Solution found [Was: Bug#667270: MAQ and MAQVIEW fail to build with GCC-4.7.]
Hi,
feel free to apply the patch which is available here
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/maq/trunk/debian/patches/gcc-4.7.patch?view=markup
into your next release.
Kind regards and thanks for providing maq as free software
Andreas.
----- Forwarded message from Charles Plessy <plessy@debian.org> -----
Date: Wed, 4 Apr 2012 13:34:06 +0900
From: Charles Plessy <plessy@debian.org>
To: maq-help@lists.sourceforge.net, 667270@bugs.debian.org
Subject: Bug#667270: MAQ and MAQVIEW fail to build
with GCC-4.7.
X-Debian-PR-Message: followup 667270
X-Debian-PR-Package: maq
X-Debian-PR-Keywords: sid wheezy
X-Debian-PR-Source: maq
Dear Maq developers,
Debian distributes Maq and Maqview, and after a mass-rebuild against GCC 4.7,
we noticed the following error:
stdhash.hh:415:81: error: 'direct_insert_aux' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
You can see below for more context, and more in particular the instructions
under “Name lookup changes” in GCC's 4.7 porting page.
http://gcc.gnu.org/gcc-4.7/porting_to.html
Do you think you can release an updated version of Maq and Maqview ?
I am sending a copy of this message in our public bug tracker
(667270@bugs.debian.org). Please feel free to do the same in your answer.
The archive is available at the following URL.
http://bugs.debian.org/667270
Have a nice day,
-- Charles Plessy, Debian Med packaging team, Tsurumi, Kanagawa, Japan.
Le Tue, Apr 03, 2012 at 11:10:41PM +0000, Matthias Klose a écrit :
> Package: maq
> Version: 0.7.1-4
> Severity: important
> Tags: sid wheezy
> User: debian-gcc@lists.debian.org
> Usertags: ftbfs-gcc-4.7
>
> The package fails to build in a test rebuild on at least amd64 with
> gcc-4.7/g++-4.7, but succeeds to build with gcc-4.6/g++-4.6. The
> severity of this report may be raised before the wheezy release.
>
> stdhash.hh:415:81: error: 'direct_insert_aux' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
>
> The full build log can be found at:
> http://people.debian.org/~lucas/logs/2012/03/29-clang-gcc47/unstable-gcc47/maq_0.7.1-4_unstable-gcc47.log
> The last lines of the build log are at the end of this report.
>
> Some hints on fixing these issues can be found at
> http://gcc.gnu.org/gcc-4.7/porting_to.html
>
> To build with GCC 4.7, either set CC=gcc-4.7 CXX=g++-4.7 explicitly,
> or install the gcc, g++, gfortran, ... packages from experimental.
>
> [...]
> g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -D_LARGEFILE64_SOURCE -c -o match.o match.cc
> match.cc: In function 'int alt_cal_mm(bit64_t)':
> match.cc:58:21: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses]
> match.cc:61:22: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses]
> match.cc: In function 'int alt_cal_err(bit64_t, bit64_t)':
> match.cc:67:21: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses]
> match.cc:70:22: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses]
> match.cc: In function 'void match_search(const match_aux_t*, match_data_t*, const nst_bfa1_t*, int, ref_canlist_t*)':
> match.cc:292:10: warning: variable 'n_reads' set but not used [-Wunused-but-set-variable]
> g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -D_LARGEFILE64_SOURCE -c -o sort_mapping.o sort_mapping.cc
> sort_mapping.cc: In function 'int ma_make_pair(const match_aux_t*, const match_info_t*, const match_info_t*, pair_info_t*)':
> sort_mapping.cc:59:62: warning: suggest parentheses around arithmetic in operand of '^' [-Wparentheses]
> g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -D_LARGEFILE64_SOURCE -c -o assemble.o assemble.cc
> assemble.cc: In function 'base_call_aux_t* assemble_cns_collect(assemble_pos_t*, const assemble_aux_t*)':
> assemble.cc:106:64: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
> g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -D_LARGEFILE64_SOURCE -c -o pileup.o pileup.cc
> g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -D_LARGEFILE64_SOURCE -c -o mapcheck.o mapcheck.cc
> mapcheck.cc: In function 'int ma_mapcheck(int, char**)':
> mapcheck.cc:60:17: warning: variable 'fpout' set but not used [-Wunused-but-set-variable]
> In file included from mapcheck.cc:11:0:
> stdhash.hh: In instantiation of 'bool hash_set_misc<keytype_t>::insert(const keytype_t&) [with keytype_t = long long unsigned int]':
> mapcheck.cc:24:45: required from here
> stdhash.hh:415:81: error: 'direct_insert_aux' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
> stdhash.hh:415:81: note: declarations in dependent base '__lh3_hash_base_class<long long unsigned int>' are not found by unqualified lookup
> stdhash.hh:415:81: note: use 'this->direct_insert_aux' instead
> make[2]: *** [mapcheck.o] Error 1
> make[2]: Leaving directory `/??PKGBUILDDIR??'
