[Debian-med-packaging] Bug#667271: MAQ and MAQVIEW fail to build with GCC-4.7.

Wed Apr 4 04:34:06 UTC 2012

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 at 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 at 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 at 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 at 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 at 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