[BioC] [R] problem loading affycoretools - solved!

Jenny Drnevich drnevich at uiuc.edu
Fri Aug 11 20:59:59 CEST 2006


Hi Martin,

The patched version works fine - thanks for pointing it out! As for 
problems installing RWinEdt, do you have WinEdt downloaded and 
installed?  www.winedt.com   I've found it to be a useful editor for R - 
well worth the nominal fee after the trial period has ended.

Cheers,
Jenny

At 01:01 PM 8/11/2006, Martin Morgan wrote:
>Hi Jenny --
>
>This sounds like a problem that is addressed in the 'patched' version
>of 2.3.1, from the CHANGES file:
>
>R 2.3.1 patched
>===============
>
>winMenuAdd() could crash when too many menus were added.  (PR#8961)
>
>The patched version is at CRAN:
>
>R Binaries --> windows --> Base and then hunt fort the link 'r-patched
>snapshot build'.
>
>I haven't been able to test this explicitly with RWinEdt, which does
>not seem to want to install easily on my computer. If this is the
>solution, then perhaps you could forward a 'solved!' note to the list?
>
>Martin
>--
>Bioconductor
>
>Jenny Drnevich <drnevich at uiuc.edu> writes:
>
> > Hi again,
> >
> > I have been playing around with the order of loading packages, and as far
> > as I can tell, there's nothing specific with affycoretools that's causing
> > my Rgui to crash (i.e., shuts down and the Microsoft 'please send error
> > report' box pops up). Instead, it has something to do with the order & 
> type
> > of packages that are loaded that add items to the menu bar by themselves,
> > or adding more options under 'Vignettes'. Specific combinations of any 3
> > of: affycoretools, RWinEdt, affyPLM or affylmGUI can cause the crash. So
> > far, I haven't been able to get it to crash without affycoretools, even if
> > I load all the dependencies by themselves, but that may just be because I
> > don't know of another package that adds to the menu bar.  After playing
> > around with this for a while, even combinations of two packages (that
> > loaded fine before) started to crash the Rgui until I rebooted my PC. I
> > remember having similar sorts of trouble a while back when manually
> > downloading zipped packages and installing them via the menu - after doing
> > a few, clicking on the menu again in the same R session would cause the
> > Rgui to crash. As this may not be specific to Bioconductor (except that 
> you
> > may not put so many items in the menu unless you're using BioC packages),
> > I'm cross posting to the R mailing list.
> >
> > Cheers,
> > Jenny
> >
> >
> > At 12:37 PM 8/10/2006, Jenny Drnevich wrote:
> >>Hi Jim & all,
> >>
> >>I'm having trouble getting affycoretools to work. I apparently had
> >>downloaded & installed affycoretools before, but had never used it. When I
> >>tried to load it today, I got an error message saying I was missing a
> >>dependent package, GOstats. So I used biocLite() to download & install
> >>GOstats & it's dependencies. Then when I tried to load affycoretools, I
> >>crashed my Rgui. I restarted the Rgui a few times in different ways, and
> >>each time I tried to load affycoretools, it crashed the Rgui. So then I
> >>went and deleted R_HOME/library/affycoretools and tried using biocLite() to
> >>get it again. This time it didn't crash, but it gave a warning message
> >>about it not containing a vignette (see below for output & sessionInfo). I
> >>checked on bioconductor.org, and there is a vignette for affycoretools. I
> >>haven't tried any of the functions yet, but I'm worried that something's
> >>amiss. Any suggestions on what to check or reload?
> >>
> >>Thanks,
> >>Jenny
> >>
> >>P.S. It was great to finally meet many of you at the BioC2006 conference!
> >>
> >>
> >>R : Copyright 2006, The R Foundation for Statistical Computing
> >>Version 2.3.1 (2006-06-01)
> >>ISBN 3-900051-07-0
> >>
> >>R is free software and comes with ABSOLUTELY NO WARRANTY.
> >>You are welcome to redistribute it under certain conditions.
> >>Type 'license()' or 'licence()' for distribution details.
> >>
> >>    Natural language support but running in an English locale
> >>
> >>R is a collaborative project with many contributors.
> >>Type 'contributors()' for more information and
> >>'citation()' on how to cite R or R packages in publications.
> >>
> >>Type 'demo()' for some demos, 'help()' for on-line help, or
> >>'help.start()' for an HTML browser interface to help.
> >>Type 'q()' to quit R.
> >>
> >>Loading required package: affy
> >>Loading required package: Biobase
> >>Loading required package: tools
> >>
> >>Welcome to Bioconductor
> >>
> >>
