Jenny Drnevich
2006-Aug-11 15:46 UTC
[R] [BioC] problem loading affycoretools (more details)
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/affycoretools_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.conductorJenny 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
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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