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/aff ycoretools_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

Hi Jenny, 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? Hmmm. That's odd. I just checked the package build, and everything looks OK for the windows build. I'm wondering if it is OK to just delete a package like that - in the past there wasn't that much involved with the installation/removal of packages, but these days there are more things going on 'under the hood', so that might be a problem. You might try remove.packages("affycoretools") and then biocLite() again. No idea why the package might be crashing R. In my experience, that almost always happens with a package that contains C code rather than something simple like affycoretools, which is R code only. Anyway, I would try removing and re-installing again. The error you are getting shouldn't be a problem - it is just complaining because the package is trying to add an entry to the vignettes menu item when it doesn't think there is one (BTW, is there a vignette in R_HOME/library/affycoretools/doc?). > > Thanks, > Jenny > > P.S. It was great to finally meet many of you at the BioC2006 conference! It was nice to meet you as well! Best, Jim > > > 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/a ffycoretools_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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

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/af fycoretools_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