subject:"\[galaxy\-dev\] package_numpy_1

Re: [galaxy-dev] package_numpy_1_7 can't be installed

2015-01-02 Thread Wang, Yu

Hi, Björn, my intention was to test a simple workflow (BASIC PROTOCOL 1
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418382/) on my local galaxy
installation.
By default, “join” function is not installed on galaxy. When I tried to install
“join”, it reported error on the installation of bx_python_0_7 (Galaxy main
tool shed).
It looks like the automated installation of bx python failed somehow.
Looking at the package, it will attempt to install NumPy 1.7.1
https://toolshed.g2.bx.psu.edu/view/devteam/package_bx_python_0_7

Then I tried to install NumPy 1.7.1 from Galaxy main tool shed, there were all
these errors from LAPACK and ATLAS.

Cheers,
Yu

di29her
w...@lrz.de

On 16 Dec 2014, at 04:07, Björn Grüning
mailto:bjo...@gruenings.eu>> wrote:

Hi Wang,

can you point me to the exact version your try to install. There is an
old numpy_1_7 package which should be deprecated. We had a lot of
trouble installing ATLAS and LAPACK and decided to deprecate all
packages which depends on LAPACK and ATLAS. Now we do not require both
libraries anymore.

Thanks,
Bjoern

Am 15.12.2014 um 18:16 schrieb Wang, Yu:
Hi, John,thanks for your answer. I installed svnversion, and compiled/installed
ATLAS/Blas/ LAPACK. I still got error messages like ATLAS/Blas/ LAPACK are not
found.
I could install package_numpy_1_9 by using galaxy main tool shed. There is
something wrong with package_numpy_1_7 on my environment.

Cheers,
Yu

di29her
w...@lrz.de

On 15 Dec 2014, at 16:12, John Chilton
mailto:jmchil...@gmail.com>>
wrote:

Looks like this - https://github.com/clarete/curdling/issues/19

I think you somehow need to install the package svn on your machine - if you
have root on that machine the command might be something like "sudo zypper
install svn" or may it is "sudo zypper install subversion". If you don't have
root on the machine I would ask the operating system maintainer or try to
compile and install svn locally and make it available to Galaxy.

Hope this helps,

-John

On Fri, Dec 12, 2014 at 7:14 AM, Wang, Yu
mailto:yu.w...@lrz.de>> wrote:
Hi, I am running galaxy on SLSE11, when I tried to install bumpy 1.7.1, I got
the following error.
Can anyone point what goes wrong here?

Error Running from numpy source directory.
/bin/sh: svnversion: command not found
/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1494:
UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
warnings.warn(AtlasNotFoundError.__doc__)
/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1503:
UserWarning:
Blas (http://www.netlib.org/blas/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [blas]) or by setting
the BLAS environment variable.
warnings.warn(BlasNotFoundError.__doc__)
/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1506:
UserWarning:
Blas (http://www.netlib.org/blas/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [blas_src]) or by setting
the BLAS_SRC environment variable.
warnings.warn(BlasSrcNotFoundError.__doc__)
/bin/sh: svnversion: command not found
/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1408:
UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
warnings.warn(AtlasNotFoundError.__doc__)
/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1419:
UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
warnings.warn(LapackNotFoundError.__doc__)
/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1422:
UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
warnings.warn(LapackSrcNotFoundError.__doc__)
error: must supply either home or prefix/exec-prefix -- not both

Cheers,
Yu

di29her
w...@lrz.de

Re: [galaxy-dev] package_numpy_1_7 can't be installed

2015-01-02 Thread Björn Grüning

Hi Wang,

can you point me to the exact version your try to install. There is an
old numpy_1_7 package which should be deprecated. We had a lot of
trouble installing ATLAS and LAPACK and decided to deprecate all
packages which depends on LAPACK and ATLAS. Now we do not require both
libraries anymore.

