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Old 07-07-2008, 08:56 PM
Andreas Tille
 
Default Help: Strange 64bit issue

Hi,

as I described at the Debian Med mailing list [1] I have some
trouble with a multiarch package. Charles Plessy and me prepared
some packaging stuff at

svn://svn.debian.org/svn/debian-med/trunk/packages/maq/trunk/

the watch file can be used to obtain the source tarball - BTW I
thought you can also use unchanged bz2 tarball as source (at least
[2] says: Bzip2 compression is supported as an alternative to gzip.)
but how to do this? For the test I rebuilded an orig.tar.gz.
When trying to build I got

fasta2bfa.o fastq2bfq.o merge.o match_aux.o match.o sort_mapping.o assemble.o pileup.o mapcheck.o get_pos.o assopt.o aux_utils.o rbcc.o subsnp.o pair_stat.o indel_soa.o maqmap.o maqmap_conv.o altchr.o submap.o rmdup.o simulate.o genran.o indel_pe.o stdaln.o indel_call.o eland2maq.o csmap2ntmap.o break_pair.o -lm -lz
/usr/bin/ld: skipping incompatible /usr/lib/gcc/i486-linux-gnu/4.3.1/libstdc++.so when searching for -lstdc++

/usr/bin/ld: skipping incompatible /usr/lib/gcc/i486-linux-gnu/4.3.1/libstdc++.a when searching for -lstdc++
/usr/bin/ld: skipping incompatible /usr/lib/gcc/i486-linux-gnu/4.3.1/libstdc++.so when searching for -lstdc++
/usr/bin/ld: skipping incompatible /usr/lib/gcc/i486-linux-gnu/4.3.1/libstdc++.a when searching for -lstdc++
/usr/bin/ld: cannot find -lstdc++
collect2: ld returned 1 exit status


Any idea how to fix this?

Kind regards

Andreas.


[1] http://lists.debian.org/debian-med/2008/07/msg00006.html
[2] http://lwn.net/Articles/139811/
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Old 07-07-2008, 09:05 PM
William Pitcock
 
Default Help: Strange 64bit issue

Hi,

If you do build-depends on gcc-multilib and g++-multilib, it should fix
this problem.

William

On Mon, 2008-07-07 at 22:56 +0200, Andreas Tille wrote:
> Hi,
>
> as I described at the Debian Med mailing list [1] I have some
> trouble with a multiarch package. Charles Plessy and me prepared
> some packaging stuff at
>
> svn://svn.debian.org/svn/debian-med/trunk/packages/maq/trunk/
>
> the watch file can be used to obtain the source tarball - BTW I
> thought you can also use unchanged bz2 tarball as source (at least
> [2] says: Bzip2 compression is supported as an alternative to gzip.)
> but how to do this? For the test I rebuilded an orig.tar.gz.
> When trying to build I got
>
> fasta2bfa.o fastq2bfq.o merge.o match_aux.o match.o sort_mapping.o assemble.o pileup.o mapcheck.o get_pos.o assopt.o aux_utils.o rbcc.o subsnp.o pair_stat.o indel_soa.o maqmap.o maqmap_conv.o altchr.o submap.o rmdup.o simulate.o genran.o indel_pe.o stdaln.o indel_call.o eland2maq.o csmap2ntmap.o break_pair.o -lm -lz
> /usr/bin/ld: skipping incompatible /usr/lib/gcc/i486-linux-gnu/4.3.1/libstdc++.so when searching for -lstdc++
> /usr/bin/ld: skipping incompatible /usr/lib/gcc/i486-linux-gnu/4.3.1/libstdc++.a when searching for -lstdc++
> /usr/bin/ld: skipping incompatible /usr/lib/gcc/i486-linux-gnu/4.3.1/libstdc++.so when searching for -lstdc++
> /usr/bin/ld: skipping incompatible /usr/lib/gcc/i486-linux-gnu/4.3.1/libstdc++.a when searching for -lstdc++
> /usr/bin/ld: cannot find -lstdc++
> collect2: ld returned 1 exit status
>
>
> Any idea how to fix this?
>
> Kind regards
>
> Andreas.
>
>
> [1] http://lists.debian.org/debian-med/2008/07/msg00006.html
> [2] http://lwn.net/Articles/139811/
> --
> http://fam-tille.de
>
>
 
Old 07-07-2008, 09:15 PM
Andreas Tille
 
Default Help: Strange 64bit issue

On Mon, 7 Jul 2008, William Pitcock wrote:


If you do build-depends on gcc-multilib and g++-multilib, it should fix
this problem.


