oligo on R 2.4.1?
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Jenny Drnevich ★ 2.2k
@jenny-drnevich-382
Last seen 7.7 years ago
Hi again, I'm having trouble making a data package for my Affy tiling array - it's not related to the arguments for makePDpackages, but because of memory limitations and the inability to install the oligo package on R 2.4.0. I have R 2.5.0 (the devel. version) installed on my PC, along with all the necessary compilers, but I don't have enough memory to make the package. I also have access to R on a server with more memory, but it's only R 2.4.0 and I doubt I could get them to install R 2.5.0 on it until it's the released version. R CMD INSTALL failed for the oligo package because it says it requires 2.5.0, but the makePlatformDesign package installed fine. I thought I would be able to make the package on the server then install it back on my PC, but according to the warnings and errors below, the oligo package is required. Is there any way for me to get around this, or am I SOL? :) Jenny > library(makePlatformDesign) Loading required package: oligo Attaching package: 'makePlatformDesign' The following object(s) are masked from package:matchprobes : complementSeq The following object(s) are masked from package:matchprobes : longestConsecutive The following object(s) are masked from package:matchprobes : matchprobes The following object(s) are masked from package:matchprobes : reverseSeq Warning messages: 1: there is no package called 'oligo' in: library(package, lib.loc = lib.loc, character.only = TRUE, logical = TRUE, 2: The oligo package could not be loaded thus the platformDesign class is not defined. in: f(libname, pkgname) > > > > makePDpackage("Mm_PromPR_v01_NCBIv35.bpmap", type="tiling", genomebuild="mg33") affymetrix tiling The package will be called pdmmpromprv01ncbiv35 Array identified as having 914 rows and 914 columns. Error in getClass(Class, where = topenv(parent.frame())) : "platformDesign" is not a defined class > > sessionInfo() R version 2.4.0 (2006-10-03) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" [7] "utils" "datasets" "base" other attached packages: makePlatformDesign affyQCReport simpleaffy made4 "0.99.20" "1.12.0" "2.8.0" "1.8.0" scatterplot3d ade4 affyPLM gcrma "0.3-24" "1.4-2" "1.10.0" "2.6.0" matchprobes affydata affycoretools biomaRt "1.6.0" "1.10.0" "1.6.0" "1.8.0" RCurl XML GOstats Category "0.8-0" "1.2-0" "2.0.4" "2.0.3" genefilter survival KEGG RBGL "1.12.0" "2.29" "1.14.1" "1.10.0" annotate GO graph limma "1.12.0" "1.14.1" "1.12.0" "2.9.1" affy affyio Biobase "1.12.1" "1.2.0" "1.12.2" > Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu
GO Survival annotate genefilter affy affydata matchprobes affyQCReport affyio oligo GO • 1.0k views
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Xinxia Peng ▴ 120
@xinxia-peng-1881
Last seen 7.7 years ago
Hi Jenny, Under Linux, you can install a local copy of both R and related packages yourself anywhere inside your home directory. I got both packages installed. Best, Xinxia -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of drnevich at uiuc.edu Sent: Thursday, February 08, 2007 11:44 AM To: bioconductor at stat.math.ethz.ch; bcarvalh at jhsph.edu Subject: [BioC] oligo on R 2.4.1? Hi again, I'm having trouble making a data package for my Affy tiling array - it's not related to the arguments for makePDpackages, but because of memory limitations and the inability to install the oligo package on R 2.4.0. I have R 2.5.0 (the devel. version) installed on my PC, along with all the necessary compilers, but I don't have enough memory to make the package. I also have access to R on a server with more memory, but it's only R 2.4.0 and I doubt I could get them to install R 2.5.0 on it until it's the released version. R CMD INSTALL failed for the oligo package because it says it requires 2.5.0, but the makePlatformDesign package installed fine. I thought I would be able to make the package on the server then install it back on my PC, but according to the warnings and errors below, the oligo package is required. Is there any way for me