[Debichem-devel] Bug#853351: comet-ms: ftbfs with GCC-7
pini
pini at pustule.org
Mon Oct 16 20:16:17 UTC 2017
Control: tags -1 + patch
Hi,
On Tue, 31 Jan 2017 09:30:22 +0000 Matthias Klose <doko at debian.org> wrote:
> Package: src:comet-ms
> Version: 2014022-3
> Severity: normal
> Tags: sid buster
> User: debian-gcc at lists.debian.org
> Usertags: ftbfs-gcc-7
>
> Please keep this issue open in the bug tracker for the package it
> was filed for. If a fix in another package is required, please
> file a bug for the other package (or clone), and add a block in this
> package. Please keep the issue open until the package can be built in
> a follow-up test rebuild.
>
> The package fails to build in a test rebuild on at least amd64 with
> gcc-7/g++-7, but succeeds to build with gcc-6/g++-6. The
> severity of this report may be raised before the buster release.
> There is no need to fix this issue in time for the stretch release.
>
> The full build log can be found at:
> http://people.debian.org/~doko/logs/gcc7-20170126/comet-ms_2014022-3_unstable_gcc7.log
> The last lines of the build log are at the end of this report.
>
> To build with GCC 7, either set CC=gcc-7 CXX=g++-7 explicitly,
> or install the gcc, g++, gfortran, ... packages from experimental.
>
> apt-get -t=experimental install g++
>
> Common build failures are new warnings resulting in build failures with
> -Werror turned on, or new/dropped symbols in Debian symbols files.
> For other C/C++ related build failures see the porting guide at
> http://gcc.gnu.org/gcc-7/porting_to.html
>
> [...]
> dpkg-source: info: applying fix-format-security-gcc-warnings.patch
> dpkg-source: info: applying fix-makefiles-to-handle-lib-debian-way-of-doing-things.patch
> dpkg-source: info: building comet-ms using existing ./comet-ms_2014022.orig.tar.gz
> dpkg-source: info: building comet-ms in comet-ms_2014022-3.debian.tar.xz
> dpkg-source: info: building comet-ms in comet-ms_2014022-3.dsc
> debian/rules build
> dh build
> dh_testdir
> dh_update_autotools_config
> dh_auto_configure
> debian/rules override_dh_auto_build
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> docbook-to-man debian/comet-ms.sgml > debian/comet-ms.1
> /usr/bin/onsgmls:debian/comet-ms.sgml:89:12:E: end tag for "PARA" omitted, but OMITTAG NO was specified
> /usr/bin/onsgmls:debian/comet-ms.sgml:87:4: start tag was here
> /usr/bin/onsgmls:debian/comet-ms.sgml:89:12: open elements: REFENTRY REFSECT1[1] PARA[1] (#PCDATA[1])
> dh_quilt_patch
> quilt --quiltrc /dev/null push -a || test $? = 2
> File series fully applied, ends at patch fix-makefiles-to-handle-lib-debian-way-of-doing-things.patch
> make
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -Wformat-security -Wextra -Wno-char-subscripts -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -I/usr/include/libmstoolkit -ICometSearch -L. Comet.cpp -c
> In file included from CometSearch/Common.h:39:0,
> from Comet.cpp:18:
> /usr/include/libmstoolkit/MSReader.h:85:80: error: invalid conversion from 'char' to 'char*' [-fpermissive]
> void writeFile(const char* c, MSFileFormat ff, MSObject& m, char* sha1Report='\0');
Patch proposal for libmstoolkit attached.
Thanks,
_g.
-------------- next part --------------
diff -Nru libmstoolkit-77.0.0/debian/changelog libmstoolkit-77.0.0/debian/changelog
--- libmstoolkit-77.0.0/debian/changelog 2015-01-13 10:25:07.000000000 +0100
+++ libmstoolkit-77.0.0/debian/changelog 2017-10-11 18:45:22.000000000 +0200
@@ -1,3 +1,10 @@
+libmstoolkit (77.0.0-1.1) UNRELEASED; urgency=medium
+
+ * Non-maintainer upload.
+ * New patch gcc-7.patch: fix FTBFS with GCC-7 (closes: #853351)
+
+ -- Gilles Filippini <pini at debian.org> Wed, 11 Oct 2017 18:45:22 +0200
+
libmstoolkit (77.0.0-1) unstable; urgency=medium
* New upstream version;
diff -Nru libmstoolkit-77.0.0/debian/patches/gcc-7.patch libmstoolkit-77.0.0/debian/patches/gcc-7.patch
--- libmstoolkit-77.0.0/debian/patches/gcc-7.patch 1970-01-01 01:00:00.000000000 +0100
+++ libmstoolkit-77.0.0/debian/patches/gcc-7.patch 2017-10-11 18:45:22.000000000 +0200
@@ -0,0 +1,26 @@
+Index: libmstoolkit/include/MSReader.h
+===================================================================
+--- libmstoolkit.orig/include/MSReader.h
++++ libmstoolkit/include/MSReader.h
+@@ -82,7 +82,7 @@ class MSReader {
+ void setPrecisionInt(int i);
+ void setPrecisionMZ(int i);
+ void writeFile(const char* c, bool text, MSObject& m);
+- void writeFile(const char* c, MSFileFormat ff, MSObject& m, char* sha1Report='\0');
++ void writeFile(const char* c, MSFileFormat ff, MSObject& m, char* sha1Report=NULL);
+
+ bool readMSTFile(const char* c, bool text, Spectrum& s, int scNum=0);
+ bool readMZPFile(const char* c, Spectrum& s, int scNum=0);
+Index: libmstoolkit/src/MSToolkit/MSReader.cpp
+===================================================================
+--- libmstoolkit.orig/src/MSToolkit/MSReader.cpp
++++ libmstoolkit/src/MSToolkit/MSReader.cpp
+@@ -688,7 +688,7 @@ void MSReader::writeSqlite(const char* c
+ string instrumentType="=";
+ for(int i=0; i<16; i++)
+ {
+- if(m.getHeader().header[i] != '\0')
++ if(m.getHeader().header[i] != NULL)
+ {
+ string headerLine = m.getHeader().header[i];
+ if(headerLine.find("CreationDate") != string::npos)
diff -Nru libmstoolkit-77.0.0/debian/patches/series libmstoolkit-77.0.0/debian/patches/series
--- libmstoolkit-77.0.0/debian/patches/series 2015-01-13 10:25:07.000000000 +0100
+++ libmstoolkit-77.0.0/debian/patches/series 2017-10-11 18:43:47.000000000 +0200
@@ -1,2 +1,3 @@
makefile.patch
+gcc-7.patch
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