Ahhh, thanks - this was a quick and very helpful hint ...

Kind regards

Andreas.

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Old 07-08-2008, 12:26 PM
Andreas Tille
 
Default Help: Strange 64bit issue

On Mon, 7 Jul 2008, William Pitcock wrote:


If you do build-depends on gcc-multilib and g++-multilib, it should fix
this problem.


As I said it fixes the build problem - but now I have a package with a
not working executable. I guess it is also a simple 64 bit problem which
might be easily solved by people with multiarch experience:


On Mon, 2008-07-07 at 22:56 +0200, Andreas Tille wrote:


svn://svn.debian.org/svn/debian-med/trunk/packages/maq/trunk/


If I build this stuff I get a package containing /usr/bin/maq (besides
some Perl scripts). The problem is:


$ /usr/bin/maq
-bash: /usr/bin/maq: cannot execute binary file
$ ldd /usr/bin/maq
ldd: exited with unknown exit code (126)


Does this ring a bell?

Kind regards

Andreas.

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Old 07-10-2008, 09:07 AM
Goswin von Brederlow
 
Default Help: Strange 64bit issue

Andreas Tille <tillea@rki.de> writes:

> On Mon, 7 Jul 2008, William Pitcock wrote:
>
>> If you do build-depends on gcc-multilib and g++-multilib, it should fix
>> this problem.
>
> As I said it fixes the build problem - but now I have a package with a
> not working executable. I guess it is also a simple 64 bit problem which
> might be easily solved by people with multiarch experience:
>
>> On Mon, 2008-07-07 at 22:56 +0200, Andreas Tille wrote:
>>>
>>> svn://svn.debian.org/svn/debian-med/trunk/packages/maq/trunk/
>
> If I build this stuff I get a package containing /usr/bin/maq (besides
> some Perl scripts). The problem is:
>
>
> $ /usr/bin/maq
> -bash: /usr/bin/maq: cannot execute binary file

That indicates your kernel can not execute that binary.

> $ ldd /usr/bin/maq
> ldd: exited with unknown exit code (126)

Usualy means the ld is missing, i.e. libc6 package missing.

> Does this ring a bell?
>
> Kind regards
>
> Andreas.

Do you have the right kernel and libc installed?

MfG
Goswin


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Old 07-10-2008, 09:37 AM
Andreas Tille
 
Default Help: Strange 64bit issue

On Thu, 10 Jul 2008, Goswin von Brederlow wrote:


$ /usr/bin/maq
-bash: /usr/bin/maq: cannot execute binary file


That indicates your kernel can not execute that binary.


$ ldd /usr/bin/maq
ldd: exited with unknown exit code (126)


Usualy means the ld is missing, i.e. libc6 package missing.


Well, I guess I would have noticed if libc would be missing:

$ ldd /usr/bin/ld
linux-gate.so.1 => (0xffffe000)
libbfd-2.18.0.20080103.so => /usr/lib/libbfd-2.18.0.20080103.so (0xb7e1f000)
libc.so.6 => /lib/i686/cmov/libc.so.6 (0xb7cd1000)
/lib/ld-linux.so.2 (0xb7f0c000)

It might be that some 64bit aware libc6 might be needed - I would have had
expected dpkg-buildpackage to add the right dependency if I use this

http://svn.debian.org/wsvn/debian-med/trunk/packages/maq/trunk/debian/control?op=file&rev=0&sc=0

control file. Am I missing something here?


Do you have the right kernel and libc installed?


What is "the right" kernel / libc???

