[med-svn] [Git][med-team/wise][master] 4 commits: gcc-14.patch: fix multiple build failures with gcc 14.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Thu Aug 15 11:03:31 BST 2024
Étienne Mollier pushed to branch master at Debian Med / wise
Commits:
a8103e2a by Étienne Mollier at 2024-08-15T11:52:43+02:00
gcc-14.patch: fix multiple build failures with gcc 14.
Note that the patch alone is not sufficient as such as motifmatrix.c
is still affected by a case of assignment to integer from pointer
without a cast which feels like a compiler bug. See #1075638.
- - - - -
aa28df9d by Étienne Mollier at 2024-08-15T11:59:26+02:00
d/control: build depends on the libfl-dev.
Apparently the missing libl.a went below the radar for building dyc.
- - - - -
afcf533d by Étienne Mollier at 2024-08-15T12:01:10+02:00
d/rules: build and provide the dyc compiler to the rest of the build.
- - - - -
f2a13fb0 by Étienne Mollier at 2024-08-15T12:02:35+02:00
Update changelog.
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/gcc-14.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+wise (2.4.1-25) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * gcc-14.patch: fix multiple build failures with gcc 14.
+ Note that the patch alone is not sufficient as such as motifmatrix.c
+ is still affected by a case of assignment to integer from pointer
+ without a cast which feels like a compiler bug. See #1075638.
+ * d/control: build depends on the libfl-dev.
+ Apparently the missing libl.a went below the radar for building dyc.
+ * d/rules: build and provide the dyc compiler to the rest of the build.
+
+ -- Étienne Mollier <emollier at debian.org> Thu, 15 Aug 2024 12:02:02 +0200
+
wise (2.4.1-24) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -10,7 +10,8 @@ Build-Depends: debhelper-compat (= 13),
texlive-extra-utils,
hevea,
docbook-to-man,
- libglib2.0-dev
+ libglib2.0-dev,
+ libfl-dev
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/wise
Vcs-Git: https://salsa.debian.org/med-team/wise.git
=====================================
debian/patches/gcc-14.patch
=====================================
@@ -0,0 +1,127 @@
+Description: fix multiple issues gone fatal with gcc 14.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075638
+Forwarded: no
+Last-Update: 2024-08-15
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- wise.orig/src/socket/functionclient.dy
++++ wise/src/socket/functionclient.dy
+@@ -190,7 +190,7 @@
+ bcopy( hp->h_addr, &server.sin_addr, hp->h_length);
+ server.sin_port = htons(port);
+
+- connect(out->socket, &server, sizeof(server));
++ connect(out->socket, (const struct sockaddr *)&server, sizeof(server));
+
+
+ return out;
+--- wise.orig/src/dyc/dynafunc.dy
++++ wise/src/dyc/dynafunc.dy
+@@ -6,6 +6,7 @@
+ #include "labelmaster.h"
+ #include "linesubs.h"
+ #include "dynashadow.h"
++#include "dyshatter.h"
+ #include "dynadb.h"
+ #include "dpimpl.h"
+ #include "dbthread.h"
+--- wise.orig/src/dyc/inputfile.c
++++ wise/src/dyc/inputfile.c
+@@ -5,7 +5,7 @@
+
+
+ static FILE * watch_file = NULL;
+-static linecount = 0;
++static int linecount = 0;
+
+
+ # line 18 "inputfile.dy"
+--- wise.orig/src/dyc/dynafunc.h
++++ wise/src/dyc/dynafunc.h
+@@ -14,6 +14,7 @@
+ #include "dbthread.h"
+ #include "probal.h"
+ #include "dynadebug.h"
++#include "dyshatter.h"
+
+
+
+--- wise.orig/src/dyc/lex.yy.c
++++ wise/src/dyc/lex.yy.c
+@@ -411,11 +411,7 @@
+ #endif
+
+ #ifndef YY_NO_INPUT
+-#ifdef __cplusplus
+ static int yyinput YY_PROTO(( void ));
+-#else
+-static int input YY_PROTO(( void ));
+-#endif
+ #endif
+
+ #if YY_STACK_USED
+@@ -1061,11 +1057,7 @@
+ #endif /* ifndef YY_NO_UNPUT */
+
+
+-#ifdef __cplusplus
+ static int yyinput()
+-#else
+-static int input()
+-#endif
+ {
+ int c;
+
+@@ -1111,11 +1103,7 @@
+
+ if ( ! yy_did_buffer_switch_on_eof )
+ YY_NEW_FILE;
+-#ifdef __cplusplus
+ return yyinput();
+-#else
+- return input();
+-#endif
+ }
+
+ case EOB_ACT_CONTINUE_SCAN:
+--- wise.orig/src/dnaindex/compressed_protein_index.dy
++++ wise/src/dnaindex/compressed_protein_index.dy
+@@ -220,7 +220,7 @@
+ {
+ fatal("For compressed protein indexes, impossible to add numbers directly");
+
+- return NULL;
++ return FALSE;
+ }
+
+ ArraySeqHead * lookup_array_head_CompressedProteinIndex(void * data,int seq_number)
+--- wise.orig/src/dnaindex/kmer_assembly_untangler.dy
++++ wise/src/dnaindex/kmer_assembly_untangler.dy
+@@ -565,7 +565,14 @@
+
+ if( have_link == 1 ) {
+ /* fprintf(stderr," ..reverse TAIL.. untangling...\n"); */
+- lift_backward_tangled_tail(kai,newpath->stack[newpath->stack_len-1],path,transferred_label,transferred_pos,transferred_len);
++ lift_backward_tangled_tail(
++ kai,
++ newpath->stack[newpath->stack_len-1],
++ path,
++ (int*)transferred_label,
++ transferred_pos,
++ transferred_len
++ );
+ }
+
+ /* pop off the top of this path */
+--- wise.orig/src/models/est_evidence.dy
++++ wise/src/models/est_evidence.dy
+@@ -139,7 +139,7 @@
+ in->utr_pot = est_utr_pot;
+ in->cds_intron_pot = est_intron_pot;
+ in->utr_intron_pot = est_intron_pot;
+- in->geu_free = free_EstEvidence;
++ in->geu_free = (int(*)(void*))free_EstEvidence;
+ in->frameshift_cds = est_cds_frameshift;
+ in->stop_pot = est_stop_pot;
+ in->start_pot = est_start_pot;
=====================================
debian/patches/series
=====================================
@@ -13,3 +13,4 @@ spelling.patch
cross.patch
implicit-function-declaration.patch
executable-is-script.patch
+gcc-14.patch
=====================================
debian/rules
=====================================
@@ -18,6 +18,12 @@ include /usr/share/dpkg/buildflags.mk
dh $@
override_dh_auto_build:
+ # The dyc compiler is needed before building the all the rest.
+ # Also, it pre-depends on the libwisebase library, otherwise
+ # linking fails.
+ dh_auto_build --sourcedirectory=src/base -- libwisebase.a
+ dh_auto_build --sourcedirectory=src/dyc -- dyc
+ PATH="$$PATH:$(CURDIR)/src/dyc" \
dh_auto_build --sourcedirectory=src -- all
$(MAKE) -C debian/manpages.d
# build documentation manually (docs/makefile is not useable)
View it on GitLab: https://salsa.debian.org/med-team/wise/-/compare/37c8e39d00fc5fa68d75171491729c657954f3ee...f2a13fb00c6c08b60f614f05464f8dd44607443f
--
View it on GitLab: https://salsa.debian.org/med-team/wise/-/compare/37c8e39d00fc5fa68d75171491729c657954f3ee...f2a13fb00c6c08b60f614f05464f8dd44607443f
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