to get around this, or am I SOL? :) Jenny > library(makePlatformDesign) Loading required package: oligo Attaching package: 'makePlatformDesign' The following object(s) are masked from package:matchprobes : complementSeq The following object(s) are masked from package:matchprobes : longestConsecutive The following object(s) are masked from package:matchprobes : matchprobes The following object(s) are masked from package:matchprobes : reverseSeq Warning messages: 1: there is no package called 'oligo' in: library(package, lib.loc = lib.loc, character.only = TRUE, logical = TRUE, 2: The oligo package could not be loaded thus the platformDesign class is not defined. in: f(libname, pkgname) > > > > makePDpackage("Mm_PromPR_v01_NCBIv35.bpmap", type="tiling", > genomebuild="mg33") affymetrix tiling The package will be called pdmmpromprv01ncbiv35 Array identified as having 914 rows and 914 columns. Error in getClass(Class, where = topenv(parent.frame())) : "platformDesign" is not a defined class > > sessionInfo() R version 2.4.0 (2006-10-03) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .U TF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UT F- 8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_ ID ENTIFICATION=C attached base packages: [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" [7] "utils" "datasets" "base" other attached packages: makePlatformDesign affyQCReport simpleaffy made4 "0.99.20" "1.12.0" "2.8.0" "1.8.0" scatterplot3d ade4 affyPLM gcrma "0.3-24" "1.4-2" "1.10.0" "2.6.0" matchprobes affydata affycoretools biomaRt "1.6.0" "1.10.0" "1.6.0" "1.8.0" RCurl XML GOstats Category "0.8-0" "1.2-0" "2.0.4" "2.0.3" genefilter survival KEGG RBGL "1.12.0" "2.29" "1.14.1" "1.10.0" annotate GO graph limma "1.12.0" "1.14.1" "1.12.0" "2.9.1" affy affyio Biobase "1.12.1" "1.2.0" "1.12.2" > Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 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
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 7.7 years ago
<drnevich at="" uiuc.edu=""> writes: > Hi again, > > I'm having trouble making a data package for my Affy tiling array - > it's not related to the arguments for makePDpackages, but because of > memory limitations and the inability to install the oligo package on R > 2.4.0. I have R 2.5.0 (the devel. version) installed on my PC, along > with all the necessary compilers, but I don't have enough memory to > make the package. I also have access to R on a server with more > memory, but it's only R 2.4.0 and I doubt I could get them to install > R 2.5.0 on it until it's the released version. R CMD INSTALL failed > for the oligo package because it says it requires 2.5.0, but the > makePlatformDesign package installed fine. I thought I would be able > to make the package on the server then install it back on my PC, but > according to the warnings and errors below, the oligo package is > required. Is there any way for me to get around this, or am I SOL? > > :) Jenny If you have a shell account on the server, you can install your own R-2.5 from source in your home directory. This isn't as difficult as it sounds (famous last words). + seth
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Jenny Drnevich ★ 2.2k
@jenny-drnevich-382
Last seen 7.7 years ago
Thanks Jim, Xinxia and Seth for the good suggestion! I wondered about doing it, and Jim's line-by-line directions were VERY helpful. Everything appeared to configure and build correctly, but adding "export PATH=/home/jdrnevich/R-devel/bin:$PATH" to my .bashrc file is not working to find my local install of R. Any other suggestions of what to try? Thanks, Jenny ---- Original message ---- >Date: Thu, 08 Feb 2007 15:13:17 -0500 >From: "James W. MacDonald" <jmacdon at="" med.umich.edu=""> >Subject: Re: [BioC] oligo on R 2.4.1? >To: drnevich at uiuc.edu >Cc: bioconductor at stat.math.ethz.ch > >Hi Jenny, > >drnevich at uiuc.edu wrote: >> Hi again, >> >> I'm having trouble making a data package for my Affy tiling array - >> it's not related to the arguments for makePDpackages, but because of >> memory limitations and the inability to install the