[med-svn] [Git][med-team/ncbi-tools6][master] 5 commits: Start work on ncbi-tools6 6.1.20170107+dfsg2-3 for #1075307.
Aaron M. Ucko (@ucko)
gitlab at salsa.debian.org
Thu Jul 25 03:16:15 BST 2024
Aaron M. Ucko pushed to branch master at Debian Med / ncbi-tools6
Commits:
e35ccc2c by Aaron M. Ucko at 2024-07-24T20:22:49-04:00
Start work on ncbi-tools6 6.1.20170107+dfsg2-3 for #1075307.
- - - - -
4dac3b8e by Aaron M. Ucko at 2024-07-24T21:58:18-04:00
Fix compilation under GCC 14 (#1075307).
* algo/blast/api/hspfilter_queue.c: Cast ersatz virtual function
implementation pointers as appropriate.
* api/asn2ff{2,4}.c, corelib/ncbimain.c, demo/trna2tbl.c,
tools/{ncbisort,pattern1}.c, vibrant/vibmain.c: Stop relying on
implicit int. (In the case of ncbisort.c, take the opportunity to
comment out an occurrence of the deprecated keyword "register.")
* desktop/seqpanel.c: Correct fputs argument order (accidentally left
unswapped when substituting it for printf years ago).
- - - - -
955797fa by Aaron M. Ucko at 2024-07-24T21:58:18-04:00
routine-update: Standards-Version: 4.7.0
- - - - -
c3f34356 by Aaron M. Ucko at 2024-07-24T21:58:18-04:00
Rely on pre-initialized dpkg-architecture variables.
Changes-By: lintian-brush
- - - - -
171835e8 by Aaron M. Ucko at 2024-07-24T21:58:18-04:00
Finalize ncbi-tools6 6.1.20170107+dfsg2-3 for unstable.
- - - - -
13 changed files:
- algo/blast/api/hspfilter_queue.c
- api/asn2ff2.c
- api/asn2ff4.c
- corelib/ncbimain.c
- debian/changelog
- debian/control
- debian/patches/debian-changes
- debian/rules
- demo/trna2tbl.c
- desktop/seqpanel.c
- tools/ncbisort.c
- tools/pattern1.c
- vibrant/vibmain.c
Changes:
=====================================
algo/blast/api/hspfilter_queue.c
=====================================
@@ -154,8 +154,8 @@ s_BlastHSPQueueNew(void* params, BlastQueryInfo* query_info)
writer = malloc(sizeof(BlastHSPWriter));
/* fill up the function pointers */
- writer->InitFnPtr = &s_BlastHSPQueueInit;
- writer->FinalFnPtr = &s_BlastHSPQueueFinal;
+ writer->InitFnPtr = (BlastHSPWriterInitFn) &s_BlastHSPQueueInit;
+ writer->FinalFnPtr = (BlastHSPWriterFinalFn) &s_BlastHSPQueueFinal;
writer->FreeFnPtr = &s_BlastHSPQueueFree;
writer->RunFnPtr = &s_BlastHSPQueueRun;
@@ -186,7 +186,7 @@ BlastHSPWriterInfo*
BlastHSPQueueInfoNew(BlastHSPQueueParams* params) {
BlastHSPWriterInfo * writer_info =
malloc(sizeof(BlastHSPWriterInfo));
- writer_info->NewFnPtr = &s_BlastHSPQueueNew;
+ writer_info->NewFnPtr = (BlastHSPWriterNewFn) &s_BlastHSPQueueNew;
writer_info->params = params;
return writer_info;
}
=====================================
api/asn2ff2.c
=====================================
@@ -1355,7 +1355,7 @@ static CharPtr GetPRFBlock (Asn2ffJobPtr ajp, GBEntryPtr gbp)
return newstring;
}
-static ChoicePID(SeqIdPtr sid)
+static Boolean ChoicePID(SeqIdPtr sid)
{
DbtagPtr db;
=====================================
api/asn2ff4.c
=====================================
@@ -1344,7 +1344,7 @@ static void UniqueGeneName(Boolean error_msgs, OrganizeFeatPtr ofp)
* Compare two ImpFeats by name and location
* returns 1 for matching features otherwise returns 0
******************************************************************************/
-static CmpImpFeat (ImpFeatPtr f1, ImpFeatPtr f2)
+static int CmpImpFeat (ImpFeatPtr f1, ImpFeatPtr f2)
{
if (f1 == NULL && f2)
return 0;
=====================================
corelib/ncbimain.c
=====================================
@@ -76,9 +76,7 @@ extern Nlm_Int2 Nlm_Main(void) __attribute__((weak));
* setups argc and argv
*
*****************************************************************************/
-#ifdef OS_MSWIN
int
-#endif
main(int argc, char *argv[])
{
Nlm_Int2 retval;
=====================================
debian/changelog
=====================================
@@ -1,3 +1,19 @@
+ncbi-tools6 (6.1.20170106+dfsg2-3) unstable; urgency=medium
+
+ * Fix compilation under GCC 14. (Closes: #1075307.)
