trouble using help() after loading IRanges and [tcl] grab failed and possible tcltk problem
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Andrew Yee ▴ 350
@andrew-yee-2667
Last seen 7.3 years ago
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]]
GO IRanges GO IRanges • 1.5k views
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@herve-pages-1542
Last seen 42 minutes ago
Seattle, WA, United States
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 at 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 at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
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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]]
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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]]
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