c
++++ ncbi-tools6-6.1.20170106/corelib/ncbitime.c
+@@ -77,6 +77,7 @@
+ #include <ncbi.h>
+ #include <ncbithr.h>
+ #include <ncbiwin.h>
++#include <stdlib.h>
+
+ #ifdef OS_UNIX
+ #include <sys/times.h>
+@@ -108,8 +109,18 @@ NLM_EXTERN time_t LIBCALL Nlm_GetSecs (
+ *****************************************************************************/
+ NLM_EXTERN Nlm_Boolean LIBCALL Nlm_GetDayTime (Nlm_DayTimePtr dtp)
+ {
++ /* This function honors the SOURCE_DATE_EPOCH specificatin
++ (https://reproducible-builds.org/specs/source-date-epoch/) */
++ const char *sde = getenv("SOURCE_DATE_EPOCH");
+ #if (defined(SOLARIS_THREADS_AVAIL) || defined(POSIX_THREADS_AVAIL) || defined(WIN32)) && !defined(OS_UNIX_DARWIN)
+- time_t t = time( NULL );
++ time_t t;
++ if (sde) {
++ t = strtoul(sde, NULL, 0);
++ if (t == 0)
++ return FALSE;
++ } else {
++ t = time( NULL );
++ }
+ #ifdef WIN32
+ static TNlmMutex localtime_lock;
+ if (NlmMutexLockEx( &localtime_lock ) != 0)
+@@ -125,7 +136,13 @@ NLM_EXTERN Nlm_Boolean LIBCALL Nlm_GetD
+ time_t ltime;
+ struct tm *dt;
+ Nlm_MemFill ((Nlm_VoidPtr) dtp, 0, sizeof(Nlm_DayTime));
+- time(<ime);
++ if (sde) {
++ ltime = strtoul(sde, NULL, 0);
++ if (ltime == 0)
++ return FALSE;
++ } else {
++ time(<ime);
++ }
+ 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
+@@ -65,6 +65,7 @@
+ #include <objmacro.h>
+ #include <macroapi.h>
+
++#include <connect/ncbi_gnutls.h>
+
+ #define ASNDISC_APP_VER "2.3"
+
+@@ -1264,6 +1265,8 @@ Int2 Main (void)
+ UseLocalAsnloadDataAndErrMsg ();
+ ErrPathReset ();
+
++ SOCK_SetupSSL(NcbiSetupGnuTls);
++
+ 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
+@@ -61,6 +61,8 @@
+
+ #include <entrez2.h>
+
++#include <connect/ncbi_gnutls.h>
++
+ #define ENTREZ_APP_VERSION "12.1"
+
+ #define MAX_QUERY_FORMS 256
+@@ -884,6 +886,8 @@ Int2 Main (void)
+ UseLocalAsnloadDataAndErrMsg ();
+ ErrPathReset ();
+
++ SOCK_SetupSSL(NcbiSetupGnuTls);
++
+ /*--------------------------------*/
+ /* Initialize the global settings */
+ /*--------------------------------*/
+@@ -1026,7 +1030,7 @@ Int2 Main (void)
+ /*--------------------------------------*/
+
+ if (useNormalServ) {
+- EntrezSetService ("Entrez2");
++ EntrezSetService ("Entrez2s");
+ } else if (useTestServ) {
+ EntrezSetService ("Entrez2Test");
+ } else if (useURL) {
+--- ncbi-tools6-6.1.20170106.orig/demo/gbseqget.c
++++ ncbi-tools6-6.1.20170106/demo/gbseqget.c
+@@ -54,6 +54,8 @@
+ #include <pmfapi.h>
+ #include <asn2gnbp.h>
+
++#include <connect/ncbi_gnutls.h>
++
+ static CharPtr ReadALine (
+ CharPtr str,
+ size_t size,
+@@ -417,6 +419,8 @@ Int2 Main (void)
+ UseLocalAsnloadDataAndErrMsg ();
+ ErrPathReset ();
+
++ SOCK_SetupSSL(NcbiSetupGnuTls);
++