oligo package on >> R 2.4.0. I have R 2.5.0 (the devel. version) installed on my PC, >> along with all the necessary compilers, but I don't have enough >> memory to make the package. I also have access to R on a server with >> more memory, but it's only R 2.4.0 and I doubt I could get them to >> install R 2.5.0 on it until it's the released version. R CMD INSTALL >> failed for the oligo package because it says it requires 2.5.0, but >> the makePlatformDesign package installed fine. I thought I would be >> able to make the package on the server then install it back on my PC, >> but according to the warnings and errors below, the oligo package is >> required. Is there any way for me to get around this, or am I SOL? > >I doubt you are SOL, unless the sysadmin has restricted your home >directory to a thimbleful of disk. If you have a reasonable amount of >disk space you can simply download the current devel version of R (the >tar.gz), then configure and build right in your home directory. > >You don't have to go any farther than > >tar xvfz R-devel_blahblahblah.tar.gz >cd R-devel >./configure >make > >Then maybe add > >export PATH=/home/jdrnevich/R-devel/bin:$PATH > >to your .bashrc file so you will find your local R install first. >Alternatively you can set your init.el file to use that directory if you >use emacs for running R. > >You can then fire up your new R-devel, run biocLite() and rock on! > >Best, > >Jim > > >> >> :) Jenny >> >> >> >>> library(makePlatformDesign) >> >> Loading required package: oligo >> >> Attaching package: 'makePlatformDesign' >> >> >> The following object(s) are masked from package:matchprobes : >> >> complementSeq >> >> The following object(s) are masked from package:matchprobes : >> >> longestConsecutive >> >> The following object(s) are masked from package:matchprobes : >> >> matchprobes >> >> The following object(s) are masked from package:matchprobes : >> >> reverseSeq >> >> Warning messages: 1: there is no package called 'oligo' in: >> library(package, lib.loc = lib.loc, character.only = TRUE, logical = >> TRUE, 2: The oligo package could not be loaded thus the >> platformDesign class is not defined. in: f(libname, pkgname) >> >>> >>> >>> makePDpackage("Mm_PromPR_v01_NCBIv35.bpmap", type="tiling", >>> genomebuild="mg33") >> >> affymetrix tiling The package will be called pdmmpromprv01ncbiv35 >> Array identified as having 914 rows and 914 columns. Error in >> getClass(Class, where = topenv(parent.frame())) : "platformDesign" is >> not a defined class >> >>> sessionInfo() >> >> R version 2.4.0 (2006-10-03) x86_64-unknown-linux-gnu >> >> locale: >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en _US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_ US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UT F-8;LC_IDENTIFICATION=C >> >> >> attached base packages: [1] "splines" "tools" "methods" >> "stats" "graphics" "grDevices" [7] "utils" "datasets" >> "base" >> >> other attached packages: makePlatformDesign affyQCReport >> simpleaffy made4 "0.99.20" "1.12.0" >> "2.8.0" "1.8.0" scatterplot3d ade4 >> affyPLM gcrma "0.3-24" "1.4-2" >> "1.10.0" "2.6.0" matchprobes affydata >> affycoretools biomaRt "1.6.0" "1.10.0" >> "1.6.0" "1.8.0" RCurl XML >> GOstats Category "0.8-0" "1.2-0" >> "2.0.4" "2.0.3" genefilter survival >> KEGG RBGL "1.12.0" "2.29" >> "1.14.1" "1.10.0" annotate GO >> graph limma "1.12.0" "1.14.1" >> "1.12.0" "2.9.1" affy affyio >> Biobase "1.12.1" "1.2.0" "1.12.2" >> >> >> >> Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist >> Roy J. Carver Biotechnology Center University of Illinois, >> Urbana-Champaign >> >> 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 >> >> 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. Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu
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drnevich at uiuc.edu wrote: > Thanks Jim, Xinxia and Seth for the good suggestion! I wondered about > doing it, and Jim's line-by-line directions were VERY helpful. > Everything appeared to configure and build correctly, but adding > "export PATH=/home/jdrnevich/R-devel/bin:$PATH" to my .bashrc file is > not working to find my local install of R. Any other suggestions of > what to try? I usually just get all red in the face and kick it a couple of times, and then things start to work ;-D Did you add the path to your .bashrc and _then_ open a shell, or are you using an existing shell? Your .bashrc file is only read when you open a shell, so if you have an existing one, it won't see the new path. On *nix I find emacs/ess to be the only way to go, even if it requires lots of teeth gnashing at the outset. Best, Jim > > Thanks, Jenny > > ---- Original message ---- > >> Date: Thu, 08 Feb 2007 15:13:17 -0500 From: "James W. MacDonald" >> <jmacdon at="" med.umich.edu=""> Subject: Re: [BioC] oligo on R 2.4.1? To: >> drnevich at uiuc.edu Cc: bioconductor at stat.math.ethz.ch >> >> Hi Jenny, >> >> drnevich at uiuc.edu wrote: >> >>> Hi again, >>> >>> I'm having trouble making a data package for my Affy tiling array >>> - it's not related to the arguments for makePDpackages, but >>> because of memory limitations and the inability to install the >>> oligo package on R 2.4.0. I have R 2.5.0 (the devel. version) >>> installed on my PC, along with all the necessary compilers, but I >>> don't have enough memory to make the package. I also have access >>> to R on a server with more memory, but it's only R 2.4.0 and I >>> doubt I could get them to install R 2.5.0 on it until it's the >>> released version. R CMD INSTALL failed for the oligo package >>> because it says it requires 2.5.0, but the makePlatformDesign >>> package installed fine. I thought I would be able to make the >>> package on the server then install it back on my PC, but >>> according to the warnings and errors below, the oligo package is >>> required. Is there any way for me to get around this, or am I >>> SOL? >> >> I doubt you are SOL, unless the sysadmin has restricted your home >> directory to a thimbleful of disk. If you have a reasonable amount >> of disk space you can simply download the current devel version of >> R (the tar.gz), then configure and build right in your home >> directory. >> >> You don't have to go any farther than >> >> tar xvfz R-devel_blahblahblah.tar.gz cd R-devel ./configure make >> >> Then maybe add >> >> export PATH=/home/jdrnevich/R-devel/bin:$PATH >> >> to your .bashrc file so you will find your local R install first. >> Alternatively you can set your init.el file to use that directory >> if you use emacs for running R. >> >> You can then fire up your new R-devel, run biocLite() and rock on! >> >> Best, >> >> Jim >> >> >> >>> :) Jenny >>> >>> >>> >>> >>>> library(makePlatformDesign) >>> >>> Loading required package: oligo >>> >>> Attaching package: 'makePlatformDesign' >>> >>> >>> The following object(s) are masked from package:matchprobes : >>> >>> complementSeq >>> >>> The following object(s) are masked from package:matchprobes : >>> >>> longestConsecutive >>> >>> The following object(s) are masked from package:matchprobes : >>> >>> matchprobes >>> >>> The following object(s) are masked from package:matchprobes : >>> >>> reverseSeq >>> >>> Warning messages: 1: there is no package called 'oligo' in: >>> library(package, lib.loc = lib.loc, character.only = TRUE, >>> logical = TRUE, 2: The oligo package could not be loaded thus the >>> platformDesign class is not defined. in: f(libname, pkgname) >>> >>> >>>> >>>> makePDpackage("Mm_PromPR_v01_NCBIv35.bpmap", type="tiling", >>>> genomebuild="mg33") >>> >>> affymetrix tiling The package will be called pdmmpromprv01ncbiv35 >>> Array identified as having 914 rows and 914 columns. Error in >>> getClass(Class, where = topenv(parent.frame())) : >>> "platformDesign" is not a defined class >>> >>> >>>> sessionInfo() >>> >>> R version 2.4.0 (2006-10-03) x86_64-unknown-linux-gnu >>> >>> locale: >>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=e n_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en _US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.U TF-8;LC_IDENTIFICATION=C >>> >>> >>> >>> attached base packages: [1] "splines" "tools" "methods" >>> "stats" "graphics" "grDevices" [7] "utils" "datasets" >>> "base" >>> >>> other