Commit Debian 3.0 (quilt) metadata

[dgit (4.3) quilt-fixup]

2 files changed, 824 insertions, 0 deletions

diff --git a/debian/patches/debian-changes b/debian/patches/debian-changes
new file mode 100644
index 00000000..f700827e
--- /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(&ltime);
++  if (sde) {
++    ltime = strtoul(sde, NULL, 0);
++    if (ltime == 0)
++      return FALSE;
++  } else {
++    time(&ltime);
++  }
+   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
+@@ -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 ();
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 00000000..7bb82529
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+debian-changes