+ 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
+@@ -55,6 +55,8 @@
+ #include <pmfapi.h>
+ #include <asn2gnbp.h>
+
++#include <connect/ncbi_gnutls.h>
++
+ #define INSDSEQGET_APP_VER "1.1"
+
+ CharPtr INSDSEQGET_APPLICATION = INSDSEQGET_APP_VER;
+@@ -423,6 +425,8 @@ Int2 Main (void)
+ UseLocalAsnloadDataAndErrMsg ();
+ ErrPathReset ();
+
++ SOCK_SetupSSL(NcbiSetupGnuTls);
++
+ 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
+@@ -50,6 +50,8 @@
+ #include <toasn3.h>
+ #include <pmfapi.h>
+
++#include <connect/ncbi_gnutls.h>
++
+ #define NPS2GPSAPP_VER "3.6"
+
+ CharPtr NPS2GPSAPPLICATION = NPS2GPSAPP_VER;
+@@ -2439,6 +2441,8 @@ Int2 Main (void)
+ UseLocalAsnloadDataAndErrMsg ();
+ ErrPathReset ();
+
++ SOCK_SetupSSL(NcbiSetupGnuTls);
++
+ if (! AllObjLoad ()) {
+ Message (MSG_FATAL, "AllObjLoad failed");
+ return 1;
+--- ncbi-tools6-6.1.20170106.orig/demo/tbl2asn.c
++++ ncbi-tools6-6.1.20170106/demo/tbl2asn.c
+@@ -8911,10 +8911,12 @@ Int2 Main (void)
+ return 1;
+ }
+
++ /*
+ if (MoreThanYearOld ()) {
+ too_old = TRUE;
+ Message (MSG_POST, "This copy of tbl2asn is more than a year old. Please download the current version.");
+ }
++ */
+
+ /* process command line arguments */
+
+@@ -9668,6 +9670,9 @@ Int2 Main (void)
+ }
+
+ if (tbl.other_failure) {
++ if (MoreThanYearOld ()) {
++ Message (MSG_POST, "This copy of tbl2asn is more than a year old. Please try again with the current version.");
++ }
+ return 1;
+ }
+
+--- ncbi-tools6-6.1.20170106.orig/desktop/bspview.c
++++ ncbi-tools6-6.1.20170106/desktop/bspview.c
+@@ -2549,13 +2549,13 @@ NLM_EXTERN void Nlm_LaunchWebPage (Char
+ }
+ #endif
+ #ifdef WIN_MOTIF
+- argv [0] = "netscape";
++ argv [0] = "sensible-browser";
+ argv [1] = url;
+ argv [2] = NULL;
+ child = fork();
+ if(child == 0) {
+- if (execvp ("netscape", argv) == -1) {
+- Message (MSG_POST, "Unable to launch netscape");
++ if (execvp ("sensible-browser", argv) == -1) {
++ Message (MSG_POST, "Unable to launch browser");
+ exit(-1);
+ }
+ }
+--- ncbi-tools6-6.1.20170106.orig/doc/firewall.html
++++ ncbi-tools6-6.1.20170106/doc/firewall.html
+@@ -133,7 +133,7 @@ in case the public access will eventuall
+
+ <p>
+ To see what ports are currently on, and their status, as reported within
+-NCBI, please refer to the following <a href="fwd_check.cgi">Firewall Daemon Presence
++NCBI, please refer to the following <a href="http://www.ncbi.nlm.nih.gov/IEB/ToolBox/NETWORK/fwd_check.cgi">Firewall Daemon Presence
+ Check</a> page. Ports marked <b>INTERNAL</b> are solely for NCBI own use, and may be
+ inaccessible from your site. That, however, does not affect availability of any
+ services that NCBI provides through other (open) firewall ports.