Thanks,
Bjoern

Am 15.12.2014 um 18:16 schrieb Wang, Yu:
> Hi, John,thanks for your answer. I installed svnversion, and 
> compiled/installed ATLAS/Blas/ LAPACK. I still got error messages like 
> ATLAS/Blas/ LAPACK are not found.
> I could install package_numpy_1_9 by using galaxy main tool shed. There is 
> something wrong with package_numpy_1_7 on my environment.
> 
> Cheers,
> Yu
> 
> di29her
> w...@lrz.de
> 
> On 15 Dec 2014, at 16:12, John Chilton 
> mailto:jmchil...@gmail.com>> wrote:
> 
> Looks like this - https://github.com/clarete/curdling/issues/19
> 
> I think you somehow need to install the package svn on your machine - if you 
> have root on that machine the command might be something like "sudo zypper 
> install svn" or may it is "sudo zypper install subversion". If you don't have 
> root on the machine I would ask the operating system maintainer or try to 
> compile and install svn locally and make it available to Galaxy.
> 
> Hope this helps,
> 
> -John
> 
> On Fri, Dec 12, 2014 at 7:14 AM, Wang, Yu 
> mailto:yu.w...@lrz.de>> wrote:
> Hi, I am running galaxy on SLSE11, when I tried to install bumpy 1.7.1, I got 
> the following error.
> Can anyone point what goes wrong here?
> 
> 
> Error   Running from numpy source directory.
> /bin/sh: svnversion: command not found
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1494:
>  UserWarning:
> Atlas (http://math-atlas.sourceforge.net/) libraries not found.
> Directories to search for the libraries can be specified in the
> numpy/distutils/site.cfg file (section [atlas]) or by setting
> the ATLAS environment variable.
>   warnings.warn(AtlasNotFoundError.__doc__)
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1503:
>  UserWarning:
> Blas (http://www.netlib.org/blas/) libraries not found.
> Directories to search for the libraries can be specified in the
> numpy/distutils/site.cfg file (section [blas]) or by setting
> the BLAS environment variable.
>   warnings.warn(BlasNotFoundError.__doc__)
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1506:
>  UserWarning:
> Blas (http://www.netlib.org/blas/) sources not found.
> Directories to search for the sources can be specified in the
> numpy/distutils/site.cfg file (section [blas_src]) or by setting
> the BLAS_SRC environment variable.
>   warnings.warn(BlasSrcNotFoundError.__doc__)
> /bin/sh: svnversion: command not found
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1408:
>  UserWarning:
> Atlas (http://math-atlas.sourceforge.net/) libraries not found.
> Directories to search for the libraries can be specified in the
> numpy/distutils/site.cfg file (section [atlas]) or by setting
> the ATLAS environment variable.
>   warnings.warn(AtlasNotFoundError.__doc__)
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1419:
>  UserWarning:
> Lapack (http://www.netlib.org/lapack/) libraries not found.
> Directories to search for the libraries can be specified in the
> numpy/distutils/site.cfg file (section [lapack]) or by setting
> the LAPACK environment variable.
>   warnings.warn(LapackNotFoundError.__doc__)
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1422:
>  UserWarning:
> Lapack (http://www.netlib.org/lapack/) sources not found.
> Directories to search for the sources can be specified in the
> numpy/distutils/site.cfg file (section [lapack_src]) or by setting
> the LAPACK_SRC environment variable.
>   warnings.warn(LapackSrcNotFoundError.__doc__)
> error: must supply either home or prefix/exec-prefix -- not both
> 
> 
> Cheers,
> Yu
> 
> di29her
> w...@lrz.de
> 
> 
> 
> 
> ___
> Please keep all replies on the list by using "reply all"
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> 
> 
> 
> 
> ___
> Please keep all replies on the list by using "reply all"
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> and other Galaxy lists, please use the interface at:
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> 
> To sear

Re: [galaxy-dev] package_numpy_1_7 can't be installed

2014-12-17 Thread Björn Grüning

Hi David,

do you get the same error message as Wang?