$ uname -a
Linux wr-linux02 2.6.22-3-686 #1 SMP Sun Feb 10 20:20:49 UTC 2008 i686 GNU/Linux

It was installed via the the Debian kernel package:

$ dpkg -l linux-image* | grep ^ii.*2.6.2
ii linux-image-2.6-686 2.6.24+13 Linux 2.6 image on PPro/Celeron/PII/PIII/P4
ii linux-image-2.6.22-3-686 2.6.22-6.lenny1 Linux 2.6.22 image on PPro/Celeron/PII/PIII/
ii linux-image-2.6.24-1-686 2.6.24-7 Linux 2.6.24 image on PPro/Celeron/PII/PIII/

(the host was not rebootet after installing 2.6.24, but the same happens
on another boc running 2.6.24)

$ dpkg -l libc6* | grep ^ii
ii libc6 2.7-10 GNU C Library: Shared libraries
ii libc6-amd64 2.7-10 GNU C Library: 64bit Shared libraries for AM
ii libc6-dev 2.7-10 GNU C Library: Development Libraries and Hea
ii libc6-dev-amd64 2.7-10 GNU C Library: 64bit Development Libraries f
ii libc6-i686 2.7-10 GNU C Library: Shared libraries [i686 optimi

Any hints

Andreas.

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Old 07-11-2008, 11:00 AM
Arthur Loiret
 
Default Help: Strange 64bit issue

On Thu, Jul 10, 2008 at 11:37:10AM +0200, Andreas Tille wrote:
>> Do you have the right kernel and libc installed?
>
> What is "the right" kernel / libc???
>
> $ uname -a
> Linux wr-linux02 2.6.22-3-686 #1 SMP Sun Feb 10 20:20:49 UTC 2008 i686 GNU/Linux
>
> It was installed via the the Debian kernel package:
>
> $ dpkg -l linux-image* | grep ^ii.*2.6.2
> ii linux-image-2.6-686 2.6.24+13 Linux 2.6 image on PPro/Celeron/PII/PIII/P4
> ii linux-image-2.6.22-3-686 2.6.22-6.lenny1 Linux 2.6.22 image on PPro/Celeron/PII/PIII/
> ii linux-image-2.6.24-1-686 2.6.24-7 Linux 2.6.24 image on PPro/Celeron/PII/PIII/
>
> (the host was not rebootet after installing 2.6.24, but the same happens
> on another boc running 2.6.24)
>
> $ dpkg -l libc6* | grep ^ii
> ii libc6 2.7-10 GNU C Library: Shared libraries
> ii libc6-amd64 2.7-10 GNU C Library: 64bit Shared libraries for AM
> ii libc6-dev 2.7-10 GNU C Library: Development Libraries and Hea
> ii libc6-dev-amd64 2.7-10 GNU C Library: 64bit Development Libraries f
> ii libc6-i686 2.7-10 GNU C Library: Shared libraries [i686 optimi

You can build 64-bit executables on any machine if supported in the toolchain
but you need a 64-bit kernel to run them, as linux-image-2.6.x-y-amd64. And of
course you need a 64-bit capable CPU to use those kernels.
 
Old 07-11-2008, 12:24 PM
Manuel Prinz
 
Default Help: Strange 64bit issue

Hi Andreas!

Am Dienstag, den 08.07.2008, 14:26 +0200 schrieb Andreas Tille:
> On Mon, 7 Jul 2008, William Pitcock wrote:
>
> > If you do build-depends on gcc-multilib and g++-multilib, it should fix
> > this problem.
>
> As I said it fixes the build problem - but now I have a package with a
> not working executable. I guess it is also a simple 64 bit problem which
> might be easily solved by people with multiarch experience:

With these fixes it still did not build on my system. I needed to change
the Build-Depends on lib64z1-dev into zlib1g-dev to get it to build in a
clean pbuilder chroot.