+@@ -143,7 +143,7 @@ TROUBLESHOOTING: You can test whether t
+ your host just by running simple <tt>telnet</tt> command (available on most
+ current systems). To know which ports, at the moment, you should be trying
+ from the list above (see the "Ports to open"), first check their status by visiting
+-<a href="fwd_check.cgi">Firewall Daemon Presence Check</a> link, then select any
++<a href="http://www.ncbi.nlm.nih.gov/IEB/ToolBox/NETWORK/fwd_check.cgi">Firewall Daemon Presence Check</a> link, then select any
+ up-and-running port and do the following (the example assumes port 5861 has
+ been shown in operational state):
+ <pre>
+@@ -175,7 +175,7 @@ functions of NCBI dispatching facilities
+
+ <p>
+ There is also an auxiliary automated UNIX shell script
+-<a href="fwd_check.sh">fwd_check.sh</a> to check all of
++<a href="../libncbi6/examples/fwd_check.sh">fwd_check.sh</a> to check all of
+ 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
+@@ -8,7 +8,7 @@
+ delay_sec="$1"
+ delay_sec=${delay_sec:="10"}
+ netcat="`which nc 2>/dev/null`"
+-temp="/tmp/`basename $0`.$$.tmp"
++temp=`mktemp`
+ 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
+@@ -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"
+ .SH NAME
+ cleanasn \- clean up irregularities in NCBI ASN.1 objects
+ .SH SYNOPSIS
+@@ -75,6 +75,10 @@ Exclude nuc\-prot sets
+ Only segmented sequences
+ .IP w
+ Exclude segmented sequences
++.IP x
++Only segmented proteins
++.IP y
++Exclude segmented proteins
+ .PD
+ .RE
+ .TP
+@@ -86,6 +90,8 @@ Sequence operations, per the flags in st
+ Compress
+ .IP d
+ Decompress
++.IP l
++Recalculated segmented sequence length
+ .IP v
+ Virtual gaps inside segmented sequence
+ .IP s
+--- /dev/null
++++ ncbi-tools6-6.1.20170106/doc/man/taxblast.1
+@@ -0,0 +1,31 @@
++.TH TAXBLAST 1 2016-12-05 NCBI "NCBI Tools User's Manual"
++.SH NAME
++taxblast \- annotate BLAST output with taxonomic details
++.SH SYNOPSIS
++.B taxblast
++[\|\fB\-\fP\|]
++[\|\fB\-d\fP\ \fIstr\fP\|]
++\fB\-i\fP\ \fIfilename\fP
++[\|\fB\-o\fP\ \fIfilename\fP\|]
++[\|\fB\-p\fP\|]
++.SH DESCRIPTION
++\fBtaxblast\fP annotates BLAST output with taxonomic details.
++.SH OPTIONS
++A summary of options is included below.
++.TP
++\fB\-\fP
++Print usage message
++.TP
++\fB\-d\fP\ \fIstr\fP
++Database used to get SeqAnnot ASN.1 (\fBnr\fP by default)
++.TP
++\fB\-i\fP\ \fIfilename\fP
++Input ASN.1 File (SeqAnnot)
++.TP
++\fB\-o\fP\ \fIfilename\fP
++Output file name (stdout by default)
++.TP
++\fB\-p\fP
++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
+@@ -1,4 +1,4 @@
+-# makefile for asntool and ncbi core routines,
++# -*- makefile -*- for asntool and ncbi core routines,
+ #
+ # $Id: makeall.unx,v 6.321 2016/12/31 22:35:10 ucko Exp $
+ #
+@@ -234,7 +234,7 @@ SRC20 = drawseq.c dotmatrx.c fea2seg.c f
+ dlgutil1.c dlgutil2.c e2trmlst.c e2docsum.c asn2graphic.c \
+ medview.c bspview.c gbfview.c gphview.c gphdraw.c gxydraw.c gtrdraw.c \
+ seqpanel.c ingengraph.c ingenext.c ingenwin.c macrodlg.c \
+- biosrc.c cdrgn.c import.c pubdesc.c seqsub.c mapgene.c prtgene.c salogif.c
++ biosrc.c cdrgn.c import.c pubdesc.c seqsub.c mapgene.c prtgene.c
+
+ SRC45 = ddvclick.c ddvgraph.c ddvopen.c ddvpanel.c
+
+@@ -392,7 +392,7 @@ OBJ20 = drawseq.o dotmatrx.o fea2seg.o f