Am 17.12.2014 um 23:10 schrieb Lapointe, David:
> I am having the same issue. The RHEL packages for atlas, blas, and lapack
> are installed, but numpy 1.7 won't install, while numpy 1.9 seems to
> install successfully.
> 
___
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] package_numpy_1_7 can't be installed

2014-12-17 Thread Lapointe, David

I am having the same issue. The RHEL packages for atlas, blas, and lapack
are installed, but numpy 1.7 won't install, while numpy 1.9 seems to
install successfully.
-- 
David Lapointe Ph.D.
Sr. Bioinformatics Specialist
Research and Geospatial Technology Services
Tufts Technology Services (TTS)
16 Dearborn Road
Somerville MA 02144

Phone:  617-627-5319
Fax: 617-627-3667
http://it.tufts.edu




On 12/16/14, 5:08 AM, "Björn Grüning"  wrote:

>Hi,
>
>Am 16.12.2014 um 10:39 schrieb Wang, Yu:
>> Hi, Björn, my intention was to test a simple workflow (BASIC PROTOCOL 1
>>http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418382/) on my local galaxy
>>installation.
>> By default, ³join² function is not installed on galaxy. When I tried to
>>install ³join², it reported error on the installation of bx_python_0_7
>>(Galaxy main tool shed).
>> It looks like the automated installation of bx python failed somehow.
>> Looking at the package, it will attempt to install NumPy 1.7.1
>> https://toolshed.g2.bx.psu.edu/view/devteam/package_bx_python_0_7
>
>I see, thanks for the information.
>Unfortunately, this is a different package from what I was talking. Have
>you compiled ATLAS or installed it with your package manager? Are you
>running a Linux or OS-X.
>
>The problem is that Galaxy tries to install:
>
>pip install numpy
>
>And this crashes because you don't have all requirements installed. If
>possible try to install LAPACK and ATLAS with your package manager, you
>need to set a lot of ENV variables if you compile it yourself.
>
>Cheers,
>Bjoern
>
>
>> Then I tried to install NumPy 1.7.1 from Galaxy main tool shed, there
>>were all these errors from LAPACK and ATLAS.
>> 
>> Cheers,
>> Yu
>> 
>> di29her
>> w...@lrz.de
>> 
>> On 16 Dec 2014, at 04:07, Björn Grüning
>>mailto:bjo...@gruenings.eu>> wrote:
>> 
>> Hi Wang,
>> 
>> can you point me to the exact version your try to install. There is an
>> old numpy_1_7 package which should be deprecated. We had a lot of
>> trouble installing ATLAS and LAPACK and decided to deprecate all
>> packages which depends on LAPACK and ATLAS. Now we do not require both
>> libraries anymore.
>> 
>> Thanks,
>> Bjoern
>> 
>> Am 15.12.2014 um 18:16 schrieb Wang, Yu:
>> Hi, John,thanks for your answer. I installed svnversion, and
>>compiled/installed ATLAS/Blas/ LAPACK. I still got error messages like
>>ATLAS/Blas/ LAPACK are not found.
>> I could install package_numpy_1_9 by using galaxy main tool shed. There
>>is something wrong with package_numpy_1_7 on my environment.
>> 
>> Cheers,
>> Yu
>> 
>> di29her
>> w...@lrz.de
>> 
>> On 15 Dec 2014, at 16:12, John Chilton
>>mailto:jmchil...@gmail.com>>om>> wrote:
>> 
>> Looks like this - https://github.com/clarete/curdling/issues/19
>> 
>> I think you somehow need to install the package svn on your machine -
>>if you have root on that machine the command might be something like
>>"sudo zypper install svn" or may it is "sudo zypper install subversion".
>>If you don't have root on the machine I would ask the operating system
>>maintainer or try to compile and install svn locally and make it
>>available to Galaxy.
>> 
>> Hope this helps,
>> 
>> -John
>> 
>> On Fri, Dec 12, 2014 at 7:14 AM, Wang, Yu
>>mailto:yu.w...@lrz.de>> wrote:
>> Hi, I am running galaxy on SLSE11, when I tried to install bumpy 1.7.1,
>>I got the following error.
>> Can anyone point what goes wrong here?
>> 
>> 
>> Error   Running from numpy source directory.
>> /bin/sh: svnversion: command not found
>> 
>>/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/nu
>>mpy/distutils/system_info.py:1494: UserWarning:
>>Atlas (http://math-atlas.sourceforge.net/) libraries not found.
>>Directories to search for the libraries can be specified in the
>>numpy/distutils/site.cfg file (section [atlas]) or by setting
>>the ATLAS environment variable.
>>  warnings.warn(AtlasNotFoundError.__doc__)
>> 
>>/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/nu
>>mpy/distutils/system_info.py:1503: UserWarning:
>>Blas (http://www.netlib.org/blas/) libraries not found.
>>Directories to search for the libraries can be specified in the
>>numpy/distutils/site.cfg file (section [blas]) or by setting
>>the BLAS environment variable.
>>  warnings.warn(BlasNotFoundError.__doc__)
>> 
>>/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/nu
>>mpy/distutils/system_info.py:1506: UserWarning:
>>Blas (http://www.netlib.org/blas/) sources not found.
>>Directories to search for the sources can be specified in the
>>numpy/distutils/site.cfg file (section [blas_src]) or by setting
>>the BLAS_SRC environment variable.
>>  warnings.warn(BlasSrcNotFoundError.__doc__)
>> /bin/sh: svnversion: command not found
>> 
>>/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/nu
>>mpy/distutils/system_info.py:1408:

