[med-svn] [Git][med-team/libgclib][master] 7 commits: CVE-2021-42006.patch: unfuzz.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Thu Nov 27 22:23:44 GMT 2025
Étienne Mollier pushed to branch master at Debian Med / libgclib
Commits:
533249d2 by Étienne Mollier at 2025-11-27T22:44:56+01:00
CVE-2021-42006.patch: unfuzz.
- - - - -
9e445e3b by Étienne Mollier at 2025-11-27T23:11:26+01:00
d/*: bump to libgclib4 SONAME.
- - - - -
a2f94570 by Étienne Mollier at 2025-11-27T23:12:14+01:00
d/control: drop redundant Rules-Requires-Root: no.
- - - - -
e73586b0 by Étienne Mollier at 2025-11-27T23:12:33+01:00
d/watch: convert to v5 Github template.
- - - - -
9276eb9a by Étienne Mollier at 2025-11-27T23:13:01+01:00
noexcept.patch: new: fix a build failure.
- - - - -
0a91a8e3 by Étienne Mollier at 2025-11-27T23:19:21+01:00
d/copyright: identify GThreads.* as ZLib material.
- - - - -
bc691cf4 by Étienne Mollier at 2025-11-27T23:22:58+01:00
d/changelog: ready for upload to experimental: NEW.
- - - - -
9 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/libgclib3.symbols.amd64 → debian/libgclib4.symbols.amd64
- debian/patches/CVE-2021-42006.patch
- debian/patches/autoconf.patch
- + debian/patches/noexcept.patch
- debian/patches/series
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+libgclib (0.12.8+ds-0+exp1) experimental; urgency=medium
+
+ * New upstream version 0.12.8+ds
+ * CVE-2021-42006.patch: unfuzz.
+ * d/*: bump to libgclib4 SONAME.
+ This is required by functions signature changes.
+ * d/control: drop redundant Rules-Requires-Root: no.
+ * d/watch: convert to v5 Github template.
+ * noexcept.patch: new: fix a build failure.
+ * d/copyright: identify GThreads.* as ZLib material.
+
+ -- Étienne Mollier <emollier at debian.org> Thu, 27 Nov 2025 23:21:58 +0100
+
libgclib (0.12.7+ds-6) unstable; urgency=medium
* d/libgclib3.symbols.amd64: flag some optional symbols. (Closes: #1097188)
=====================================
debian/control
=====================================
@@ -12,13 +12,12 @@ Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/libgclib
Vcs-Git: https://salsa.debian.org/med-team/libgclib.git
Homepage: https://github.com/gpertea/gclib
-Rules-Requires-Root: no
Package: libgclib-dev
Architecture: any
Multi-Arch: same
Section: libdevel
-Depends: libgclib3 (= ${binary:Version}),
+Depends: libgclib4 (= ${binary:Version}),
${misc:Depends}
Description: header files for Genome Code Lib (GCLib)
This is an eclectic gathering of (mostly) C++ code which upstream used
@@ -37,7 +36,7 @@ Description: header files for Genome Code Lib (GCLib)
Header files of Genome Code Lib. It is mainly known for being
used by StringTie but with its own release cycle.
-Package: libgclib3
+Package: libgclib4
Architecture: any
Multi-Arch: same
Section: libs
=====================================
debian/copyright
=====================================
@@ -10,7 +10,7 @@ License: Artistic-2.0
Files: GThreads.*
Copyright: 2010 Marcus Geelnard
(with minor modifications by Geo Pertea)
-License: custom
+License: ZLib
This software is provided 'as-is', without any express or implied
warranty. In no event will the authors be held liable for any damages
arising from the use of this software.