+ dlgutil1.o dlgutil2.o e2trmlst.o e2docsum.o asn2graphic.o \
+ medview.o bspview.o gbfview.o gphview.o gphdraw.o gxydraw.o gtrdraw.o \
+ seqpanel.o ingengraph.o ingenext.o ingenwin.o macrodlg.o \
+- biosrc.o cdrgn.o import.o pubdesc.o seqsub.o mapgene.o prtgene.o salogif.o
++ biosrc.o cdrgn.o import.o pubdesc.o seqsub.o mapgene.o prtgene.o
+
+ OBJ45 = ddvclick.o ddvgraph.o ddvopen.o ddvpanel.o
+
+@@ -491,14 +491,14 @@ ln-if-absent: ../make/ln-if-absent
+ nocopy : sources $(THR_OBJ) $(LIB1) $(LIBTLS) $(LIB2) $(LIB3) $(DLIB4) $(DLIB400) \
+ $(LIB5) $(DLIB20) $(DLIB45) $(LIB22) $(LIB23) $(LIBCOMPADJ) \
+ $(DLIB28) $(DLIB30) $(DLIB3000) \
+- $(DLIB34) $(DLIB37) $(DLIB38) $(LIB50) $(LIB60) $(LIB61) $(NCBI_SHLIBS)
++ $(DLIB34) $(DLIB37) $(DLIB38) $(LIB60) $(LIB61) $(NCBI_SHLIBS)
+
+ sources : $(SRCALL)
+
+ ## To clean out the directory without removing make
+ ##
+ clean :
+- -rm -f *.[acho]
++ -rm -f *.[acho] *.glo
+
+ .NO_PARALLEL: copy $(ULIB4) $(ULIB30)
+
+@@ -656,10 +656,12 @@ shlib.sol :
+ cd ../shlib; make -f $(MAKESHLIB) `ls *.a | sed "s/\.a/.so/"` NCBI_OTHERLIBS=$(OTHERLIBS)
+ rm -f ../shlib/*.a
+
+-#
+-# Linux shared libs are built the same in the same manner as for SGI
+-#
+-shlib.lnx : shlib.sgi
++shlib.lnx :
++ -mkdir ../shlib
++ -rm -f ../shlib/*.a
++ ln $(NCBI_LIBDIR)/*.a ../shlib
++ cd ../shlib; make -f $(MAKESHLIB) `ls *.a | sed "s/\.a/.so.$(NCBI_VERSION_MAJOR)/"` SH1="$(CC) -o" SH2="-shared *.o"
++ rm -f ../shlib/*.a
+
+ shlib.sgi :
+ -mkdir ../shlib
+@@ -792,7 +794,7 @@ copy :
+ cp -fp ../algo/blast/core/*.h ../include/algo/blast/core
+ - mkdir -p ../include/algo/blast/composition_adjustment
+ $(SRCCOPY) ../algo/blast/composition_adjustment/*.c .
+- $(SRCCOPY) ../algo/blast/composition_adjustment/*.h ../include
++# $(SRCCOPY) ../algo/blast/composition_adjustment/*.h ../include
+ 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
+@@ -1,4 +1,4 @@
+-# makefile for demo programs
++# -*- makefile -*- for demo programs
+ #
+ # $Id: makedemo.unx,v 6.96 2016/08/31 19:05:26 ucko Exp $
+ #
+--- ncbi-tools6-6.1.20170106.orig/make/makenet.unx
++++ ncbi-tools6-6.1.20170106/make/makenet.unx
+@@ -1,4 +1,4 @@
+-# makefile for network demo programs and network entrez
++# -*- makefile -*- for network demo programs and network entrez
+ #
+ # $Id: makenet.unx,v 6.261 2016/08/25 15:37:04 ucko Exp $
+ # test, ignore
+@@ -330,6 +330,8 @@ OBJ46 = id2.o id2sgen.o
+
+ # objects & sources needed for versions of network demo programs
+
++OBJCN3D = cn3dmain.o
++
+ OBJDDV = ddvmain.o
+
+ OBJUDV = udvmain.o
+@@ -445,10 +447,12 @@ shlib.sol :
+ cd ../shlib; make -f $(MAKESHLIB) `ls *.a | sed "s/\.a/.so/"` NCBI_OTHERLIBS=$(OTHERLIBS)
+ rm -f ../shlib/*.a
+
+-#
+-# Linux shared libs are built the same in the same manner as for SGI
+-#
+-shlib.lnx : shlib.sgi
++shlib.lnx :
++ -mkdir ../shlib
++ -rm -f ../shlib/*.a
++ ln $(NCBI_LIBDIR)/*.a ../shlib
++ cd ../shlib; make -f $(MAKESHLIB) `ls *.a | sed "s/\.a/.so.$(NCBI_VERSION_MAJOR)/"` SH1="$(CC) -o" SH2="-shared *.o"
++ rm -f ../shlib/*.a
+
+ shlib.sgi :
+ -mkdir ../shlib
+@@ -518,7 +522,7 @@ copy :
+ $(SRCCOPY) ../network/vibnet/*.h ../include
+ $(SRCCOPY) ../cdromlib/*.h ../include
+ -$(SRCCOPY) ../network/wwwblast/Src/*.c .