> make[1]: *** [all] Error 2
> make: *** [debian/stamp-makefile-build] Error 2
> dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
>
>
>
> _______________________________________________
> Debian-med-packaging mailing list
> Debian-med-packaging@lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
Le Tue, Apr 03, 2012 at 11:10:42PM +0000, Matthias Klose a écrit :
> Package: maqview
> Version: 0.2.5-1
> Severity: important
> Tags: sid wheezy
> User: debian-gcc@lists.debian.org
> Usertags: ftbfs-gcc-4.7
>
> The package fails to build in a test rebuild on at least amd64 with
> gcc-4.7/g++-4.7, but succeeds to build with gcc-4.6/g++-4.6. The
> severity of this report may be raised before the wheezy release.
>
> stdhash.hh:496:81: error: 'direct_insert_aux' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
>
> The full build log can be found at:
> http://people.debian.org/~lucas/logs/2012/03/29-clang-gcc47/unstable-gcc47/maqview_0.2.5-1_unstable-gcc47.log
> The last lines of the build log are at the end of this report.
>
> Some hints on fixing these issues can be found at
> http://gcc.gnu.org/gcc-4.7/porting_to.html
>
> To build with GCC 4.7, either set CC=gcc-4.7 CXX=g++-4.7 explicitly,
> or install the gcc, g++, gfortran, ... packages from experimental.
>
> [...]
> gcc -DHAVE_CONFIG_H -I. -DHAVE_FREEGLUT -g -O2 -Wall -W -DMAQ_LONGREADS -MT btree.o -MD -MP -MF .deps/btree.Tpo -c -o btree.o btree.c
> mv -f .deps/btree.Tpo .deps/btree.Po
> gcc -DHAVE_CONFIG_H -I. -DHAVE_FREEGLUT -g -O2 -Wall -W -DMAQ_LONGREADS -MT maqmap_index.o -MD -MP -MF .deps/maqmap_index.Tpo -c -o maqmap_index.o maqmap_index.c
> maqmap_index.c: In function 'notify':
> maqmap_index.c:43:69: warning: unused parameter 'pos' [-Wunused-parameter]
> maqmap_index.c: In function 'read_map_index':
> maqmap_index.c:387:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
> maqmap_index.c: In function 'read_map_next_to':
> maqmap_index.c:403:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
> mv -f .deps/maqmap_index.Tpo .deps/maqmap_index.Po
> gcc -DHAVE_CONFIG_H -I. -DHAVE_FREEGLUT -g -O2 -Wall -W -DMAQ_LONGREADS -MT zrio.o -MD -MP -MF .deps/zrio.Tpo -c -o zrio.o zrio.c
> zrio.c: In function 'get_max_dist':
> zrio.c:437:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
> zrio.c: In function 'build_index':
> zrio.c:466:24: warning: variable 'state' set but not used [-Wunused-but-set-variable]
> mv -f .deps/zrio.Tpo .deps/zrio.Po
> g++ -DHAVE_CONFIG_H -I. -DHAVE_FREEGLUT -g -O2 -MT stdhashc.o -MD -MP -MF .deps/stdhashc.Tpo -c -o stdhashc.o stdhashc.cc
> In file included from stdhashc.cc:2:0:
> stdhash.hh: In instantiation of 'bool hash_map_misc<keytype_t, valtype_t>::insert(const keytype_t&, const valtype_t&) [with keytype_t = unsigned int; valtype_t = int]':
> stdhashc.cc:72:51: required from here
> stdhash.hh:496:81: error: 'direct_insert_aux' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
> stdhash.hh:496:81: note: declarations in dependent base '__lh3_hash_base_class<unsigned int>' are not found by unqualified lookup
> stdhash.hh:496:81: note: use 'this->direct_insert_aux' instead
> make[2]: *** [stdhashc.o] Error 1
> make[2]: Leaving directory `/??PKGBUILDDIR??'
> make[1]: *** [all] Error 2
> dh_auto_build: make -j1 returned exit code 2
> make[1]: Leaving directory `/??PKGBUILDDIR??'
> make: *** [build-arch] Error 2
> dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
>
>
>
> _______________________________________________
> Debian-med-packaging mailing list
> Debian-med-packaging@lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
--
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan
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