Re: [galaxy-dev] package_numpy_1_7 can't be installed

2014-12-16 Thread Björn Grüning

Hi,

Am 16.12.2014 um 10:39 schrieb Wang, Yu:
> Hi, Björn, my intention was to test a simple workflow (BASIC PROTOCOL 1 
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418382/) on my local galaxy 
> installation.
> By default, “join” function is not installed on galaxy. When I tried to 
> install “join”, it reported error on the installation of bx_python_0_7 
> (Galaxy main tool shed).
> It looks like the automated installation of bx python failed somehow.
> Looking at the package, it will attempt to install NumPy 1.7.1
> https://toolshed.g2.bx.psu.edu/view/devteam/package_bx_python_0_7

I see, thanks for the information.
Unfortunately, this is a different package from what I was talking. Have
you compiled ATLAS or installed it with your package manager? Are you
running a Linux or OS-X.

The problem is that Galaxy tries to install:

pip install numpy

And this crashes because you don't have all requirements installed. If
possible try to install LAPACK and ATLAS with your package manager, you
need to set a lot of ENV variables if you compile it yourself.

Cheers,
Bjoern


> Then I tried to install NumPy 1.7.1 from Galaxy main tool shed, there were 
> all these errors from LAPACK and ATLAS.
> 
> Cheers,
> Yu
> 
> di29her
> w...@lrz.de
> 
> On 16 Dec 2014, at 04:07, Björn Grüning 
> mailto:bjo...@gruenings.eu>> wrote:
> 
> Hi Wang,
> 
> can you point me to the exact version your try to install. There is an
> old numpy_1_7 package which should be deprecated. We had a lot of
> trouble installing ATLAS and LAPACK and decided to deprecate all
> packages which depends on LAPACK and ATLAS. Now we do not require both
> libraries anymore.
> 
> Thanks,
> Bjoern
> 
> Am 15.12.2014 um 18:16 schrieb Wang, Yu:
> Hi, John,thanks for your answer. I installed svnversion, and 
> compiled/installed ATLAS/Blas/ LAPACK. I still got error messages like 
> ATLAS/Blas/ LAPACK are not found.
> I could install package_numpy_1_9 by using galaxy main tool shed. There is 
> something wrong with package_numpy_1_7 on my environment.
> 
> Cheers,
> Yu
> 
> di29her
> w...@lrz.de
> 
> On 15 Dec 2014, at 16:12, John Chilton 
> mailto:jmchil...@gmail.com>> 
> wrote:
> 
> Looks like this - https://github.com/clarete/curdling/issues/19
> 
> I think you somehow need to install the package svn on your machine - if you 
> have root on that machine the command might be something like "sudo zypper 
> install svn" or may it is "sudo zypper install subversion". If you don't have 
> root on the machine I would ask the operating system maintainer or try to 
> compile and install svn locally and make it available to Galaxy.
> 
> Hope this helps,
> 
> -John
> 
> On Fri, Dec 12, 2014 at 7:14 AM, Wang, Yu 
> mailto:yu.w...@lrz.de>> wrote:
> Hi, I am running galaxy on SLSE11, when I tried to install bumpy 1.7.1, I got 