+- -$(SRCCOPY) ../network/wwwblast/Src/*.h ../include
++# -$(SRCCOPY) ../network/wwwblast/Src/*.h ../include
+ $(SRCCOPY) ../cdromlib/accentr.c .
+ $(SRCCOPY) ../cdromlib/accutils.c .
+ -$(SRCCOPY) ../sequin/*.* .
+@@ -952,6 +956,11 @@ accvdb.o : accvdb.c
+ ##
+
+
++Cn3D : $(OBJCN3D) $(BENTREZLIBS) netentcf $(BLIB36)
++ $(CC) -o Cn3D $(LDFLAGS) $(OBJCN3D) $(LIB31) $(LIB3000) $(LIB20) \
++ $(LIB45) $(LIB22) $(LIB8) $(LIB7) \
++ $(LIB400) $(LIB2) $(LIB1) $(VIBLIBS) $(OGLLIBS)
++
+ ddv : $(OBJDDV)
+ $(CC) -o ddv $(LDFLAGS) $(OBJDDV) $(LIB41) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \
+ $(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) $(LIB23) \
+@@ -1097,8 +1106,8 @@ asnval_dbx_psf.o : asnval.c
+ # asndisc program (asndisc)
+ asndisc : asndisc.c
+ $(CC) -g -o asndisc $(LDFLAGS) asndisc.c $(THREAD_OBJ) $(LIB41) \
+- $(NETCLILIB) $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) \
+- $(OTHERLIBS) $(THREAD_OTHERLIBS)
++ $(NETCLILIB) $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIBTLS) $(LIB1) \
++ $(GNUTLS_LIBS) $(OTHERLIBS) $(THREAD_OTHERLIBS)
+
+ # asndisc_psf, uses PUBSEQBioseqFetchEnable instead of PubSeqFetchEnable
+ # should be used only internally within NCBI.
+@@ -1150,17 +1159,19 @@ diffshift : diffshift.c
+ # gbseqget program (gbseqget)
+ gbseqget : gbseqget.c
+ $(CC) -g -o gbseqget $(LDFLAGS) gbseqget.c $(LIB41) $(NETCLILIB) \
+- $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS)
++ $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIBTLS) $(LIB1) \
++ $(GNUTLS_LIBS) $(OTHERLIBS)
+
+ # insdseqget program (insdseqget)
+ insdseqget : insdseqget.c
+ $(CC) -g -o insdseqget $(LDFLAGS) insdseqget.c $(LIB41) $(NETCLILIB) \
+- $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS)
++ $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIBTLS) $(LIB1) \
++ $(GNUTLS_LIBS) $(OTHERLIBS)
+
+ # nps2gps program (nps2gps)
+ nps2gps : nps2gps.c
+ $(CC) -g -o nps2gps $(LDFLAGS) nps2gps.c $(LIB23) $(LIBCOMPADJ) \
+- $(LIB2) $(LIB1) $(OTHERLIBS)
++ $(LIB2) $(LIBTLS) $(LIB1) $(GNUTLS_LIBS) $(OTHERLIBS)
+
+ # trna2sap program (trna2sap)
+ trna2sap : trna2sap.c
+@@ -1181,7 +1192,8 @@ testent2 : testent2.c
+ entrez2 : entrez2.c
+ $(CC) -g -o entrez2 $(LDFLAGS) entrez2.c $(LIB41) $(LIB6) $(LIB20) \
+ $(LIB61) $(LIB60) $(LIB22) $(LIB23) $(LIBCOMPADJ) \
+- $(LIB2) $(LIB4) $(LIB1) $(VIBLIBS) $(OTHERLIBS)
++ $(LIB2) $(LIB4) $(LIBTLS) $(LIB1) \
++ $(GNUTLS_LIBS) $(VIBLIBS) $(OTHERLIBS)
+ $(VIB_POST_LINK) entrez2
+
+ # demo program (spidey)
+--- ncbi-tools6-6.1.20170106.orig/make/makeshlb.unx
++++ ncbi-tools6-6.1.20170106/make/makeshlb.unx
+@@ -1,4 +1,4 @@
+-#
++# -*- makefile -*-
+ #
+ # $Id: makeshlb.unx,v 6.1 1999/03/18 17:31:11 beloslyu Exp $
+ #
+@@ -12,7 +12,115 @@ SH1 = ld -G -o
+ SH2 = `lorder *.o | tsort` $(NCBI_OTHERLIBS)
