[Debian-med-packaging] [andreas at an3as.eu: More help for ams statements needed (Was: [Help] Need help for architecture specific code)]

Fri Sep 5 13:24:44 UTC 2014

Hi Alex,

just to have a public, web-search enabled record I'm moving the
conversation to our list.  In the case below it looks really different.
While I'm continue to be reluctant to use an outdated copy of a gcc
header file I would recommend skipping my patch - even if I would really
like to hear upstreams reasoning for doing this.  But it seems they are
not very responsive to requests like this.

Thanks for your work on this

     Andreas.

On Fri, Sep 05, 2014 at 03:16:41PM +0200, Alex Mestiashvili wrote:
> On 09/05/2014 02:46 PM, Andreas Tille wrote:
> >Hi Alex,
> >
> >On Fri, Sep 05, 2014 at 02:15:46PM +0200, Alex Mestiashvili wrote:
> >>On 09/05/2014 01:50 PM, Andreas Tille wrote:
> >>>Hi Alex,
> >>>
> >>>I guess I was to quick to assume bowtie2 might be available also for
> >>>other architectures.  While I keep on thinking that running the test
> >>>suite also at build time I'm afraid my patch will not really help.
> >>Hi Andreas,
> >>I see, thank you. And I can confirm that bowtie2 doesn't work on
> >>i386 - just tried to build bowtie2 for i386 and it has failed.
> >... which comes somehow expected now.  Is this the same error like here:
> >
> >    https://buildd.debian.org/status/fetch.php?pkg=bowtie&arch=i386&ver=1.0.1-2&stamp=1409911500
> >
> >ebwt.h: Assembler messages:
> >ebwt.h:1909: Error: invalid instruction suffix for `popcnt'
> >ebwt.h:1909: Error: invalid instruction suffix for `popcnt'
> >ebwt.h:1909: Error: invalid instruction suffix for `popcnt'
> >ebwt.h:1909: Error: invalid instruction suffix for `popcnt'
> >make[2]: *** [bowtie-build] Error 1
> >
> >
> 
> No, it is different, the build log is attached.
> 
> Regards,
> Alex