> > On Mon, 2008-07-07 at 22:56 +0200, Andreas Tille wrote:
> >>
> >> svn://svn.debian.org/svn/debian-med/trunk/packages/maq/trunk/
>
> If I build this stuff I get a package containing /usr/bin/maq (besides
> some Perl scripts). The problem is:
>
>
> $ /usr/bin/maq
> -bash: /usr/bin/maq: cannot execute binary file
> $ ldd /usr/bin/maq
> ldd: exited with unknown exit code (126)

I cannot reproduce this on my amd64 machine. With the change mentioned
above it builds fine and I'm able to run /usr/bin/maq on both lenny and
sid. Some output:

$ /usr/bin/maq 2>&1 | head -n 4

Program: maq (Mapping and Assembly with Qualities)
Version: 0.6.7
Contact: Heng Li <lh3@sanger.ac.uk>

$ file /usr/bin/maq
/usr/bin/maq: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), for
GNU/Linux 2.6.8, dynamically linked (uses shared libs), stripped

$ ldd /usr/bin/maq
linux-vdso.so.1 => (0x00007fff2d7fe000)
libz.so.1 => /usr/lib/libz.so.1 (0x00002abe7d4cd000)
libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00002abe7d6e4000)
libm.so.6 => /lib/libm.so.6 (0x00002abe7d9f0000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00002abe7dc70000)
libc.so.6 => /lib/libc.so.6 (0x00002abe7de87000)
/lib64/ld-linux-x86-64.so.2 (0x00002abe7d2b1000)

Best regards
Manuel
 
Old 07-11-2008, 12:40 PM
Andreas Tille
 
Default Help: Strange 64bit issue

On Fri, 11 Jul 2008, Manuel Prinz wrote:


With these fixes it still did not build on my system. I needed to change
the Build-Depends on lib64z1-dev into zlib1g-dev to get it to build in a
clean pbuilder chroot.


Well, I guess that lib64z1-dev will not exist for amd64 and that this
whole mess is just caused by the multiarch stuff. It's the first time
that I have to deal with this and I have the impression that I try to
add just problems with no real profit for the user of the program.
Probably I should just exclude the -m64 switch when building for i386
and everything will work fine.

BTW, how could I specify arch dependant Build-Depends (in case some
hint might reveal a multiarch solution)?


I cannot reproduce this on my amd64 machine. With the change mentioned
above it builds fine and I'm able to run /usr/bin/maq on both lenny and
sid. Some output:


I expect this in 64bit machines - but Charles had problems on hie PowerPC
as well ...

Kind regards

Andreas.

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Old 07-11-2008, 12:55 PM
Mark Brown
 
Default Help: Strange 64bit issue

On Fri, Jul 11, 2008 at 02:40:17PM +0200, Andreas Tille wrote:
> On Fri, 11 Jul 2008, Manuel Prinz wrote:

> >With these fixes it still did not build on my system. I needed to change
> >the Build-Depends on lib64z1-dev into zlib1g-dev to get it to build in a
> >clean pbuilder chroot.

> Well, I guess that lib64z1-dev will not exist for amd64 and that this
> whole mess is just caused by the multiarch stuff. It's the first time

It doesn't exist for AMD64 - it is 64 bit native so there is no need to
produce a 64 bit cross verson of anything. There is lib32z1 on amd64,
allowing 32 bit binaries to be built in an amd64 environment.

> that I have to deal with this and I have the impression that I try to
> add just problems with no real profit for the user of the program.
> Probably I should just exclude the -m64 switch when building for i386
> and everything will work fine.

That is almost certainly what you want to do. If you build with -m64
you will produce an amd64 binary. This can be run on i386 systems with
an appropriate processor, kernel and runtime environment but won't run
on systems where one or more of those isn't available and shouldn't be
the standard thing for the Debian port.

Depending on the needs of the package it may make sense to provide both
an i386 native and a cross-built amd64 binary in the i386 port.

> >I cannot reproduce this on my amd64 machine. With the change mentioned
> >above it builds fine and I'm able to run /usr/bin/maq on both lenny and
> >sid. Some output:

> I expect this in 64bit machines - but Charles had problems on hie PowerPC
> as well ...

PowerPC also supports mixed 64/32 bit environments so the situation is
similar to that on x86 and x86-64. When running on a G5 or other 64 bit
processor with an appropriate kernel it is possible to execute 64 bit
PowerPC programs, even using the 32 bit PowerPC port.

--
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