+
+ %.so: %.a
+- rm -f *.o __*
++ rm -f *.o *.glo __*
+ ar x $<
++ case $< in \
++ *OGL.a) for f in *.glo; do mv $$f `basename $$f .glo`.o; done ;; \
++ esac
+ $(SH1) $@ $(SH2)
+ rm -f *.o __*
++
++so=so.$(NCBI_VERSION_MAJOR).$(NCBI_VERSION_MINOR)
++
++%.$(so): %.a
++ $(CC) -shared -Wl,-soname=$*.so.$(NCBI_VERSION_MAJOR) -o $@ \
++ -Wl,--whole-archive $< -Wl,--no-whole-archive $(LDFLAGS) \
++ $($*_deps) $($*_sysdeps)
++
++%.so.$(NCBI_VERSION_MAJOR): %.$(so)
++ ln -s $< $@
++ ln -s $< $*.so
++
++# Make libncbiCacc and libncbiacc pointers to libncbiNacc, since it's
++# the most useful variant in the usual (net-only) case. Do the same
++# for libnetentr, and link the static version into libncbiNacc.so, due
++# to a circular dependency.
++libnetentr.$(so) libncbiCacc.$(so) libncbiacc.$(so):
++ ln -s libncbiNacc.$(so) $@
++
++# Standardize on the OpenGL-enabled versions of Vibrant, since there's
++# no longer any real penalty in doing so.
++libvibrant.$(so):
++ ln -s libvibrantOGL.$(so) $@
++libncbicn3d.$(so):
++ ln -s libncbicn3dOGL.$(so) $@
++
++libblast_deps = libblastcompadj.$(so) libncbi.$(so)
++libblast_sysdeps = -lm
++libblastapi_deps = libblast.$(so) libncbitool.$(so) libncbiobj.$(so) \
++ libncbi.$(so)
++libblastapi_sysdeps = -lm
++libblastcompadj_sysdeps = -lm
++libconnssl_deps = libncbi.$(so)
++libconnssl_sysdeps = -lgnutls
++libncbi_sysdeps = -lm
++# libncbiCacc_deps = libncbicdr.$(so) libnetentr.a libnetcli.$(so)
++libncbiNacc_deps = libncbicdr.$(so) libnetentr.a libnetcli.$(so) \
++ libncbiobj.$(so) libncbi.$(so)
++libncbiNacc_sysdeps = -lm
++# libncbiacc_deps = libncbicdr.$(so)
++libncbicdr_deps = libncbiobj.$(so) libncbi.$(so)
++libncbiid1_deps = libncbiobj.$(so) libnetcli.$(so) libncbi.$(so)
++libncbimla_deps = libncbiobj.$(so) libnetcli.$(so) libncbi.$(so)
++libncbimmdb_deps = libncbiid1.$(so) libncbitool.$(so) libncbiobj.$(so) \
++ libncbi.$(so)
++libncbimmdb_sysdeps = -lm
++libncbiobj_deps = libncbi.$(so)
++libncbiobj_sysdeps = -lm
++libncbitool_deps = libblastcompadj.$(so) libncbiobj.$(so) libncbi.$(so)
++libncbitool_sysdeps = -lm
++libncbitxc2_deps = libncbitool.$(so) libnetcli.$(so) libncbiobj.$(so) \
++ libncbi.$(so)
++libncbitxc2_sysdeps = -lm
++libnetblast_deps = libncbitool.$(so) libnetcli.$(so) libncbiobj.$(so) \
++ libncbi.$(so)
++libnetcli_deps = libncbi.$(so)
++# libnetentr_deps = libncbiacc.$(so) libnetcli.$(so)
++libvibgif_deps = libncbi.$(so)
++libvibgif_sysdeps = -lm
++
++libddvlib_deps = libncbidesk.$(so) libvibrantOGL.$(so) \
++ libncbitool.$(so) libncbiobj.$(so) libncbi.$(so)
++libncbicn3d_deps = libncbiNacc.$(so) libddvlib.$(so) libncbidesk.$(so) \
++ libncbimmdb.$(so) libncbitool.$(so) libncbiobj.$(so) \
++ libncbi.$(so)
++libncbicn3dOGL_deps = $(libncbicn3d_deps) libvibrantOGL.$(so)
++libncbicn3dOGL_sysdeps = -lm