> >>      Vignettes contain introductory material.
> >>
> >>      To view, simply type 'openVignette()' or start with 'help(Biobase)'.
> >>
> >>      For details on reading vignettes, see the openVignette help page.
> >>
> >>
> >>Loading required package: affyio
> >>Loading required package: affydata
> >>Loading required package: Biobase
> >>Loading required package: gcrma
> >>Loading required package: matchprobes
> >>Loading required package: reposTools
> >>Loading required package: simpleaffy
> >>Loading required package: genefilter
> >>Loading required package: survival
> >>Loading required package: splines
> >>Welcome to 'affyQCReport' V 1.6-1
> >>Further information available at: www.bifix.org
> >>        mailto: craig.parman at bifix.org
> >>Loading required package: ade4
> >>Loading required package: scatterplot3d
> >>
> >>  > source("http://bioconductor.org/biocLite.R")
> >>  > biocLite("affycoretools")
> >>
> >>Running getBioC version 0.1.6 with R version 2.3.1
> >>Running biocinstall version 1.8.4 with R version 2.3.1
> >>Your version of R requires version 1.8 of Bioconductor.
> >>trying URL
> >>'http://bioconductor.org/packages/1.8/bioc/bin/windows/contrib/2.3/affyc 
> oretools_1.4.0.zip'
> >>Content type 'application/zip' length 10626563 bytes
> >>opened URL
> >>downloaded 10377Kb
> >>
> >>package 'affycoretools' successfully unpacked and MD5 sums checked
> >>
> >>The downloaded packages are in
> >>          C:\Documents and Settings\drnevich\Local
> >>Settings\Temp\RtmpfRnlqb\downloaded_packages
> >>updating HTML package descriptions
> >>
> >>  > library(affycoretools)
> >>
> >>Loading required package: GOstats
> >>Loading required package: graph
> >>Loading required package: Ruuid
> >>Loading required package: GO
> >>Loading required package: annotate
> >>Loading required package: RBGL
> >>Loading required package: xtable
> >>
> >>Attaching package: 'xtable'
> >>
> >>
> >>          The following object(s) are masked from package:graph :
> >>
> >>           label
> >>
> >>Loading required package: multtest
> >>Loading required package: Category
> >>Loading required package: KEGG
> >>Loading required package: hgu95av2
> >>Warning message:
> >>affycoretools contains no vignette, nothing is added to the menu bar in:
> >>addVigs2WinMenu("affycoretools")
> >>
> >>  > sessionInfo()
> >>Version 2.3.1 (2006-06-01)
> >>i386-pc-mingw32
> >>
> >>attached base packages:
> >>[1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices"
> >>[7] "utils"     "datasets"  "base"
> >>
> >>other attached packages:
> >>affycoretools       GOstats      Category      hgu95av2          KEGG
> >>        "1.4.0"       "1.6.0"       "1.4.1"      "1.12.0"      "1.12.0"
> >>       multtest        xtable          RBGL      annotate            GO
> >>       "1.10.2"       "1.3-2"       "1.8.1"      "1.10.0"      "1.12.0"
> >>          graph         Ruuid         made4 scatterplot3d          ade4
> >>       "1.10.4"      "1.10.0"       "1.6.0"      "0.3-24"       "1.4-1"
> >>   affyQCReport    simpleaffy    genefilter      survival    reposTools
> >>       "1.10.0"       "2.6.0"      "1.10.1"        "2.26"      "1.10.0"
> >>        affyPLM         gcrma   matchprobes      affydata          affy
> >>        "1.8.0"       "2.4.1"       "1.4.0"       "1.8.0"      "1.10.0"
> >>         affyio       Biobase         limma       RWinEdt
> >>        "1.0.0"      "1.10.0"       "2.7.2"       "1.7-4"
> >>  >
> >>
> >>
> >>Jenny Drnevich, Ph.D.
> >>
> >>Functional Genomics Bioinformatics Specialist
> >>W.M. Keck Center for Comparative and Functional Genomics
> >>Roy J. Carver Biotechnology Center
> >>University of Illinois, Urbana-Champaign
> >>
> >>330 ERML
> >>1201 W. Gregory Dr.
> >>Urbana, IL 61801
> >>USA
> >>
> >>ph: 217-244-7355
> >>fax: 217-265-5066
> >>e-mail: drnevich at uiuc.edu
> >>
> >>_______________________________________________
> >>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
> >
> > Jenny Drnevich, Ph.D.
> >
> > Functional Genomics Bioinformatics Specialist
> > W.M. Keck Center for Comparative and Functional Genomics
> > Roy J. Carver Biotechnology Center
> > University of Illinois, Urbana-Champaign
> >
> > 330 ERML
> > 1201 W. Gregory Dr.
> > Urbana, IL 61801
> > USA
> >
> > ph: 217-244-7355
> > fax: 217-265-5066
> > e-mail: drnevich at uiuc.edu
> >
> > ______________________________________________
> > R-help at stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide 
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.



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