Bugs item #1956434, was opened at 2008-05-02 22:42
Message generated for change (Comment added) made by lgautier
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Category: None
Group: None
Status: Open
>Resolution: Fixed
Priority: 5
Private: No
Submitted By: Faheem Mitha (fmitha)
Assigned to: Nobody/Anonymous (nobody)
Summary: rpy 1.0~rc1segfault with bioconductor packages
Initial Comment:
Hi,
I'm getting a segfault with rpy, 1.0~rc1-2 on Debian etch, with the CRAN
backport of 2.6.2.
Faheem.
**************************************************************************
Debian package info.
**************************************************************************
||/ Name Version Description
+++-===============================-===============================-==============================================================================
ii python-rpy 1.0~rc1-2 Python
interface to the GNU R language and environment
ii r-base-core 2.6.2-1~etchcran.1 GNU R core
of statistical computing language and environment
****************************************************************************
Script to reproduce
****************************************************************************
from rpy import r
r.library("affy")
r.library("hu6800cdf")
fnames = [u'AD8.CEL', u'L01.CEL', u'L02.CEL', u'L04.CEL', u'L05.CEL',
u'L06.CEL']
celdat = r.ReadAffy(filenames = fnames, celfile_path = 'data')
*****************************************************************
Run output
****************************************************************
[EMAIL PROTECTED]:/tmp$ python rpy_bug.py
RHOME= /usr/lib64/R
RVERSION= 2.6.2
RVER= 2062
RUSER= /home/faheem
Loading Rpy version 2062 .. Done.
Creating the R object 'r' .. Done
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: affyio
Loading required package: preprocessCore
Error: segfault from C stack overflow
Segmentation fault
****************************************************************
R package info obtained from sessionInfo.
****************************************************************
> sessionInfo()
R version 2.6.2 (2008-02-08)
x86_64-pc-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;L
C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] tools stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] hu6800cdf_2.0.0 affy_1.16.0 preprocessCore_1.0.0
[4] affyio_1.6.1 Biobase_1.16.3
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17
----------------------------------------------------------------------
>Comment By: lgautier (lgautier)
Date: 2008-09-19 08:48
Message:
Seems to be working with rpy2 and R-2.7:
import rpy2.robjects as ro
ro.r.library("affy")
cel = ro.r["read.affybatch"]("GSM177882.CEL.gz")
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