++libncbidesk_deps = libblastapi.$(so) libncbimmdb.$(so) libncbitool.$(so) \
++ libvibrantOGL.$(so) libncbiobj.$(so) libncbi.$(so)
++libncbidesk_sysdeps = -lm
++libvibnet_deps = libncbiNacc.$(so) libncbidesk.$(so) libncbimmdb.$(so) \
++ libvibrantOGL.$(so) libncbitool.$(so) \
++ libncbicdr.$(so) libncbiobj.$(so) libncbi.$(so)
++# libvibrant_deps = libncbi.$(so)
++# libvibrant_sysdeps = $(VIBLIBS)
++# for ddvcolor stuff
++libvibrantOGL_deps = libncbiobj.$(so) libncbi.$(so)
++libvibrantOGL_sysdeps = $(OGLLIBS) $(VIBLIBS) -lm
++
++# XXX - is there a way to express these programmatically?
++libblast.$(so): $(libblast_deps)
++libblastapi.$(so): $(libblastapi_deps)
++libconnssl.$(so): $(libconnssl_deps)
++# libncbiCacc.$(so): $(libncbiCacc_deps)
++libncbiNacc.$(so): $(libncbiNacc_deps)
++# libncbiacc.$(so): $(libncbiacc_deps)
++libncbicdr.$(so): $(libncbicdr_deps)
++libncbiid1.$(so): $(libncbiid1_deps)
++libncbimla.$(so): $(libncbimla_deps)
++libncbimmdb.$(so): $(libncbimmdb_deps)
++libncbiobj.$(so): $(libncbiobj_deps)
++libncbitool.$(so): $(libncbitool_deps)
++libncbitxc2.$(so): $(libncbitxc2_deps)
++libnetblast.$(so): $(libnetblast_deps)
++libnetcli.$(so): $(libnetcli_deps)
++# libnetentr.$(so): $(libnetentr_deps)
++
++libddvlib.$(so): $(libddvlib_deps)
++# libncbicn3d.$(so): $(libncbicn3d_deps)
++libncbicn3dOGL.$(so): $(libncbicn3dOGL_deps)
++libncbidesk.$(so): $(libncbidesk_deps)
++libvibgif.$(so): $(libvibgif_deps)
++libvibnet.$(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
+@@ -10167,7 +10167,10 @@ static Int2 FDBFinish (FormatDBPtr
+ return 1;
+
+ MemSet(dateTime, 0, DATETIME_LENGTH);
+- Nlm_DayTimeStr(dateTime, TRUE, TRUE);
++ /* SOURCE_DATE_EPOCH specification: "If the value is malformed, the
++ build process SHOULD exit with a non-zero error code." */
++ if (!Nlm_DayTimeStr(dateTime, TRUE, TRUE))
++ return 1;
+
+ /* 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
+@@ -548,9 +548,8 @@ static Boolean NS_LoadNetscape(const cha
+ }
+
+ /* ---------- child process ------------ */
+- if (execlp("netscape", "netscape", url, NULL) < 0 &&
+- execl(NETSCAPE_PATH, NETSCAPE_PATH, url, NULL) < 0) {
+- Message(MSG_ERROR, "Failure to open URL in netscape window");
++ if (execlp("sensible-browser", "sensible-browser", url, NULL) < 0) {
++ Message(MSG_ERROR, "Failure to open URL in browser window");
+ exit(1);
+ }
+
+--- ncbi-tools6-6.1.20170106.orig/vibrant/shim3d.c
++++ ncbi-tools6-6.1.20170106/vibrant/shim3d.c
+@@ -321,6 +321,7 @@
+
+ #ifdef _PNG
+ #include <png.h> /* must go berore ncbi headers */
++#include <zlib.h>
+ #ifndef png_jmpbuf
+ #define png_jmpbuf(x) ((x)->jmpbuf)
+ #endif
+@@ -339,7 +340,8 @@ NLM_EXTERN void LIBCALL Nlm_HeapSort PRO
+ #include <ddvcolor.h>
+
+ #if defined(_OPENGL) && defined(_PNG)