+ - algo/blast/api/hspfilter_queue.c: Cast ersatz virtual function
+ implementation pointers as appropriate.
+ - api/asn2ff{2,4}.c, corelib/ncbimain.c, demo/trna2tbl.c,
+ tools/{ncbisort,pattern1}.c, vibrant/vibmain.c: Stop relying on
+ implicit int. (In the case of ncbisort.c, take the opportunity to
+ comment out an occurrence of the deprecated keyword "register.")
+ - desktop/seqpanel.c: Correct fputs argument order (accidentally left
+ unswapped when substituting it for printf years ago).
+ * Standards-Version: 4.7.0 (routine-update)
+ * Rely on pre-initialized dpkg-architecture variables (routine-update)
+
+ -- Aaron M. Ucko <ucko at debian.org> Wed, 24 Jul 2024 21:56:34 -0400
+
ncbi-tools6 (6.1.20170106+dfsg2-2) unstable; urgency=medium
* Don't rely on any implicit function declarations. (Closes: #1066356.)
=====================================
debian/control
=====================================
@@ -14,7 +14,7 @@ Build-Depends-Arch: csh | c-shell,
libxmu-dev
Build-Depends-Indep: icoutils,
imagemagick
-Standards-Version: 4.6.2
+Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/ncbi-tools6
Vcs-Git: https://salsa.debian.org/med-team/ncbi-tools6.git
Homepage: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/
=====================================
debian/patches/debian-changes
=====================================
@@ -19,6 +19,50 @@ Combined patches from git.
}
#ifdef OS_MAC
+--- ncbi-tools6-6.1.20170106+dfsg2.orig/algo/blast/api/hspfilter_queue.c
++++ ncbi-tools6-6.1.20170106+dfsg2/algo/blast/api/hspfilter_queue.c
+@@ -154,8 +154,8 @@ s_BlastHSPQueueNew(void* params, BlastQu
+ writer = malloc(sizeof(BlastHSPWriter));
+
+ /* fill up the function pointers */
+- writer->InitFnPtr = &s_BlastHSPQueueInit;
+- writer->FinalFnPtr = &s_BlastHSPQueueFinal;
++ writer->InitFnPtr = (BlastHSPWriterInitFn) &s_BlastHSPQueueInit;
++ writer->FinalFnPtr = (BlastHSPWriterFinalFn) &s_BlastHSPQueueFinal;
+ writer->FreeFnPtr = &s_BlastHSPQueueFree;
+ writer->RunFnPtr = &s_BlastHSPQueueRun;
+
+@@ -186,7 +186,7 @@ BlastHSPWriterInfo*
+ BlastHSPQueueInfoNew(BlastHSPQueueParams* params) {
+ BlastHSPWriterInfo * writer_info =
+ malloc(sizeof(BlastHSPWriterInfo));
+- writer_info->NewFnPtr = &s_BlastHSPQueueNew;
++ writer_info->NewFnPtr = (BlastHSPWriterNewFn) &s_BlastHSPQueueNew;
+ writer_info->params = params;
+ return writer_info;
+ }
+--- ncbi-tools6-6.1.20170106+dfsg2.orig/api/asn2ff2.c
++++ ncbi-tools6-6.1.20170106+dfsg2/api/asn2ff2.c
+@@ -1355,7 +1355,7 @@ static CharPtr GetPRFBlock (Asn2ffJobPtr
+ return newstring;
+ }
+
+-static ChoicePID(SeqIdPtr sid)
++static Boolean ChoicePID(SeqIdPtr sid)
+ {
+
+ DbtagPtr db;
+--- ncbi-tools6-6.1.20170106+dfsg2.orig/api/asn2ff4.c
++++ ncbi-tools6-6.1.20170106+dfsg2/api/asn2ff4.c
+@@ -1344,7 +1344,7 @@ static void UniqueGeneName(Boolean error
+ * Compare two ImpFeats by name and location
+ * returns 1 for matching features otherwise returns 0
+ ******************************************************************************/
+-static CmpImpFeat (ImpFeatPtr f1, ImpFeatPtr f2)
++static int CmpImpFeat (ImpFeatPtr f1, ImpFeatPtr f2)
+ {
+ if (f1 == NULL && f2)
+ return 0;
--- ncbi-tools6-6.1.20170106+dfsg2.orig/api/asn2gnb2.c
+++ ncbi-tools6-6.1.20170106+dfsg2/api/asn2gnb2.c
@@ -58,7 +58,7 @@
@@ -123,7 +167,17 @@ Combined patches from git.