=====================================
debian/libgclib3.symbols.amd64 → debian/libgclib4.symbols.amd64
=====================================
@@ -1,4 +1,4 @@
-libgclib.so.3 libgclib3 #MINVER#
+libgclib.so.4 libgclib4 #MINVER#
* Build-Depends-Package: libgclib-dev
CLASSCODE_OVL_RANK at Base 0.11.4
COLOR_buf at Base 0.11.4
@@ -25,7 +25,7 @@ libgclib.so.3 libgclib3 #MINVER#
_Z10g2bit2baseh at Base 0.11.4
_Z10gcdb_allocj at Base 0.11.4
_Z10getFileExtPKc at Base 0.11.4
- _Z10getOvlDataR6GffObjS0_bi at Base 0.12.7
+ _Z10getOvlDataR6GffObjS0_bib at Base 0.12.8
_Z10parseFloatRPcRf at Base 0.11.4
_Z10replaceStrRPcS_ at Base 0.11.4
_Z10startsWithPKcS0_ at Base 0.11.4
@@ -61,6 +61,7 @@ libgclib.so.3 libgclib3 #MINVER#
_Z12reverseCharsPci at Base 0.11.4
_Z12to_unix_pathPc at Base 0.12.7
_Z12translateDNAPKcRii at Base 0.11.4
+ _Z12txCmpByExonsPvS_ at Base 0.12.8
_Z13color_resetbgP8_IO_FILE at Base 0.11.4
_Z13color_resetfgP8_IO_FILE at Base 0.11.4
(arch-bits=64)_Z13commaprintnumm at Base 0.11.4
@@ -79,13 +80,16 @@ libgclib.so.3 libgclib3 #MINVER#
_Z14gffnames_unrefRP8GffNames at Base 0.11.4
_Z14gfo_cmpRefByIDPvS_ at Base 0.11.4
_Z14translateCodonPKc at Base 0.11.4
+ _Z14txCmpByIntronsPvS_ at Base 0.12.8
_Z15printEditScriptP12GXEditScript at Base 0.11.4
+ _Z15seTxCompareProcPPvS0_ at Base 0.12.8
_Z15transcriptMatchR6GffObjS0_Rii at Base 0.11.10
_Z15uint32_pack_bigPcj at Base 0.11.4
_Z16BED_addAttributeP8_IO_FILERiPKcz at Base 0.11.4
_Z16DefLTCompareProcI4GSegEiPvS1_ at Base 0.11.4
_Z16gthreads_errExitiPKc at Base 0.11.4
- _Z16singleExonTMatchR6GffObjS0_Rii at Base 0.11.10
+ _Z16singleExonTMatchR6GffObjS0_RiiPi at Base 0.12.8
+ _Z16txStructureMatchR6GffObjS0_di at Base 0.12.8
_Z15transcriptMatchR6GffObjS0_Rii at Base 0.11.10
_Z17GreedyAlignRegionPKciiS0_iiP16CGreedyAlignDataP8CAlnTrimb at Base 0.11.4
_Z17GreedyAlignRegionPKciiS0_iiiiiP16CGreedyAlignDataP8CAlnTrimb at Base 0.11.4
@@ -97,6 +101,7 @@ libgclib.so.3 libgclib3 #MINVER#
_Z6GErrorPKcz at Base 0.11.4
_Z6GfopenPKcPc at Base 0.11.4
_Z6GmkdirPKcbi at Base 0.11.4
+ _Z6GrmdirPKc at Base 0.12.8
_Z6GstrEqPKcS0_ at Base 0.11.4
_Z6loCasePKc at Base 0.11.4
_Z6upCasePKc at Base 0.11.4
@@ -324,10 +329,7 @@ libgclib.so.3 libgclib3 #MINVER#
_ZN5GListI6GXBandE18DefaultCompareProcEPvS2_ at Base 0.11.4
_ZN5GListI6GXSeedE18DefaultCompareProcEPvS2_ at Base 0.11.4
_ZN5GListI6GffObjE18DefaultCompareProcEPvS2_ at Base 0.11.4
- (optional)_ZN5GListI6NucOriE18DefaultCompareProcEPvS2_ at Base 0.11.4
- (optional)_ZN5GListI7GffAttrE18DefaultCompareProcEPvS2_ at Base 0.11.4
_ZN5GListI7GffExonE18DefaultCompareProcEPvS2_ at Base 0.11.4
- (optional)_ZN5GListI8SeqDelOpE18DefaultCompareProcEPvS2_ at Base 0.11.4
_ZN5GListI9GFastaRecE18DefaultCompareProcEPvS2_ at Base 0.11.4
_ZN5GListI9GXAlnInfoE18DefaultCompareProcEPvS2_ at Base 0.11.4
_ZN5GPVecI11GffNameInfoE15DefaultFreeProcEPv at Base 0.11.4
=====================================
debian/patches/CVE-2021-42006.patch
=====================================