attached packages: makePlatformDesign affyQCReport >>> simpleaffy made4 "0.99.20" "1.12.0" >>> "2.8.0" "1.8.0" scatterplot3d ade4 >>> affyPLM gcrma "0.3-24" "1.4-2" "1.10.0" >>> "2.6.0" matchprobes affydata affycoretools >>> biomaRt "1.6.0" "1.10.0" "1.6.0" "1.8.0" >>> RCurl XML GOstats Category "0.8-0" >>> "1.2-0" "2.0.4" "2.0.3" genefilter survival >>> KEGG RBGL "1.12.0" "2.29" "1.14.1" >>> "1.10.0" annotate GO graph limma >>> "1.12.0" "1.14.1" "1.12.0" "2.9.1" affy >>> affyio Biobase "1.12.1" "1.2.0" "1.12.2" >>> >>> >>> >>> Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics >>> Specialist Roy J. Carver Biotechnology Center University of >>> Illinois, Urbana-Champaign >>> >>> 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 >>> >>> 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. > > Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist > Roy J. Carver Biotechnology Center University of Illinois, > Urbana-Champaign > > 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 > > ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu -- 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.
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Dear Jenny, > Thanks Jim, Xinxia and Seth for the good suggestion! I wondered about > doing it, and Jim's line-by-line directions were VERY helpful. > Everything appeared to configure and build correctly, but adding > "export PATH=/home/jdrnevich/R-devel/bin:$PATH" to my .bashrc file is > not working to find my local install of R. Any other suggestions of > what to try? As an alternative to editing PATH, I find it convenient to create a little file (shell script) in my $HOME/bin directory, of the name "R" and with contents like #!/bin/sh exec /home/huber/R-2.4.1/bin/R $* On many systems, $HOME/bin is already in the PATH. That way you can easily juggle between different versions of R, set environment variables like "LD_LIBRARY_PATH" locally just for this R (not interfering with other software), prepend "nice -n 19" etc. Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
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Last seen 4 hours ago
United States
Hi Jenny, drnevich at uiuc.edu wrote: > Hi again, > > I'm having trouble making a data package for my Affy tiling array - > it's not related to the arguments for makePDpackages, but because of > memory limitations and the inability to install the oligo package on > R 2.4.0. I have R 2.5.0 (the devel. version) installed on my PC, > along with all the necessary compilers, but I don't have enough > memory to make the package. I also have access to R on a server with > more memory, but it's only R 2.4.0 and I doubt I could get them to > install R 2.5.0 on it until it's the released version. R CMD INSTALL > failed for the oligo package because it says it requires 2.5.0, but > the makePlatformDesign package installed fine. I thought I would be > able to make the package on the server then install it back on my PC, > but according to the warnings and errors below, the oligo package is > required. Is there any way for me to get around this, or am I SOL? I doubt you are SOL, unless the sysadmin has restricted your home directory to a thimbleful of disk. If you have a reasonable amount of disk space you can simply download the current devel version of R (the tar.gz), then configure and build right in your home directory. You don't have to go any farther than tar xvfz R-devel_blahblahblah.tar.gz cd R-devel ./configure make Then maybe add export PATH=/home/jdrnevich/R-devel/bin:$PATH to your .bashrc file so you will find your local R install first. Alternatively you can set your init.el file to use that directory if you use emacs for running R. You can then fire up your new R-devel, run biocLite() and rock on! Best, Jim > > :) Jenny > > > >> library(makePlatformDesign) > > Loading required package: oligo > > Attaching package: 'makePlatformDesign' > > > The following object(s) are masked from package:matchprobes : > > complementSeq > > The following object(s) are masked from package:matchprobes : > > longestConsecutive > > The following object(s) are masked from package:matchprobes : > > matchprobes > > The following object(s) are masked from package:matchprobes : > > reverseSeq > > Warning messages: 1: there is no package called 'oligo' in: > library(package, lib.loc = lib.loc, character.only = TRUE, logical = > TRUE, 2: The oligo package could not be loaded thus the > platformDesign class is not defined. in: f(libname, pkgname) > >> >> >> makePDpackage("Mm_PromPR_v01_NCBIv35.bpmap", type="tiling", >> genomebuild="mg33") > > affymetrix tiling The package will be called pdmmpromprv01ncbiv35 > Array identified as having 914 rows and 914 columns. Error in > getClass(Class, where = topenv(parent.frame())) : "platformDesign" is > not a defined class > >> sessionInfo() > > R version 2.4.0 (2006-10-03) x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF -8;LC_IDENTIFICATION=C > > > attached base packages: [1] "splines" "tools" "methods" > "stats" "graphics" "grDevices" [7] "utils" "datasets" > "base" > > other attached packages: makePlatformDesign affyQCReport > simpleaffy made4 "0.99.20" "1.12.0" > "2.8.0" "1.8.0" scatterplot3d ade4 > affyPLM gcrma "0.3-24" "1.4-2" > "1.10.0" "2.6.0" matchprobes affydata > affycoretools biomaRt "1.6.0" "1.10.0" > "1.6.0" "1.8.0" RCurl XML > GOstats Category "0.8-0" "1.2-0" > "2.0.4" "2.0.3" genefilter survival > KEGG RBGL "1.12.0" "2.29" > "1.14.1" "1.10.0" annotate GO > graph limma "1.12.0" "1.14.1" > "1.12.0" "2.9.1" affy affyio > Biobase "1.12.1" "1.2.0" "1.12.2" > > > > Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist > Roy J. Carver Biotechnology Center University of Illinois, > Urbana-Champaign > > 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 > > 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.
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Jenny Drnevich ★ 2.2k
@jenny-drnevich-382
Last seen 7.7 years ago
Hi Seth, Yes, I did log out and back... I'll have to ask my sys admin when he gets back on Monday. The local call worked - thanks! People like me who don't really know how computers work need detailed instructions :) Jenny At 03:33 PM 2/8/2007, Seth Falcon wrote: ><drnevich at="" uiuc.edu=""> writes: > > > Thanks Jim, Xinxia and Seth for the good suggestion! I wondered about > > doing it, and Jim's line-by-line directions were VERY > > helpful. Everything appeared to configure and build correctly, but > > adding "export PATH=/home/jdrnevich/R-devel/bin:$PATH" to my .bashrc > > file is not working to find my local install of R. Any other > > suggestions of what to try? > >Did you logout and back after editing .bashrc? > >Anyhow, you should at least be able to call your locally built R using >a full path: > > $ ~/R-devel/bin/R > >+ seth 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
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 7.7 years ago
Wolfgang Huber <huber at="" ebi.ac.uk=""> writes: > As an alternative to editing PATH, I find it convenient to create a > little file (shell script) in my $HOME/bin directory, of the name "R" > and with contents like > > #!/bin/sh > exec /home/huber/R-2.4.1/bin/R $* > > On many systems, $HOME/bin is already in the PATH. That way you can > easily juggle between different versions of R, set environment variables > like "LD_LIBRARY_PATH" locally just for this R (not interfering with > other software), prepend "nice -n 19" etc. I use this approach as well. Since I always have both the current R release and a devel version of R around, I need to keep them straight. So I have scripts ~/bin/R-2.4 and ~/bin/R-2.5 (and a symlink called R for whichever I'm using most often). When running multiple R's it is a good idea to keep your package libraries separate. So I also have ~/RLIB/2.4 and ~/RLIB/2.5. My script is then: #!/bin/bash export R_LIBS=/Users/seth/RLIB/2.5 /Users/seth/proj/builds/R-2.5/bin/R "$@" So when I invoke R-2.5, I get the desired R_LIBS. The use of "$@" is a subtle point, but as I understand it, it keeps the args intact so the script you are calling does expansion, etc. + seth
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