Question: recipe for installing and using Bioconductor with Mac OS X 10.3 and R GUI 1.9
0
gravatar for Marc Salit
15.5 years ago by
Marc Salit80
Marc Salit80 wrote:
Dear Colleagues -- I've been trying unsuccessfully to use Bioconductor (mostly the affy package) on a Mac with OS X 10.3.3, running R with a GUI, either 1.8.1 or 1.9.0 beta. I've tried to install Bioconductor with getBioC.R, which doesn't work all the way, and also tried to use a shell command to install downloaded packages, a la R CMD INSTALL /path/to/pkg_version.tar.gz , which also doesn't work all the way (stops when it can't find a 'make' command in SHLIB. Suggestions? Caveats? Will this work? Shall I give up and 'switch' back to a PC??? Cheers & TIA, Marc Salit -- Dr. Marc Salit Research Chemist NIST Chemical Science and Technology Laboratory 100 Bureau Drive, Stop 8391 Gaithersburg, MD 20899-8391 email: Salit@NIST.gov voice: +1 301 975-3646 fax: +1 301 869-0413 -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 897 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040413/723b395c/attachment.bin
gui • 853 views
ADD COMMENTlink modified 15.5 years ago • written 15.5 years ago by Marc Salit80
Answer: recipe for installing and using Bioconductor with Mac OS X 10.3 and R GUI 1.9
0
gravatar for Kasper Daniel Hansen
15.5 years ago by
Kasper Daniel Hansen630 wrote:
On Tue, Apr 13, 2004 at 05:15:51PM -0400, Marc Salit wrote: > I've been trying unsuccessfully to use Bioconductor (mostly the affy > package) on a Mac with OS X 10.3.3, running R with a GUI, either 1.8.1 > or 1.9.0 beta. I've tried to install Bioconductor with getBioC.R, which > doesn't work all the way, and also tried to use a shell command to > install downloaded packages, a la R CMD INSTALL > /path/to/pkg_version.tar.gz , which also doesn't work all the way > (stops when it can't find a 'make' command in SHLIB. You do not gives us much to work with here. While not a Mac user myself, it would help if we could see the output from the failed build. However, it seems you have problems building some C code. Have you installed the packages mentioned in the R for MacOS FAQ from the R-project/CRAN homepage? -- Kasper Daniel Hansen, Research Assistant Department of Biostatistics, University of Copenhagen
ADD COMMENTlink written 15.5 years ago by Kasper Daniel Hansen630
Answer: recipe for installing and using Bioconductor with Mac OS X 10.3 and R GUI 1.9
0
gravatar for Simon Kidd
15.5 years ago by
Simon Kidd180
Simon Kidd180 wrote:
At 5.15pm -0400 13/4/04, Marc Salit wrote: >Dear Colleagues -- > >I've been trying unsuccessfully to use Bioconductor (mostly the affy >package) on a Mac with OS X 10.3.3, running R with a GUI, either >1.8.1 or 1.9.0 beta. I've tried to install Bioconductor with >getBioC.R, which doesn't work all the way, and also tried to use a >shell command to install downloaded packages, a la R CMD INSTALL >/path/to/pkg_version.tar.gz , which also doesn't work all the way >(stops when it can't find a 'make' command in SHLIB. > >Suggestions? Caveats? Will this work? Shall I give up and 'switch' >back to a PC??? Ive installed R1.9 beta from : <http: www.economia.unimi.it="" r=""/> and then used its gui to install the Bioconductor Affy (and a few others) packages. Other than some problems with tcltk and limmaGUI and what I think is a different problem with simpleaffy things have worked (as much as I can tell). This is with OSX10.3.3, and the X11 and the developer tools which came with it. Simon
ADD COMMENTlink written 15.5 years ago by Simon Kidd180
On Tue, 13 Apr 2004, Simon Kidd wrote: ... > others) packages. Other than some problems with tcltk and limmaGUI ... Yes, last time I installed limmaGUI on Mac OS X, it certainly took some effort. One issue with Mac OS X is that there are two different tcltk's : Aqua Tcl/Tk and X11 Tcl/Tk, and they are not compatible. So if you are installing the Tcl/Tk extensions requied by limmaGUI (Tktable and BWidget) you have to be careful you don't mix these Tcl/Tk versions, otherwise you will get strange errors like "undefined systemWindowBody color". To see your Tcl/Tk search path, type : library(tcltk) tclvalue("auto_path") I think the R-Mac experts (Jan de Leeuw, Stefano Iacus etc.) have been working pretty hard to make the R-Tcl/Tk stuff easier to install on OS X. While I don't use a Mac regularly, I do have access to Macs so if anyone has any specific questions about installing limmaGUI on OS X, I'd be happy to help. There are a few rough notes on http://bioinf.wehi.edu.au/limmaGUI/ Regards, James
ADD REPLYlink written 15.5 years ago by James Wettenhall1000
Answer: recipe for installing and using Bioconductor with Mac OS X 10.3 and R GUI 1.9
0
gravatar for Floor Stam