/*****************************************************************************
*
-@@ -95,7 +96,12 @@ main(int argc, char *argv[])
+@@ -75,9 +76,7 @@
+ * setups argc and argv
+ *
+ *****************************************************************************/
+-#ifdef OS_MSWIN
+ int
+-#endif
+ main(int argc, char *argv[])
+ {
+ Nlm_Int2 retval;
+@@ -95,7 +94,12 @@ main(int argc, char *argv[])
/* Initialize connection library's logger, registry and lock */
CONNECT_Init(0);
@@ -355,6 +409,17 @@ Combined patches from git.
return 1;
}
+--- ncbi-tools6-6.1.20170106+dfsg2.orig/demo/trna2tbl.c
++++ ncbi-tools6-6.1.20170106+dfsg2/demo/trna2tbl.c
+@@ -229,7 +229,7 @@ static void RunTrnaScan (void)
+ }
+ }
+
+-main (int argc, char *argv[])
++int main (int argc, char *argv[])
+
+ {
+ RunTrnaScan ();
--- ncbi-tools6-6.1.20170106+dfsg2.orig/desktop/bspview.c
+++ ncbi-tools6-6.1.20170106+dfsg2/desktop/bspview.c
@@ -2549,13 +2549,13 @@ NLM_EXTERN void Nlm_LaunchWebPage (Char
@@ -374,6 +439,26 @@ Combined patches from git.
exit(-1);
}
}
+--- ncbi-tools6-6.1.20170106+dfsg2.orig/desktop/seqpanel.c
++++ ncbi-tools6-6.1.20170106+dfsg2/desktop/seqpanel.c
+@@ -8662,7 +8662,7 @@ WriteAlignmentInterleaveToFileEx
+ seqbuf, alnbuf, &alnbuf_len,
+ show_substitutions);
+ MemCpy (printed_line + label_len + 1 + coord_len, alnbuf, alnbuf_len);
+- fputs (fp, printed_line);
++ fputs (printed_line, fp);
+ }
+ fprintf (fp, "\n");
+ start = stop + 1;
+@@ -8758,7 +8758,7 @@ extern void WriteAlignmentContiguousToFi
+ seqbuf, alnbuf, &alnbuf_len,
+ show_substitutions);
+ MemCpy (printed_line, alnbuf, alnbuf_len);
+- fputs (fp, printed_line);
++ fputs (printed_line, fp);
+ start = stop + 1;
+ stop += seq_chars_per_row;
+ }
--- ncbi-tools6-6.1.20170106+dfsg2.orig/doc/dispatcher.html
+++ ncbi-tools6-6.1.20170106+dfsg2/doc/dispatcher.html
@@ -9,15 +9,15 @@
@@ -869,6 +954,29 @@ Combined patches from git.
+libvibnet.$(so): $(libvibnet_deps)
+# libvibrant.$(so): $(libvibrant_deps)
+libvibrantOGL.$(so): $(libvibrantOGL_deps)
+--- ncbi-tools6-6.1.20170106+dfsg2.orig/tools/ncbisort.c
++++ ncbi-tools6-6.1.20170106+dfsg2/tools/ncbisort.c
+@@ -696,7 +696,7 @@ static SORTErrorCode SORTFindLines(SORTB
+ of the fraction. Strings not of this form are considered to be zero. */
+ static Int4 SORTFracCompare(register UcharPtr a, register UcharPtr b)
+ {
+- register tmpa = UCHAR(*a), tmpb = UCHAR(*b);
++ /* register */ int tmpa = UCHAR(*a), tmpb = UCHAR(*b);
+
+ if (tmpa == '.' && tmpb == '.') {
+ do
+--- ncbi-tools6-6.1.20170106+dfsg2.orig/tools/pattern1.c
++++ ncbi-tools6-6.1.20170106+dfsg2/tools/pattern1.c
+@@ -741,7 +741,8 @@ static void or(Int4 *a, Int4 *b, pattern
+
+ /*Do a word-by-word bit-wise or of a and b and put the result in
+ result; return 1 if there are any non-zero words*/
+-static and(Int4 *result, Int4 *a, Int4 *b, patternSearchItems *patternSearch)
++static Int4 and(Int4 *result, Int4 *a, Int4 *b,
++ patternSearchItems *patternSearch)
+ {
+ Int4 i; /*index over words*/
+ Int4 returnValue = 0;
--- ncbi-tools6-6.1.20170106+dfsg2.orig/tools/readdb.c
+++ ncbi-tools6-6.1.20170106+dfsg2/tools/readdb.c
@@ -10167,7 +10167,10 @@ static Int2 FDBFinish (FormatDBPtr
@@ -980,6 +1088,15 @@ Combined patches from git.
