Re: [Rpy] importr regression in 2.3?
In data martedì 12 marzo 2013 17:03:26, Luca Beltrame ha scritto: This package provides a series of classes, in this case I wanted to access the kegg class. Just as a small correction, it's a R list containing classes. It's present in the package environment but not loaded by importr. – Luca Beltrame, Ph.D. - Translational Genomics Unit Oncology Department, Mario Negri Institute signature.asc Description: This is a digitally signed message part. -- Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester Wave(TM): Endpoint Security, Q1 2013 and remains a good choice in the endpoint security space. For insight on selecting the right partner to tackle endpoint security challenges, access the full report. http://p.sf.net/sfu/symantec-dev2dev___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list
Re: [Rpy] importr regression in 2.3?
On 2013-03-12 17:06, Luca Beltrame wrote: In data martedì 12 marzo 2013 17:03:26, Luca Beltrame ha scritto: This package provides a series of classes, in this case I wanted to access the kegg class. Just as a small correction, it's a R list containing classes. It's present in the package environment but not loaded by importr. The error message in full would certainly help guessing what is happening. Best, L. -- Luca Beltrame, Ph.D. - Translational Genomics Unit Oncology Department, Mario Negri Institute -- Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester Wave(TM): Endpoint Security, Q1 2013 and remains a good choice in the endpoint security space. For insight on selecting the right partner to tackle endpoint security challenges, access the full report. http://p.sf.net/sfu/symantec-dev2dev ___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list -- Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester Wave(TM): Endpoint Security, Q1 2013 and remains a good choice in the endpoint security space. For insight on selecting the right partner to tackle endpoint security challenges, access the full report. http://p.sf.net/sfu/symantec-dev2dev___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list
Re: [Rpy] importr regression in 2.3?
In data martedì 12 marzo 2013 17:07:39, Laurent Gautier ha scritto: Hello Laurent, The error message in full would certainly help guessing what is happening. Simply put, this list vector used to be loaded in the package namespace, but is not loaded anymore on package import. hasattr(graphite, kegg) False rpy2.__version__ '2.3.3' The exact error is, in fact AttributeError: 'SignatureTranslatedPackage' object has no attribute 'kegg' I just confirmed the fact that it worked on a machine with 2.2.x. In [6]: hasattr(graphite, kegg) Out[6]: True In [8]: rpy2.__version__ Out[8]: '2.2.5' – Luca Beltrame, Ph.D. - Translational Genomics Unit Oncology Department, Mario Negri Institute signature.asc Description: This is a digitally signed message part. -- Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester Wave(TM): Endpoint Security, Q1 2013 and remains a good choice in the endpoint security space. For insight on selecting the right partner to tackle endpoint security challenges, access the full report. http://p.sf.net/sfu/symantec-dev2dev___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list
Re: [Rpy] importr regression in 2.3?
On 2013-03-12 16:44, Luca Beltrame wrote: Hello, I've been using importr successfully with the 2.2.x series, but since upgrading today to the 2.3.x series I noticed a change in behavior. I noticed this with the graphite package from Bioconductor: graphite = importr(graphite) This package provides a series of classes, in this case I wanted to access the kegg class. With 2.2.x, this graphite.kegg worked while in 2.3.x causes AttributeError. Where I can start digging to find the problem? I tried it myself and now I understand what is happening. Two things: - There were changes in R regarding datasets in packages and exported symbols, that forced me to make changes to the way the datasets are accessed (see below). - There is something odd happening with the names of those datasets (probably an error in rpy2) The way to get the data is currently: kegg_env = graphite.__rdata__.fetch(kegg (pathways)) kegg = kegg_env['kegg'] Not as easy as it was, I agree... L. -- Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester Wave(TM): Endpoint Security, Q1 2013 and remains a good choice in the endpoint security space. For insight on selecting the right partner to tackle endpoint security challenges, access the full report. http://p.sf.net/sfu/symantec-dev2dev ___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list -- Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester Wave(TM): Endpoint Security, Q1 2013 and remains a good choice in the endpoint security space. For insight on selecting the right partner to tackle endpoint security challenges, access the full report. http://p.sf.net/sfu/symantec-dev2dev___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list
Re: [Rpy] importr regression in 2.3?
In data martedì 12 marzo 2013 17:23:12, Laurent Gautier ha scritto: - There is something odd happening with the names of those datasets (probably an error in rpy2) Do you want me to open a bug on bitbucket to ensure this quirk is not forgotten in case someone else bumps into it? kegg_env = graphite.__rdata__.fetch(kegg (pathways)) kegg = kegg_env['kegg'] I did something similar using wherefrom(), in fact. -- Luca Beltrame, Ph.D. - Translational Genomics Unit Oncology Department, Mario Negri Institute signature.asc Description: This is a digitally signed message part. -- Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester Wave(TM): Endpoint Security, Q1 2013 and remains a good choice in the endpoint security space. For insight on selecting the right partner to tackle endpoint security challenges, access the full report. http://p.sf.net/sfu/symantec-dev2dev___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list
Re: [Rpy] importr regression in 2.3?
On 2013-03-12 17:25, Luca Beltrame wrote: In data martedì 12 marzo 2013 17:23:12, Laurent Gautier ha scritto: - There is something odd happening with the names of those datasets (probably an error in rpy2) Do you want me to open a bug on bitbucket to ensure this quirk is not forgotten in case someone else bumps into it? Yes. Better to open a bug report (and even better send a pull request with a patch ;-) ). Thanks. kegg_env = graphite.__rdata__.fetch(kegg (pathways)) kegg = kegg_env['kegg'] I did something similar using wherefrom(), in fact. L. -- Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester Wave(TM): Endpoint Security, Q1 2013 and remains a good choice in the endpoint security space. For insight on selecting the right partner to tackle endpoint security challenges, access the full report. http://p.sf.net/sfu/symantec-dev2dev ___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list