> the following error.
> Can anyone point what goes wrong here?
> 
> 
> Error   Running from numpy source directory.
> /bin/sh: svnversion: command not found
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1494:
>  UserWarning:
>Atlas (http://math-atlas.sourceforge.net/) libraries not found.
>Directories to search for the libraries can be specified in the
>numpy/distutils/site.cfg file (section [atlas]) or by setting
>the ATLAS environment variable.
>  warnings.warn(AtlasNotFoundError.__doc__)
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1503:
>  UserWarning:
>Blas (http://www.netlib.org/blas/) libraries not found.
>Directories to search for the libraries can be specified in the
>numpy/distutils/site.cfg file (section [blas]) or by setting
>the BLAS environment variable.
>  warnings.warn(BlasNotFoundError.__doc__)
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1506:
>  UserWarning:
>Blas (http://www.netlib.org/blas/) sources not found.
>Directories to search for the sources can be specified in the
>numpy/distutils/site.cfg file (section [blas_src]) or by setting
>the BLAS_SRC environment variable.
>  warnings.warn(BlasSrcNotFoundError.__doc__)
> /bin/sh: svnversion: command not found
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1408:
>  UserWarning:
>Atlas (http://math-atlas.sourceforge.net/) libraries not found.
>Directories to search for the libraries can be specified in the
>numpy/distutils/site.cfg file (section [atlas]) or by setting
>the ATLAS environment variable.
>  warnings.warn(AtlasNotFoundError.__doc__)
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1419:
>  UserWarning:
>Lapack (http://www.netlib.org/lapack/) libraries not found.
>Directories to search for the libraries

Re: [galaxy-dev] package_numpy_1_7 can't be installed

2014-12-15 Thread Wang, Yu

Hi, John,thanks for your answer. I installed svnversion, and compiled/installed
ATLAS/Blas/ LAPACK. I still got error messages like ATLAS/Blas/ LAPACK are not
found.
I could install package_numpy_1_9 by using galaxy main tool shed. There is
something wrong with package_numpy_1_7 on my environment.

Cheers,
Yu

di29her
w...@lrz.de

On 15 Dec 2014, at 16:12, John Chilton
mailto:jmchil...@gmail.com>> wrote:

Looks like this - https://github.com/clarete/curdling/issues/19

Hope this helps,

-John

Cheers,
Yu

di29her
w...@lrz.de

___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] package_numpy_1_7 can't be installed

2014-12-15 Thread John Chilton

Looks like this - https://github.com/clarete/curdling/issues/19

I think you somehow need to install the package svn on your machine - if
you have root on that machine the command might be something like "sudo
zypper install svn" or may it is "sudo zypper install subversion". If you
don't have root on the machine I would ask the operating system maintainer
or try to compile and install svn locally and make it available to Galaxy.

