Build test on gbrowse2 fails

[Wes Barris]

Hi,

I am getting this error when running Build test on a freshly downloaded
copy of gbrowse2:

wes@bioweb> sudo ./Build test
NOTE: Run ./Build reconfig to change existing configuration.
.
.
.
gcc -I/usr/local/src/bioinformatics/gbrowse2/Generic-Genome-Browser/libalign -I/usr/lib/perl5/5.8.5/i386-linux-thread-multi/CORE -DXS_VERSION="1.9971" -DVERSION="1.9971" -fPIC -c -D_REENTRANT
-D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -m32 -march=i386 -mtune=pentium4 -o
lib/Bio/Graphics/Browser2/CAlign.o lib/Bio/Graphics/Browser2/CAlign.c
lib/Bio/Graphics/Browser2/CAlign.c: In function `boot_Bio__Graphics__Browser2__CAlign':
lib/Bio/Graphics/Browser2/CAlign.c:295: error: `PL_unitcheckav' undeclared (first use in this function)
lib/Bio/Graphics/Browser2/CAlign.c:295: error: (Each undeclared identifier is reported only once
lib/Bio/Graphics/Browser2/CAlign.c:295: error: for each function it appears in.)
error building lib/Bio/Graphics/Browser2/CAlign.o from 'lib/Bio/Graphics/Browser2/CAlign.c' at /usr/lib/perl5/site_perl/5.8.5/ExtUtils/CBuilder/Base.pm line 110.

Is gbrowse2 in a buildable state right now?
--
Wes Barris <wes.barris@...>

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[Dave Clements, GMOD Help Desk-2]

Hi Wes,

I'm guessing from subsequent emails that you got past this problem?

Thanks,

Dave C

On Mon, Nov 9, 2009 at 3:59 PM, Wes Barris <wes.barris@...> wrote:

> Hi,
>
> I am getting this error when running Build test on a freshly downloaded
> copy of gbrowse2:
>
> wes@bioweb> sudo ./Build test
> NOTE: Run ./Build reconfig to change existing configuration.
> .
> .
> .
> gcc -I/usr/local/src/bioinformatics/gbrowse2/Generic-Genome-Browser/libalign -I/usr/lib/perl5/5.8.5/i386-linux-thread-multi/CORE -DXS_VERSION="1.9971" -DVERSION="1.9971" -fPIC -c -D_REENTRANT
> -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -m32 -march=i386 -mtune=pentium4 -o
> lib/Bio/Graphics/Browser2/CAlign.o lib/Bio/Graphics/Browser2/CAlign.c
> lib/Bio/Graphics/Browser2/CAlign.c: In function `boot_Bio__Graphics__Browser2__CAlign':
> lib/Bio/Graphics/Browser2/CAlign.c:295: error: `PL_unitcheckav' undeclared (first use in this function)
> lib/Bio/Graphics/Browser2/CAlign.c:295: error: (Each undeclared identifier is reported only once
> lib/Bio/Graphics/Browser2/CAlign.c:295: error: for each function it appears in.)
> error building lib/Bio/Graphics/Browser2/CAlign.o from 'lib/Bio/Graphics/Browser2/CAlign.c' at /usr/lib/perl5/site_perl/5.8.5/ExtUtils/CBuilder/Base.pm line 110.
>
> Is gbrowse2 in a buildable state right now?
> --
> Wes Barris <wes.barris@...>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

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[Wes Barris]

Dave Clements, GMOD Help Desk wrote:
> Hi Wes,
>
> I'm guessing from subsequent emails that you got past this problem?

Hi Dave,

No, I have not got past this.  I am unable to build gbrowse2.