@@ -4,9 +4,9 @@ Bug-Debian: https://bugs.debian.org/996591
Author: Andreas Tille <tille at debian.org>
Last-Update: 2021-10-18
---- a/gff.cpp
-+++ b/gff.cpp
-@@ -405,7 +405,7 @@ GffLine::GffLine(GffReader* reader, cons
+--- libgclib.orig/gff.cpp
++++ libgclib/gff.cpp
+@@ -487,7 +487,7 @@
GMALLOC(dupline, llen+1);
memcpy(dupline, l, llen+1);
skipLine=true; //clear only if we make it to the end of this function
@@ -15,7 +15,7 @@ Last-Update: 2021-10-18
int i=0;
int tidx=1;
t[0]=line;
-@@ -430,6 +430,10 @@ GffLine::GffLine(GffReader* reader, cons
+@@ -512,6 +512,10 @@
track=t[1];
ftype=t[2];
info=t[8];
=====================================
debian/patches/autoconf.patch
=====================================
@@ -86,7 +86,7 @@ Index: libgclib/configure.ac
+
+AM_INIT_AUTOMAKE([1.6 foreign dist-zip tar-ustar filename-length-max=299])
+
-+LIB_VERSION=3:0
++LIB_VERSION=4:0
+
+AC_SUBST([VERSION])
+AC_SUBST([LIB_VERSION])
=====================================
debian/patches/noexcept.patch
=====================================
@@ -0,0 +1,28 @@
+Description: fix different exception specifier
+ This change fixes the following symptom, occurring when attempting to
+ build the GAlnExtend.cpp using gcc-15:
+ .
+ In file included from GAlnExtend.h:7,
+ from GAlnExtend.cpp:1:
+ GList.hh:375:22: error: declaration of ‘GList<OBJ>::GList(GList<OBJ>&&) noexcept’ has a different exception specifier -Wtemplate-body]
+ 375 | template <class OBJ> GList<OBJ>::GList(GList<OBJ>&& other) noexcept:
+ | ^~~~~~~~~~
+ GList.hh:101:5: note: from previous declaration ‘GList<OBJ>::GList(GList<OBJ>&&)’
+ 101 | GList(GList<OBJ>&& list); //move constructor
+ | ^~~~~
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2025-11-27
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- libgclib.orig/GList.hh
++++ libgclib/GList.hh
+@@ -372,7 +372,7 @@
+ }
+
+ //move constructor
+-template <class OBJ> GList<OBJ>::GList(GList<OBJ>&& other) noexcept:
++template <class OBJ> GList<OBJ>::GList(GList<OBJ>&& other) noexcept(false):
+ GPVec<OBJ>(std::move(other)), fUnique(other.fUnique), fCompareProc(other.fCompareProc){
+ //other.fUnique = false;
+ //other.fCompareProc = nullptr;
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
autoconf.patch
CVE-2021-42006.patch
+noexcept.patch
=====================================
debian/watch
=====================================
@@ -1,5 +1,8 @@
-version=4
+Version: 5
-opts="mode=git,dversionmangle=auto,repack,repacksuffix=+ds" \
-https://github.com/gpertea/gclib.git \
-refs/tags/v?([\d\.\d]+)
+Template: Github
+Owner: gpertea
+Project: gclib
+Dversionmangle: auto
+Repack: yes
+Repacksuffix: +ds
View it on GitLab: https://salsa.debian.org/med-team/libgclib/-/compare/efeb748ea4299471948e1056cdcf3c79a0e7c4c1...bc691cf4fa378b949ee529647015c057d7c3f6b4
--
View it on GitLab: https://salsa.debian.org/med-team/libgclib/-/compare/efeb748ea4299471948e1056cdcf3c79a0e7c4c1...bc691cf4fa378b949ee529647015c057d7c3f6b4
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