+-TOGL_Data *Cn3D_GetCurrentOGLData(void); /* in cn3dxprt.c */
++/* In cn3dxprt.c; declared weak here to avoid dependency loops. */
++extern TOGL_Data *Cn3D_GetCurrentOGLData(void) __attribute__((weak));
+ #endif
+
+
+@@ -2939,7 +2941,15 @@ void Nlm_SaveImagePNG(Nlm_Char *fname)
+ png_structp png_ptr = NULL;
+ png_infop info_ptr = NULL;
+ Nlm_Boolean doInterlacing = TRUE;
+- TOGL_Data *OGL_Data = (TOGL_Data *)(Cn3D_GetCurrentOGLData());
++ TOGL_Data *OGL_Data;
++
++ if (!Cn3D_GetCurrentOGLData) {
++ Message(MSG_ERROR, "PNG output unavailable; "
++ "please relink application with -lncbicn3d.");
++ return;
++ }
++
++ OGL_Data = (TOGL_Data *)(Cn3D_GetCurrentOGLData());
+
+ #if defined(WIN_MOTIF)
+ GLint glSize;
+@@ -3720,4 +3730,3 @@ void Nlm_AddHalfWorm3D(Nlm_Picture3D pic
+ if (fblock)
+ MemFree(fblock);
+ }
+-
+--- ncbi-tools6-6.1.20170106.orig/vibrant/vibmain.c
++++ ncbi-tools6-6.1.20170106/vibrant/vibmain.c
+@@ -44,6 +44,21 @@
+
+
+
++extern Nlm_Int2 Nlm_Main(void) __attribute__((weak));
++
++static Nlm_Int2 s_CallNlmMain(void)
++{
++ if (Nlm_Main) {
++ return Nlm_Main();
++ } else {
++ ErrPost(0, 0, "Neither main nor Nlm_Main defined by program.");
++ return -1;
++ }
++}
++
++#define Nlm_Main s_CallNlmMain
++
++
+ #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
+@@ -6818,7 +6818,7 @@ extern void Nlm_VibMainPrelude (int argc
+ Nlm_InitPrompt ();
+ Nlm_InitSlate ();
+ Nlm_InitTexts ();
+- if (! Nlm_SetupWindows ()) return;
++ if (! Nlm_SetupWindows ()) exit(1);
+ Nlm_RegisterWindows ();
+ Nlm_RegisterTexts ();
+ Nlm_RegisterSlates ();
=====================================
debian/patches/series
=====================================
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+debian-changes
=====================================
debian/source/format
=====================================
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
=====================================
debian/source/include-binaries
=====================================
--- /dev/null
+++ b/debian/source/include-binaries
@@ -0,0 +1 @@
+debian/tests/test-data/nc0305.aso.gz
=====================================
debian/source/options
=====================================
--- /dev/null
+++ b/debian/source/options
@@ -0,0 +1 @@
+single-debian-patch
=====================================
debian/source/patch-header
=====================================
--- /dev/null
+++ b/debian/source/patch-header
@@ -0,0 +1 @@
+Combined patches from git.
View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/compare/edfa9b84c7fa34e800e1b2fe1cc70d59a1cee424...48f368cbae4c19629394db7392f7a99ba92e73de
---
View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/compare/edfa9b84c7fa34e800e1b2fe1cc70d59a1cee424...48f368cbae4c19629394db7392f7a99ba92e73de
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