> Thanks,
>
> Dave C
>
> On Mon, Nov 9, 2009 at 3:59 PM, Wes Barris <wes.barris@...> wrote:
>> Hi,
>>
>> I am getting this error when running Build test on a freshly downloaded
>> copy of gbrowse2:
>>
>> wes@bioweb> sudo ./Build test
>> NOTE: Run ./Build reconfig to change existing configuration.
>> .
>> .
>> .
>> gcc -I/usr/local/src/bioinformatics/gbrowse2/Generic-Genome-Browser/libalign -I/usr/lib/perl5/5.8.5/i386-linux-thread-multi/CORE -DXS_VERSION="1.9971" -DVERSION="1.9971" -fPIC -c -D_REENTRANT
>> -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -m32 -march=i386 -mtune=pentium4 -o
>> lib/Bio/Graphics/Browser2/CAlign.o lib/Bio/Graphics/Browser2/CAlign.c
>> lib/Bio/Graphics/Browser2/CAlign.c: In function `boot_Bio__Graphics__Browser2__CAlign':
>> lib/Bio/Graphics/Browser2/CAlign.c:295: error: `PL_unitcheckav' undeclared (first use in this function)
>> lib/Bio/Graphics/Browser2/CAlign.c:295: error: (Each undeclared identifier is reported only once
>> lib/Bio/Graphics/Browser2/CAlign.c:295: error: for each function it appears in.)
>> error building lib/Bio/Graphics/Browser2/CAlign.o from 'lib/Bio/Graphics/Browser2/CAlign.c' at /usr/lib/perl5/site_perl/5.8.5/ExtUtils/CBuilder/Base.pm line 110.
>>
>> Is gbrowse2 in a buildable state right now?
>> --
>> Wes Barris <wes.barris@...>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
>> trial. Simplify your report design, integration and deployment - and focus on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse@...
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>

--
Wes Barris <wes.barris@...>

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[Wes Barris]

Dave Clements, GMOD Help Desk wrote:
> Hi Wes,
>
> I'm guessing from subsequent emails that you got past this problem?

I updated all of the ExtUtils perl modules.  I then did a new SVN
checkout of gbrowse2 and got this revision:

# Checked out revision 22245.

The ./Build test step hangs here:

Copying sample_data/yeast_scaffolds/chromosomes.gff3 -> blib/database/yeast_scaffolds/chromosomes.gff3
t/01yeast.t ............... ok
t/02.rearchitecture.t ..... 1/90 Can't locate object method "parse_fh" via package "Bio::Graphics::Browser2::DataSource" at
/usr/local/src/bioinformatics/gbrowse2/Generic-Genome-Browser/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 981.
t/02.rearchitecture.t ..... Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 4/90 subtests
t/03.render.t ............. 45/148 invalid track Motif at /usr/local/src/bioinformatics/gbrowse2/Generic-Genome-Browser/t/../lib/Bio/Graphics/Browser2/Render.pm line 1828.
*** glibc detected *** double free or corruption (!prev): 0x0b5d62d8 ***

I had received this same error/hang a few weeks and and posted a question
but did not receive any responses.

Does this error mean anything to anyone?

> Thanks,
>
> Dave C
>
> On Mon, Nov 9, 2009 at 3:59 PM, Wes Barris <wes.barris@...> wrote:
>> Hi,
>>
>> I am getting this error when running Build test on a freshly downloaded
>> copy of gbrowse2:
>>
>> wes@bioweb> sudo ./Build test
>> NOTE: Run ./Build reconfig to change existing configuration.
>> .
>> .
>> .
>> gcc -I/usr/local/src/bioinformatics/gbrowse2/Generic-Genome-Browser/libalign -I/usr/lib/perl5/5.8.5/i386-linux-thread-multi/CORE -DXS_VERSION="1.9971" -DVERSION="1.9971" -fPIC -c -D_REENTRANT
>> -D_GNU_SOURCE -DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -m32 -march=i386 -mtune=pentium4 -o
>> lib/Bio/Graphics/Browser2/CAlign.o lib/Bio/Graphics/Browser2/CAlign.c
>> lib/Bio/Graphics/Browser2/CAlign.c: In function `boot_Bio__Graphics__Browser2__CAlign':
>> lib/Bio/Graphics/Browser2/CAlign.c:295: error: `PL_unitcheckav' undeclared (first use in this function)
>> lib/Bio/Graphics/Browser2/CAlign.c:295: error: (Each undeclared identifier is reported only once
>> lib/Bio/Graphics/Browser2/CAlign.c:295: error: for each function it appears in.)
>> error building lib/Bio/Graphics/Browser2/CAlign.o from 'lib/Bio/Graphics/Browser2/CAlign.c' at /usr/lib/perl5/site_perl/5.8.5/ExtUtils/CBuilder/Base.pm line 110.
>>
>> Is gbrowse2 in a buildable state right now?
>> --
>> Wes Barris <wes.barris@...>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
>> trial. Simplify your report design, integration and deployment - and focus on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse@...
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>

--
Wes Barris <wes.barris@...>

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