Hope this helps,

-John

On Fri, Dec 12, 2014 at 7:14 AM, Wang, Yu  wrote:
>
>  Hi, I am running galaxy on SLSE11, when I tried to install bumpy 1.7.1, I
> got the following error.
> Can anyone point what goes wrong here?
>
>
>   Error Running from numpy source directory.
> /bin/sh: svnversion: command not found
>
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1494:
>  UserWarning:
> Atlas (http://math-atlas.sourceforge.net/) libraries not found.
> Directories to search for the libraries can be specified in the
> numpy/distutils/site.cfg file (section [atlas]) or by setting
> the ATLAS environment variable.
>   warnings.warn(AtlasNotFoundError.__doc__)
>
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1503:
>  UserWarning:
> Blas (http://www.netlib.org/blas/) libraries not found.
> Directories to search for the libraries can be specified in the
> numpy/distutils/site.cfg file (section [blas]) or by setting
> the BLAS environment variable.
>   warnings.warn(BlasNotFoundError.__doc__)
>
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1506:
>  UserWarning:
> Blas (http://www.netlib.org/blas/) sources not found.
> Directories to search for the sources can be specified in the
> numpy/distutils/site.cfg file (section [blas_src]) or by setting
> the BLAS_SRC environment variable.
>   warnings.warn(BlasSrcNotFoundError.__doc__)
> /bin/sh: svnversion: command not found
>
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1408:
>  UserWarning:
> Atlas (http://math-atlas.sourceforge.net/) libraries not found.
> Directories to search for the libraries can be specified in the
> numpy/distutils/site.cfg file (section [atlas]) or by setting
> the ATLAS environment variable.
>   warnings.warn(AtlasNotFoundError.__doc__)
>
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1419:
>  UserWarning:
> Lapack (http://www.netlib.org/lapack/) libraries not found.
> Directories to search for the libraries can be specified in the
> numpy/distutils/site.cfg file (section [lapack]) or by setting
> the LAPACK environment variable.
>   warnings.warn(LapackNotFoundError.__doc__)
>
> /home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1422:
>  UserWarning:
> Lapack (http://www.netlib.org/lapack/) sources not found.
> Directories to search for the sources can be specified in the
> numpy/distutils/site.cfg file (section [lapack_src]) or by setting
> the LAPACK_SRC environment variable.
>   warnings.warn(LapackSrcNotFoundError.__doc__)
> error: must supply either home or prefix/exec-prefix -- not both
>
>
> Cheers,
> Yu
>
> di29her
> w...@lrz.de
>
>
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
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>
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[galaxy-dev] package_numpy_1_7 can't be installed

2014-12-13 Thread Wang, Yu

Hi, I am running galaxy on SLSE11, when I tried to install bumpy 1.7.1, I got 
the following error.
Can anyone point what goes wrong here?


Error   Running from numpy source directory.
/bin/sh: svnversion: command not found
/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1494:
 UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
  warnings.warn(AtlasNotFoundError.__doc__)
/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1503:
 UserWarning:
Blas (http://www.netlib.org/blas/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [blas]) or by setting
the BLAS environment variable.
  warnings.warn(BlasNotFoundError.__doc__)
/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1506:
 UserWarning:
Blas (http://www.netlib.org/blas/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [blas_src]) or by setting
the BLAS_SRC environment variable.
  warnings.warn(BlasSrcNotFoundError.__doc__)
/bin/sh: svnversion: command not found
/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1408:
 UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
  warnings.warn(AtlasNotFoundError.__doc__)
/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1419:
 UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
  warnings.warn(LapackNotFoundError.__doc__)
/home/wang/galaxy-dist/database/tmp/tmp-toolshed-mtdMR9ITC/numpy-1.7.1/numpy/distutils/system_info.py:1422:
 UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
  warnings.warn(LapackSrcNotFoundError.__doc__)
error: must supply either home or prefix/exec-prefix -- not both


Cheers,
Yu

di29her
w...@lrz.de



___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

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Re: [galaxy-dev] package_numpy_1_7 can't be installed

Re: [galaxy-dev] package_numpy_1_7 can't be installed

Re: [galaxy-dev] package_numpy_1_7 can't be installed

Re: [galaxy-dev] package_numpy_1_7 can't be installed

Re: [galaxy-dev] package_numpy_1_7 can't be installed

Re: [galaxy-dev] package_numpy_1_7 can't be installed

Re: [galaxy-dev] package_numpy_1_7 can't be installed

[galaxy-dev] package_numpy_1_7 can't be installed

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