15.5 years ago by
Floor Stam90
Floor Stam90 wrote:
...and make sure you have the Xtools installed. Affy and some other packages like xml do not install without them. floor > Dear Colleagues -- > > I've been trying unsuccessfully to use Bioconductor (mostly the affy > package) on a Mac with OS X 10.3.3, running R with a GUI, either 1.8.1 > or 1.9.0 beta. I've tried to install Bioconductor with getBioC.R, > which doesn't work all the way, and also tried to use a shell command > to install downloaded packages, a la R CMD INSTALL > /path/to/pkg_version.tar.gz , which also doesn't work all the way > (stops when it can't find a 'make' command in SHLIB. > > Suggestions? Caveats? Will this work? Shall I give up and 'switch' > back to a PC??? > > Cheers & TIA, > Marc Salit > > -- > Dr. Marc Salit > Research Chemist > NIST > Chemical Science and Technology Laboratory > 100 Bureau Drive, Stop 8391 > Gaithersburg, MD 20899-8391 > email: Salit@NIST.gov > voice: +1 301 975-3646 > fax: +1 301 869-0413_______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1211 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040414/ce1f4f12/attachment.bin
ADD COMMENTlink written 15.5 years ago by Floor Stam90
Answer: recipe for installing and using Bioconductor with Mac OS X 10.3 and R GUI 1.9
0
gravatar for Marc Salit
15.5 years ago by
Marc Salit80
Marc Salit80 wrote:
Dear Colleagues -- Thanks for the hints, though I'm still stuck. Here's what happens when I run the R 1.9.0 Beta GUI and go to the Packages menu, and try to download the affy bundle from the Bioconductor sub-menu: > local({source(paste(getOption('BIOC'), 'getBioC.R',sep='/'), local=TRUE); getBioC('affy', destdir=.libPaths()[1])}) Running getBioC version 1.2.54.... If you encounter problems, first make sure that you are running the latest version of getBioC() which can be found at: www.bioconductor.org/getBioC.R Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. Loading required package: reposTools [1] "Attempting to download genefilter from http://www.bioconductor.org/repository/release1.3/package/Source" [1] "Download complete." [1] "Installing genefilter" [1] "Attempting to download multtest from http://www.bioconductor.org/repository/release1.3/package/Source" [1] "Download complete." [1] "Installing multtest" Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users [1] "Attempting to download XML from http://www.bioconductor.org//CRANrepository" [1] "Download complete." [1] "Installing XML" Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users [1] "Attempting to download XML from http://www.bioconductor.org//CRANrepository" [1] "Download complete." [1] "Installing XML" [1] "Attempting to download MAGEML from http://www.bioconductor.org/repository/release1.3/package/Source" [1] "Download complete." [1] "Installing MAGEML" [1] "Attempting to download affyPLM from http://www.bioconductor.org/repository/release1.3/package/Source" [1] "Download complete." [1] "Installing affyPLM" [1] "Attempting to download matchprobes from http://www.bioconductor.org/repository/release1.3/package/Source" [1] "Download complete." [1] "Installing matchprobes" [1] "Attempting to download makecdfenv from http://www.bioconductor.org/repository/release1.3/package/Source" [1] "Download complete." [1] "Installing makecdfenv" From URL: http://www.bioconductor.org/repository/release1.3/package/Source genefilter version 1.3.1 multtest version 1.3.7 MAGEML version 1.0.6 affyPLM version 1.0.0 matchprobes version 1.0.0 makecdfenv version 1.4.1 From URL: http://www.bioconductor.org//CRANrepository XML version 0.95-6 XML version 0.95-6 Warning messages: 1: 'package.description' is deprecated. Use 'packageDescription' instead. See help("Deprecated") 2: 'package.description' is deprecated. Use 'packageDescription' instead. See help("Deprecated") 3: Installation of package genefilter had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 4: Installation of package multtest had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 5: Installation of package XML had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 6: Installation of package XML had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 7: Installation of package MAGEML had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 8: Installation of package affyPLM had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 9: Installation of package matchprobes had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 10: Installation of package makecdfenv had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) > library(affy) Error: package affy was built for powerpc-apple-darwin7.2.0 > Any ideas??? Thanks in advance, Marc Salit On Apr 13, 2004, at 5:15 PM, Marc Salit wrote: > Dear Colleagues -- > > I've been trying unsuccessfully to use Bioconductor (mostly the affy > package) on a Mac with OS X 10.3.3, running R with a GUI, either 1.8.1 > or 1.9.0 beta. I've tried to install Bioconductor with getBioC.R, > which doesn't work all the way, and also tried to use a shell command > to install downloaded packages, a la R CMD INSTALL > /path/to/pkg_version.tar.gz , which also doesn't work all the way > (stops when it can't find a 'make' command in SHLIB. > > Suggestions? Caveats? Will this work? Shall I give up and 'switch' > back to a PC??? > > Cheers & TIA, > Marc Salit > -- Dr. Marc Salit Research Chemist NIST Chemical Science and Technology Laboratory 100 Bureau Drive, Stop 8391 Gaithersburg, MD 20899-8391 email: Salit@NIST.gov voice: +1 301 975-3646 fax: +1 301 869-0413_______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 5161 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040415/2f6ea23b/attachment.bin
ADD COMMENTlink written 15.5 years ago by Marc Salit80
Answer: recipe for installing and using Bioconductor with Mac OS X 10.3 and R GUI 1.9
0
gravatar for Marc Salit
15.5 years ago by
Marc Salit80
Marc Salit80 wrote:
Dear Colleagues -- A little follow-up is in order -- I've got things going, more or less. Mostly more. Thanks for the suggestions, which mostly got me on track. Bioconductor things seem to work in general, it was the affy package I was having trouble with. I am still having problems with the 'widget' tools, but have received some leads on that (problems with tcltk). Ok, so I'm running R release version Version 1.9.0 (2004-04-12) , on Mac OS X 10.3.3 on a PowerMac G5 2.0 GHz dual processor. Some things that I did in order to get going: 1) I installed the Apple Mac OSX developer's tools, which are needed to compile source. 2) I changed owner and permissions on the R.Framework directory, and everything underneath it to permit r/w access to all users. (From some of the error messages I was receiving, it seemed that this was necessary, though your mileage may vary...) 3) I downloaded the development version of the affy package (affy_1.4.23.tar.gz) and installed from the command line. The 'released' version (affy_1.3.28.tar.gz) would not install this way, it died while building help for normalize.invariantset (see below). normalize.contrast text html latex example normalize.invariantset text html latex ERROR: command (e.g. \url) inside \link ERROR: building help failed for package 'affy' ** Removing '/Library/Frameworks/R.framework/Versions/1.9.0/Resources/library/affy ' And, my problems with tcltk: > package.manager() loading package: widgetTools Loading required package: tcltk Error in fun(...) : this isn't a Tk applicationcouldn't connect to display ":0" Error: .onLoad failed in loadNamespace Error in f(libname, pkgname) : Package tcltk not able to be loaded! Error in library(pkgs[i], character.only = TRUE) : .First.lib failed > dchip <- expresso(widget=TRUE) Loading required package: tkWidgets Error in expresso(widget = TRUE) : library tkWidgets could not be found ! In addition: Warning message: There is no package called 'tkWidgets' in: library(package, character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts, > package.manager() loading package: tcltk Error in fun(...) : this isn't a Tk applicationcouldn't connect to display ":0" Error: .onLoad failed in loadNamespace Error in library(pkgs[i], character.only = TRUE) : package/namespace load failed Best regards, Marc Salit On Apr 13, 2004, at 5:15 PM, Marc Salit wrote: > Dear Colleagues -- > > I've been trying unsuccessfully to use Bioconductor (mostly the affy > package) on a Mac with OS X 10.3.3, running R with a GUI, either 1.8.1 > or 1.9.0 beta. I've tried to install Bioconductor with getBioC.R, > which doesn't work all the way, and also tried to use a shell command > to install downloaded packages, a la R CMD INSTALL > /path/to/pkg_version.tar.gz , which also doesn't work all the way > (stops when it can't find a 'make' command in SHLIB. > > Suggestions? Caveats? Will this work? Shall I give up and 'switch' > back to a PC??? > > Cheers & TIA, > Marc Salit > > -- > Dr. Marc Salit > Research Chemist > NIST > Chemical Science and Technology Laboratory > 100 Bureau Drive, Stop 8391 > Gaithersburg, MD 20899-8391 > email: Salit@NIST.gov > voice: +1 301 975-3646 > fax: +1 301 869-0413_______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 3825 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040421/54479d8c/attachment-0001.bin
ADD COMMENTlink written 15.5 years ago by Marc Salit80
