Re: [galaxy-dev] Error / import rpy module
Hi Sarah you need to install the rpy module: http://rpy.sourceforge.net/rpy.html As a warning: we have been struggling to get rpy to work with newer versions of R. In or experience in only works with R version 2.9 and older. Thanks to a recent effort of our sysadmin, we can now use it with 2.15 - which is good, but not great, as our default version of R is now 3.0 Although we haven't started to us it, I recommend using rpy2: http://rpy.sourceforge.net/rpy2.html Most tools have been refactored by John Chilton see: http://dev.list.galaxyproject.org/rpy2-Core-Tools-td4659832.html Regards, Hans-Rudolf On 06/05/2013 10:19 AM, Sarah Maman wrote: Hello, Some Galaxy tools failed to import rpy module and displays the following message: Traceback (most recent call last): File /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/plotting/histogram.py, line 5, in module from rpy import * ImportError: No module named rpy For instance, the tool Regrouping (tools/stats/grouping.py) have been refactored in 2011 by Kanwei Li to use numpy instead of rpy. And this tool runs on my local instance of Galaxy. But I would like to be able use rpy module instead of refactor the others tools. Could you, please, help me to understand why the eggs ' import does not allow the use of rpy module? How to debug these tools? Thnaks in advance, Sarah ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Error / import rpy module
On Wed, Jun 5, 2013 at 9:42 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Sarah you need to install the rpy module: http://rpy.sourceforge.net/rpy.html As a warning: we have been struggling to get rpy to work with newer versions of R. In or experience in only works with R version 2.9 and older. Thanks to a recent effort of our sysadmin, we can now use it with 2.15 - which is good, but not great, as our default version of R is now 3.0 According to the rpy list, using the latest code from SVN you should be able to get rpy v1 to work under R 3.0.1, http://sourceforge.net/mailarchive/message.php?msg_id=30999482 Although we haven't started to us it, I recommend using rpy2: http://rpy.sourceforge.net/rpy2.html Indeed - rpy v1 is still being maintained in SVN, but hasn't had an official release with these fixed for over two years. Most tools have been refactored by John Chilton see: http://dev.list.galaxyproject.org/rpy2-Core-Tools-td4659832.html We're not making heavy use of rpy in Galaxy yet, but I hope John's good work switching to rpy2 gets integrated soon. Peter ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Error / import rpy module
Thanks a lot for these explantions, I have downloded refactored tools (rpy2 is more suited to our R version). Unfortunatly, galaxy still do not import rpy2 .. Traceback (most recent call last): File /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/plotting/histogram.py, line 6, in module import rpy2.robjects as robjects ImportError: No module named rpy2.robjects Moreover our rpy2 module is avalaible and listed in our python. Maybe a problem with Python ? Thanks in advance, Sarah Hans-Rudolf Hotz a écrit : Hi Sarah you need to install the rpy module: http://rpy.sourceforge.net/rpy.html As a warning: we have been struggling to get rpy to work with newer versions of R. In or experience in only works with R version 2.9 and older. Thanks to a recent effort of our sysadmin, we can now use it with 2.15 - which is good, but not great, as our default version of R is now 3.0 Although we haven't started to us it, I recommend using rpy2: http://rpy.sourceforge.net/rpy2.html Most tools have been refactored by John Chilton see: http://dev.list.galaxyproject.org/rpy2-Core-Tools-td4659832.html Regards, Hans-Rudolf On 06/05/2013 10:19 AM, Sarah Maman wrote: Hello, Some Galaxy tools failed to import rpy module and displays the following message: Traceback (most recent call last): File /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/plotting/histogram.py, line 5, in module from rpy import * ImportError: No module named rpy For instance, the tool Regrouping (tools/stats/grouping.py) have been refactored in 2011 by Kanwei Li to use numpy instead of rpy. And this tool runs on my local instance of Galaxy. But I would like to be able use rpy module instead of refactor the others tools. Could you, please, help me to understand why the eggs ' import does not allow the use of rpy module? How to debug these tools? Thnaks in advance, Sarah -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*-- ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Error / import rpy module
Three quick comments on this thread:
- A real short-coming of my colleague JJ is that he doesn't possess a
tenth the ego that I do, so he doesn't care, but I think it is
important he gets credit. He did 85% of the work, and the harder 85%
at that, so they should be called the JJ changes.
- It is possible to get rpy working with newer versions of R (at least
3.0.0) because CloudBioLinux is configured this way and it seems to
work for me. (Not that there aren't other problems -
https://github.com/chapmanb/cloudbiolinux/commit/302072341696390dc1cf3ae1dd88a9c1ca35a4fa).