#ifdef WIN_MAC
#ifdef OS_UNIX_DARWIN
int main (int argc, char *argv[])
+@@ -103,7 +118,7 @@ main (int argc, char *argv[], char *envp
+ exit (retval);
+ }
+ #else
+-main (int argc, char *argv[])
++int main (int argc, char *argv[])
+ {
+ Nlm_Int2 retval;
+
--- ncbi-tools6-6.1.20170106+dfsg2.orig/vibrant/vibwndws.c
+++ ncbi-tools6-6.1.20170106+dfsg2/vibrant/vibwndws.c
@@ -6818,7 +6818,7 @@ extern void Nlm_VibMainPrelude (int argc
=====================================
debian/rules
=====================================
@@ -114,7 +114,7 @@ override_dh_auto_clean:
-rm -f debian/*.menu $(ICONS)
chmod -x debian/makemenu debian/installman
-DEB_HOST_MULTIARCH ?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH)
+include /usr/share/dpkg/architecture.mk
destlibdir=debian/tmp/usr/lib/$(DEB_HOST_MULTIARCH)
icon_in = link/mswin/ncbilogo.ico
hi = debian/ncbi-data/usr/share/icons/hicolor
=====================================
demo/trna2tbl.c
=====================================
@@ -229,7 +229,7 @@ static void RunTrnaScan (void)
}
}
-main (int argc, char *argv[])
+int main (int argc, char *argv[])
{
RunTrnaScan ();
=====================================
desktop/seqpanel.c
=====================================
@@ -8662,7 +8662,7 @@ WriteAlignmentInterleaveToFileEx
seqbuf, alnbuf, &alnbuf_len,
show_substitutions);
MemCpy (printed_line + label_len + 1 + coord_len, alnbuf, alnbuf_len);
- fputs (fp, printed_line);
+ fputs (printed_line, fp);
}
fprintf (fp, "\n");
start = stop + 1;
@@ -8758,7 +8758,7 @@ extern void WriteAlignmentContiguousToFile
seqbuf, alnbuf, &alnbuf_len,
show_substitutions);
MemCpy (printed_line, alnbuf, alnbuf_len);
- fputs (fp, printed_line);
+ fputs (printed_line, fp);
start = stop + 1;
stop += seq_chars_per_row;
}
=====================================
tools/ncbisort.c
=====================================
@@ -696,7 +696,7 @@ static SORTErrorCode SORTFindLines(SORTBufferPtr buf, SORTLinesPtr lines,
of the fraction. Strings not of this form are considered to be zero. */
static Int4 SORTFracCompare(register UcharPtr a, register UcharPtr b)
{
- register tmpa = UCHAR(*a), tmpb = UCHAR(*b);
+ /* register */ int tmpa = UCHAR(*a), tmpb = UCHAR(*b);
if (tmpa == '.' && tmpb == '.') {
do
=====================================
tools/pattern1.c
=====================================
@@ -741,7 +741,8 @@ static void or(Int4 *a, Int4 *b, patternSearchItems *patternSearch)
/*Do a word-by-word bit-wise or of a and b and put the result in
result; return 1 if there are any non-zero words*/
-static and(Int4 *result, Int4 *a, Int4 *b, patternSearchItems *patternSearch)
+static Int4 and(Int4 *result, Int4 *a, Int4 *b,
+ patternSearchItems *patternSearch)
{
Int4 i; /*index over words*/
Int4 returnValue = 0;
=====================================
vibrant/vibmain.c
=====================================
@@ -118,7 +118,7 @@ main (int argc, char *argv[], char *envp[])
exit (retval);
}
#else
-main (int argc, char *argv[])
+int main (int argc, char *argv[])
{
Nlm_Int2 retval;
View it on GitLab: https://salsa.debian.org/med-team/ncbi-tools6/-/compare/b2ceceb766083a3efd5cb42c157a058d0577240f...171835e81a1b7968bd3fe876d756711af0e0126d
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