Patient Colleagues -- Further follow-up, thanks mostly to Robert Gentleman and Stefano Iacus... It was suggested that I not live with the permissions open in the R framework (because of the security holes that leaves), and that I take another shot at installing the latest version of R GUI for the Mac and the packages as pre-compiled binaries. I dragged the permission- changed R.framework directory tree to the trash, emptied the trash, and started over with the fresh package. Slightly longer story made short: this all worked. I installed the package from the CRAN website, and then used the menu option Packages|Bioconductor|Individual Packages|Ready-to-use Binary to install biobase, affy, and the widget tools. Then I ran the X windows server in Mac OS X (to accommodate the Tcl/tk stuff) before calling expresso with widget=TRUE. Viola. Thanks for the help. Now to converge on some consistent, credible, coherent expression measures... Best regards, Marc Salit -- Dr. Marc Salit Research Chemist NIST Chemical Science and Technology Laboratory 100 Bureau Drive, Stop 8391 Gaithersburg, MD 20899-8391 email: Salit domain NIST.gov voice: +1 301 975-3646 fax: +1 301 869-0413 On Apr 21, 2004, at 6:43 PM, Marc Salit wrote: > Dear Colleagues -- > > A little follow-up is in order -- I've got things going, more or less. > Mostly more. Thanks for the suggestions, which mostly got me on track. > Bioconductor things seem to work in general, it was the affy package > I was having trouble with. I am still having problems with the > 'widget' tools, but have received some leads on that (problems with > tcltk). > > Ok, so I'm running R release version Version 1.9.0 (2004-04-12) , on > Mac OS X 10.3.3 on a PowerMac G5 2.0 GHz dual processor. > > Some things that I did in order to get going: > 1) I installed the Apple Mac OSX developer's tools, which are needed > to compile source. > > 2) I changed owner and permissions on the R.Framework directory, and > everything underneath it to permit r/w access to all users. (From some > of the error messages I was receiving, it seemed that this was > necessary, though your mileage may vary...) > > 3) I downloaded the development version of the affy package > (affy_1.4.23.tar.gz) and installed from the command line. The > 'released' version (affy_1.3.28.tar.gz) would not install this way, it > died while building help for normalize.invariantset (see below). > > normalize.contrast text html latex example > normalize.invariantset text html latex > > ERROR: command (e.g. \url) inside \link > ERROR: building help failed for package 'affy' > ** Removing > '/Library/Frameworks/R.framework/Versions/1.9.0/Resources/library/ > affy' > > And, my problems with tcltk: > > > package.manager() > loading package: widgetTools > Loading required package: tcltk > Error in fun(...) : this isn't a Tk applicationcouldn't connect to > display ":0" > Error: .onLoad failed in loadNamespace > Error in f(libname, pkgname) : Package tcltk not able to be loaded! > Error in library(pkgs[i], character.only = TRUE) : > .First.lib failed > > dchip <- expresso(widget=TRUE) > Loading required package: tkWidgets > Error in expresso(widget = TRUE) : library tkWidgets could not be > found ! > In addition: Warning message: > There is no package called 'tkWidgets' in: library(package, > character.only = TRUE, logical = TRUE, warn.conflicts = > warn.conflicts, > > package.manager() > loading package: tcltk > Error in fun(...) : this isn't a Tk applicationcouldn't connect to > display ":0" > Error: .onLoad failed in loadNamespace > Error in library(pkgs[i], character.only = TRUE) : > package/namespace load failed > > Best regards, > Marc Salit > > On Apr 13, 2004, at 5:15 PM, Marc Salit wrote: > >> Dear Colleagues -- >> >> I've been trying unsuccessfully to use Bioconductor (mostly the affy >> package) on a Mac with OS X 10.3.3, running R with a GUI, either >> 1.8.1 or 1.9.0 beta. I've tried to install Bioconductor with >> getBioC.R, which doesn't work all the way, and also tried to use a >> shell command to install downloaded packages, a la R CMD INSTALL >> /path/to/pkg_version.tar.gz , which also doesn't work all the way >> (stops when it can't find a 'make' command in SHLIB. >> >> Suggestions? Caveats? Will this work? Shall I give up and 'switch' >> back to a PC??? >> >> Cheers & TIA, >> Marc Salit >> >> -- >> Dr. Marc Salit >> Research Chemist >> NIST >> Chemical Science and Technology Laboratory >> 100 Bureau Drive, Stop 8391 >> Gaithersburg, MD 20899-8391 >> email: Salit@NIST.gov >> voice: +1 301 975-3646 >> fax: +1 301 869-0413_______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 5364 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040422/ea79ed40/attachment.bin
ADD REPLYlink written 15.5 years ago by Marc Salit80
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 310 users visited in the last hour