Re: [galaxy-user] runtime warning with pysam egg
On Apr 29, 2011, at 9:10 AM, Nate Coraor wrote:
Shantanu Pavgi wrote:
Hi,
I am getting following warning when I start the galaxy server. I am using
latest revision (50e249442c5a) of galaxy-dist. Am I missing anything in the
configuration here?
{{{
$ ./run.sh
/home/galaxy/.python-eggs/pysam-0.4.1_kanwei_ae2bd50d9945-py2.6-linux-x86_64-ucs2.egg-tmp/csamtools.so:6:
RuntimeWarning: __builtin__.file size changed, may indicate binary
incompatibility
###t#|}###b###S#5#D###i)###[x,m
###<#=LB###q##.:##$2###rDM###E3A#j###
Hi Shantanu,
This warning is safe to ignore. I haven't had a chance to look in to
why this occurs, but it does not affect normal Galaxy operation.
--nate
thanks for the reply.
--
shantanu.
___
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Re: [galaxy-user] runtime warning with pysam egg
Shantanu Pavgi wrote:
>
> Hi,
>
> I am getting following warning when I start the galaxy server. I am using
> latest revision (50e249442c5a) of galaxy-dist. Am I missing anything in the
> configuration here?
>
> {{{
> $ ./run.sh
>
> /home/galaxy/.python-eggs/pysam-0.4.1_kanwei_ae2bd50d9945-py2.6-linux-x86_64-ucs2.egg-tmp/csamtools.so:6:
> RuntimeWarning: __builtin__.file size changed, may indicate binary
> incompatibility
> ###t#|}###b###S#5#D###i)###[x,m
>
> ###<#=LB###q##.:##$2###rDM###E3A#j###
Hi Shantanu,
This warning is safe to ignore. I haven't had a chance to look in to
why this occurs, but it does not affect normal Galaxy operation.
--nate
> python path is:
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/numpy-1.3.0-py2.6-linux-x86_64-ucs2.egg,
>
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/pysam-0.4.1_kanwei_ae2bd50d9945-py2.6-linux-x86_64-ucs2.egg,
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Whoosh-0.3.18-py2.6.egg,
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs2.egg,
>
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs2.egg,
>
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/bx_python-0.7.0_14b6a6c95da6-py2.6-linux-x86_64-ucs2.egg,
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/amqplib-0.6.1-py2.6.egg,
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/pexpect-2.4-py2.6.egg,
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg,/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Babel-0.9.4-py2.6.egg,
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Beaker-1.4-py2.6.egg,
> /share/apps/gal!
ax!
> y/galaxy-dist-50e249442c5a/eggs/Mako-0.2.5-py2.6.egg,
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/WebHelpers-0.2-py2.6.egg,
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg,
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/wchartype-0.1-py2.6.egg,
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/elementtree-1.2.6_20050316-py2.6.egg,
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/docutils-0.7-py2.6.egg,
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/WebOb-0.8.5-py2.6.egg,
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Routes-1.12.3-py2.6.egg,
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs2.egg,
>
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/PasteDeploy-1.3.3-py2.6.egg,
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/PasteScript-1.7.3-py2.6.egg,
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Paste-1.6-py2.6.egg,
> /share/apps/galaxy/galaxy-dist-50e249442c5a/lib, /share/apps/gal!
ax!
> y/python/2.6.6/lib/python26.zip,
> /share/apps/galaxy/python/2.6.6/lib/python2.6,
> /share/apps/galaxy/python/2.6.6/lib/python2.6/plat-linux2,
> /share/apps/galaxy/python/2.6.6/lib/python2.6/lib-tk,
> /share/apps/galaxy/python/2.6.6/lib/python2.6/lib-old,
> /share/apps/galaxy/python/2.6.6/lib/python2.6/lib-dynload,
> /share/apps/galaxy/python/2.6.6/lib/python2.6/site-packages
> galaxy.datatypes.registry DEBUG 2011-04-25 12:37:54,637 Loading
> datatypes from datatypes_conf.xml
> galaxy.datatypes.registry DEBUG 2011-04-25 12:37:54,650 Loaded display
> application 'ucsc_bam' for datatype 'bam', inherit=False
> ...
> ...
> ...
>
> }}}
>
> --
> Thanks,
> Shantanu.
> ___
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org. Please keep all replies on the list by
> using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
[galaxy-user] runtime warning with pysam egg
Hi,
I am getting following warning when I start the galaxy server. I am using
latest revision (50e249442c5a) of galaxy-dist. Am I missing anything in the
configuration here?
{{{
$ ./run.sh
/home/galaxy/.python-eggs/pysam-0.4.1_kanwei_ae2bd50d9945-py2.6-linux-x86_64-ucs2.egg-tmp/csamtools.so:6:
RuntimeWarning: __builtin__.file size changed, may indicate binary
incompatibility
###t#|}###b###S#5#D###i)###[x,m
###<#=LB###q##.:##$2###rDM###E3A#j###
python path is:
/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/numpy-1.3.0-py2.6-linux-x86_64-ucs2.egg,
/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/pysam-0.4.1_kanwei_ae2bd50d9945-py2.6-linux-x86_64-ucs2.egg,
/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Whoosh-0.3.18-py2.6.egg,
/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs2.egg,
/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs2.egg,
/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/bx_python-0.7.0_14b6a6c95da6-py2.6-linux-x86_64-ucs2.egg,
/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/amqplib-0.6.1-py2.6.egg,
/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/pexpect-2.4-py2.6.egg,
/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg,/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Babel-0.9.4-py2.6.egg,
/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Beaker-1.4-py2.6.egg,
/share/apps/galax!
y/galaxy-dist-50e249442c5a/eggs/Mako-0.2.5-py2.6.egg,
/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/WebHelpers-0.2-py2.6.egg,
/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg,
/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/wchartype-0.1-py2.6.egg,
/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/elementtree-1.2.6_20050316-py2.6.egg,
/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/docutils-0.7-py2.6.egg,
/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/WebOb-0.8.5-py2.6.egg,
/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Routes-1.12.3-py2.6.egg,
/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs2.egg,
/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/PasteDeploy-1.3.3-py2.6.egg,
/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/PasteScript-1.7.3-py2.6.egg,
/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Paste-1.6-py2.6.egg,
/share/apps/galaxy/galaxy-dist-50e249442c5a/lib, /share/apps/galax!
y/python/2.6.6/lib/python26.zip,
/share/apps/galaxy/python/2.6.6/lib/python2.6,
/share/apps/galaxy/python/2.6.6/lib/python2.6/plat-linux2,
/share/apps/galaxy/python/2.6.6/lib/python2.6/lib-tk,
/share/apps/galaxy/python/2.6.6/lib/python2.6/lib-old,
/share/apps/galaxy/python/2.6.6/lib/python2.6/lib-dynload,
/share/apps/galaxy/python/2.6.6/lib/python2.6/site-packages
galaxy.datatypes.registry DEBUG 2011-04-25 12:37:54,637 Loading
datatypes from datatypes_conf.xml
galaxy.datatypes.registry DEBUG 2011-04-25 12:37:54,650 Loaded display
application 'ucsc_bam' for datatype 'bam', inherit=False
...
...
...
}}}
--
Thanks,
Shantanu.
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