CloudBioLinux is configured to get its rpy packages here
http://watson.nci.nih.gov/cran_mirror/bin/linux/ubuntu/{precise,quantal}
which has versions compatible with R 3.0.0.
- Finally, an idea - Death to RPY - The BoF. Everyone with a stake
in this meets with laptops at the Galaxy conference together and we
divvy up the remaining tools to convert (hopefully one tool per
person). Every person is also assigned two of the existing converted
tools to retest and clean up. As they are completed they are given to
a core Galaxy developer (Nate, Dannon, Daniel, any volunteers?) to
collect, re-retest, and okay. The changes are then committed all
together at the end and the next Galaxy release contains no
dependencies on rpy.
These tools are not updated frequently, so the advantage of these all
being upgraded in one commit before being shipped off to the tool shed
is that an institution that is really stuck on rpy1 for whatever
reason can just undo that single commit and keep going with the old
tools indefinitely.
If anybody with commit access signs on I will be happy create a BoF
page and attend this.
Thanks,
-John
On Wed, Jun 5, 2013 at 4:23 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Wed, Jun 5, 2013 at 9:42 AM, Hans-Rudolf Hotz h...@fmi.ch wrote:
Hi Sarah
you need to install the rpy module:
http://rpy.sourceforge.net/rpy.html
As a warning: we have been struggling to get rpy to work with newer versions
of R. In or experience in only works with R version 2.9 and older. Thanks to
a recent effort of our sysadmin, we can now use it with 2.15 - which is
good, but not great, as our default version of R is now 3.0
According to the rpy list, using the latest code from SVN
you should be able to get rpy v1 to work under R 3.0.1,
http://sourceforge.net/mailarchive/message.php?msg_id=30999482
Although we haven't started to us it, I recommend using rpy2:
http://rpy.sourceforge.net/rpy2.html
Indeed - rpy v1 is still being maintained in SVN, but
hasn't had an official release with these fixed for
over two years.
Most tools have been refactored by John Chilton
see: http://dev.list.galaxyproject.org/rpy2-Core-Tools-td4659832.html
We're not making heavy use of rpy in Galaxy yet, but I
hope John's good work switching to rpy2 gets integrated
soon.
Peter
___
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in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
___
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:
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To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] Error / import rpy module
On Wed, Jun 5, 2013 at 2:18 PM, John Chilton chil...@msi.umn.edu wrote:
Three quick comments on this thread:
- A real short-coming of my colleague JJ is that he doesn't possess a
tenth the ego that I do, so he doesn't care, but I think it is
important he gets credit. He did 85% of the work, and the harder 85%
at that, so they should be called the JJ changes.
- It is possible to get rpy working with newer versions of R (at least
3.0.0) because CloudBioLinux is configured this way and it seems to
work for me. (Not that there aren't other problems -
https://github.com/chapmanb/cloudbiolinux/commit/302072341696390dc1cf3ae1dd88a9c1ca35a4fa).
CloudBioLinux is configured to get its rpy packages here
http://watson.nci.nih.gov/cran_mirror/bin/linux/ubuntu/{precise,quantal}
which has versions compatible with R 3.0.0.
- Finally, an idea - Death to RPY - The BoF. Everyone with a stake
in this meets with laptops at the Galaxy conference together and we
divvy up the remaining tools to convert (hopefully one tool per
person). Every person is also assigned two of the existing converted
tools to retest and clean up. As they are completed they are given to
a core Galaxy developer (Nate, Dannon, Daniel, any volunteers?) to
collect, re-retest, and okay. The changes are then committed all
together at the end and the next Galaxy release contains no
dependencies on rpy.
These tools are not updated frequently, so the advantage of these all
being upgraded in one commit before being shipped off to the tool shed
is that an institution that is really stuck on rpy1 for whatever
reason can just undo that single commit and keep going with the old
tools indefinitely.
If anybody with commit access signs on I will be happy create a BoF
page and attend this.
Thanks,
-John
If you all can pull that off in Oslo, great. Otherwise a piecewise
conversion seems a sensible plan B, where both rpy (v1) and rpy2
are installed and things are updated on a tool by tool basis.
The BoF group might also have some collective wisdom on how
to deal with the question of multiple versions of R/BioConductor
given this is important for reproducibility of many more complex
and rapidly developed R tools.
Peter
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and other Galaxy lists, please use the interface at:
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