>  debian/rules build
> dh build
>    dh_testdir
>    dh_auto_configure
>    debian/rules override_dh_auto_build
> make[1]: Entering directory '/tmp/buildd/bowtie2-2.2.3'
> dh_auto_build -- EXTRA_FLAGS=-Wl,-z,relro CPPFLAGS=-D_FORTIFY_SOURCE=2
> make[2]: Entering directory '/tmp/buildd/bowtie2-2.2.3'
> /usr/bin/g++ -O3 -m64 -msse2  -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2  -funroll-loops -g3 -Wl,-z,relro\"" -Wl,-z,relro \
>         -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall \
>          \
>         -o bowtie2-build-s bt2_build.cpp \
>         ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp bowtie_build_main.cpp \
>         -lpthread
> In file included from bt2_build.cpp:20:0:
> /usr/include/c++/4.9/iostream:38:28: fatal error: bits/c++config.h: No such file or directory
>  #include <bits/c++config.h>
>                             ^
> compilation terminated.
> In file included from /usr/include/stdint.h:25:0,
>                  from /usr/lib/gcc/i586-linux-gnu/4.9/include/stdint.h:9,
>                  from ccnt_lut.cpp:20:
> /usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
>  #  include <sys/cdefs.h>
>                          ^
> compilation terminated.
> In file included from ref_read.h:23:0,
>                  from ref_read.cpp:20:
> /usr/include/c++/4.9/iostream:38:28: fatal error: bits/c++config.h: No such file or directory
>  #include <bits/c++config.h>
>                             ^
> compilation terminated.
> In file included from /usr/include/stdint.h:25:0,
>                  from /usr/lib/gcc/i586-linux-gnu/4.9/include/stdint.h:9,
>                  from alphabet.cpp:20:
> /usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
>  #  include <sys/cdefs.h>
>                          ^
> compilation terminated.
> In file included from edit.cpp:20:0:
> /usr/include/c++/4.9/iostream:38:28: fatal error: bits/c++config.h: No such file or directory
>  #include <bits/c++config.h>
>                             ^
> compilation terminated.
> In file included from bt2_idx.cpp:20:0:
> /usr/include/c++/4.9/string:38:28: fatal error: bits/c++config.h: No such file or directory
>  #include <bits/c++config.h>
>                             ^
> compilation terminated.
> In file included from bt2_io.cpp:20:0:
> /usr/include/c++/4.9/string:38:28: fatal error: bits/c++config.h: No such file or directory
>  #include <bits/c++config.h>
>                             ^
> compilation terminated.
> In file included from bt2_util.cpp:20:0:
> /usr/include/c++/4.9/string:38:28: fatal error: bits/c++config.h: No such file or directory
>  #include <bits/c++config.h>
>                             ^
> compilation terminated.
> In file included from reference.cpp:20:0:
> /usr/include/c++/4.9/string:38:28: fatal error: bits/c++config.h: No such file or directory
>  #include <bits/c++config.h>
>                             ^
> compilation terminated.
> In file included from /usr/include/c++/4.9/algorithm:60:0,
>                  from ds.h:23,
>                  from ds.cpp:20:
> /usr/include/c++/4.9/utility:68:28: fatal error: bits/c++config.h: No such file or directory
>  #include <bits/c++config.h>
>                             ^
> compilation terminated.
> In file included from multikey_qsort.h:23:0,
>                  from multikey_qsort.cpp:20:
> /usr/include/c++/4.9/iostream:38:28: fatal error: bits/c++config.h: No such file or directory
>  #include <bits/c++config.h>
>                             ^
> compilation terminated.
> In file included from limit.cpp:20:0:
> /usr/include/c++/4.9/limits:42:28: fatal error: bits/c++config.h: No such file or directory
>  #include <bits/c++config.h>
>                             ^
> compilation terminated.
> In file included from /usr/include/stdint.h:25:0,
>                  from /usr/lib/gcc/i586-linux-gnu/4.9/include/stdint.h:9,
>                  from random_source.h:23,
>                  from random_source.cpp:20:
> /usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
>  #  include <sys/cdefs.h>
>                          ^
> compilation terminated.
> In file included from tinythread.cpp:24:0:
> /usr/include/c++/4.9/exception:37:28: fatal error: bits/c++config.h: No such file or directory
>  #include <bits/c++config.h>
>                             ^
> compilation terminated.
> In file included from /usr/include/stdint.h:25:0,
>                  from /usr/lib/gcc/i586-linux-gnu/4.9/include/stdint.h:9,
>                  from diff_sample.h:23,
>                  from diff_sample.cpp:20:
> /usr/include/features.h:374:25: fatal error: sys/cdefs.h: No such file or directory
>  #  include <sys/cdefs.h>
>                          ^
> compilation terminated.
> In file included from bowtie_build_main.cpp:20:0:
> /usr/include/c++/4.9/iostream:38:28: fatal error: bits/c++config.h: No such file or directory
>  #include <bits/c++config.h>
>                             ^
> compilation terminated.
> Makefile:232: recipe for target 'bowtie2-build-s' failed
> make[2]: *** [bowtie2-build-s] Error 1
> make[2]: Leaving directory '/tmp/buildd/bowtie2-2.2.3'
> dh_auto_build: make -j1 EXTRA_FLAGS=-Wl,-z,relro CPPFLAGS=-D_FORTIFY_SOURCE=2 returned exit code 2
> debian/rules:13: recipe for target 'override_dh_auto_build' failed
> make[1]: *** [override_dh_auto_build] Error 2
> make[1]: Leaving directory '/tmp/buildd/bowtie2-2.2.3'
> debian/rules:10: recipe for target 'build' failed
> make: *** [build] Error 2
> dpkg-buildpackage: error: debian/rules build gave error exit status 2
> 

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