Just to follow up, I've been able to get it to work without any errors after shutting down various X11 windows. At one point, I got an X11 fatal IO error: please save work and shut down R. So, I don't have a great explanation on my end. Andrew 2010/3/4 Andrew Yee <yee@post.harvard.edu> > Thanks for checking. Note, I'm accessing Linux through putty on my Windows > machine. I've also encountered this problem when I'm using Linux directly. > > > Here's my sessionInfo() > > R version 2.10.1 (2009-12-14) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] IRanges_1.4.11 > > > > 2010/3/4 Hervé Pagès <hpages@fhcrc.org> > > Hi Andrew, >> >> I'm running BioC 2.5 + R 2.10.1 on a Linux system too but I can't >> reproduce this (I'm not even asked to choose between base::sort >> and IRanges::sort). >> >> Please provide the output of sessionInfo() that you get just after >> a fresh R start immediately followed by library(IRanges). >> >> Thanks, >> H. >> >> >> Andrew Yee wrote: >> >>> I'm not sure where to begin with this problem, but here I go. I'm >>> running >>> this on a Linux system using R 2.10.1 >>> >>> I've installed the IRanges package. However, when I enter help(sort), it >>> shows that the topic 'sort' was found both in the IRanges and the base >>> package. However, it ultimately returns an error message, >>> >>> Error in structure(.External("dotTclObjv", objv, PACKAGE="tcltk"), class >>> = >>> "tclObj") : >>> [tcl] grab failed: window not viewable. >>> >>> Am I missing something obvious? >>> >>> Thanks, >>> Andrew >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> -- >> Hervé Pagès >> >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N, M2-B876 >> P.O. Box 19024 >> Seattle, WA 98109-1024 >> >> E-mail: hpages@fhcrc.org >> Phone: (206) 667-5791 >> Fax: (206) 667-1319 >> > > [[alternative HTML version deleted]]