[Debian-med-packaging] [andreas at an3as.eu: More help for ams statements needed (Was: [Help] Need help for architecture specific code)]
Alex Mestiashvili
alex at biotec.tu-dresden.de
Fri Sep 5 13:42:16 UTC 2014
On 09/05/2014 03:24 PM, Andreas Tille wrote:
> 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 While I'm continue to be reluctant to use an outdated copy of a gcc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.
Hi Andreas,
I just refreshed that we had to patch upstream's makefile and tweak
d/rules in order to build it on i386 ( when it was still possible -
version 2.2.0 )
after we decided to drop support for other architectures, the
corresponding patch and d/rules were removed/updated.
So most probably the current reason of build failure has nothing to do
with your last patch.
Regards,
Alex
[0]
http://anonscm.debian.org/cgit/debian-med/bowtie2.git/tree/debian/patches/fix_makefile_machine_detection.patch?id=b57d0e715a2c3d38bf7c39377c4ffff72ce70a1e
[1]
http://anonscm.debian.org/cgit/debian-med/bowtie2.git/tree/debian/rules?id=b57d0e715a2c3d38bf7c39377c4ffff72ce70a1e
>
> 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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