Hello Rafa, Benilton, and others, I didn't get a chance to sit on the "Advancing in Feature-Level Analyses for Microarray Data" workshop[1] while at BioC2006, so I thought I'd try to work from the slides. However, I'm running into some issues, which is not surprising given that I'm new to R and BioConductor. As an example of one issue, I'd like to try out the makePlatformDesign package as explained on slide 56 of the tutorial- slides using our own data. Here is the transcript of the results, where R's working directory is C:/tmp: <quote> 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. > library(makePlatformDesign) Loading required package: affyio Loading required package: oligo Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()' or start with 'help(Biobase)'. For details on reading vignettes, see the openVignette help page. Warning messages: 1: package 'makePlatformDesign' was built under R version 2.4.0 2: package 'affyio' was built under R version 2.4.0 3: package 'oligo' was built under R version 2.4.0 > > makePDpackage("d:/2006-01-30_Orion_ogha2.ndf", + "d:/77786_532.xys", + manufacturer="nimblegen", type="tiling") nimblegen tiling The package will be called pd20060130orionogha2 Reading d:/2006-01-30_Orion_ogha2.ndf Assuming a simple design (NOT multiple-wells). Creating package in C:/tmp/pd20060130orionogha2 [1] "pd20060130orionogha2" > > install.packages("C:/tmp/pd20060130orionogha2", repos=NULL) Error in gzfile(file, "r") : unable to open connection In addition: Warning messages: 1: error 1 in extracting from zip file 2: cannot open compressed file 'pd20060130orionogha2/DESCRIPTION' > <quote> We've googled for the error message "Error in gzfile ..." without any fruitful hits. Any ideas why we are getting this error? Wrong version of R? Wrong version of BioConductor? Wrong configuration? Wrong sequence of commands? Wrong data format? Something else? Trying to install the package from the command line yielded these results: <quote> C:\tmp>R CMD INSTALL pd20060130orionogha2 'R' is not recognized as an internal or external command, operable program or batch file. C:\tmp>path PATH=D:\oracle\ora92\bin;C:\Program Files\Oracle\jre\1.3.1\bin;C: \Program Files\Oracle\jre\1.1.8\bin;C:\WINDOWS\system32;C:\WINDOWS;C: \WINDOWS\System32\Wbem;D:\j2sdk1.4.2_05\bin; </quote> I suspect this is because the path to R needs to specified in the PATH variable. When we explicitly used the path to R, we then got errors about requiring perl. Before we go down the path of missing dependencies (e.g. perl, gcc, and who knows what else) I thought I'd post here to make sure that we were not overlooking the obvious. This is for R running on Windows 2003 server. [1] http://www.bioconductor.org/workshops/2006/BioC2006/labs/bcarvalho/ Regards, - Robert Citek <rwcitek at="" oriongenomics.com="">

Hi Robert, thanks for sharing your experience with us. The slides assumed the use of a Unix-like environment, which often provides compilers and perl. This is not the case when we're working under MS-Windows and therefore I recommend you to take a look at the following pages: http://stat.ethz.ch/R-manual/R-devel/doc/manual/R-admin.html#The- Windows-toolset http://www.murdoch-sutherland.com/Rtools/ They explain how to setup your system so you can build R packages under Windows (I'm sorry for not adding those to the slides). You're doing good so far. You already have the source for your Platform Design environment and building the package as the pages above recommend will give you a ZIP file which you'll be able to install. Please, do not hesitate in contacting me if you get any further questions, cheers, b. On Aug 9, 2006, at 8:19 PM, Robert Citek wrote: > Hello Rafa, Benilton, and others, > > I didn't get a chance to sit on the "Advancing in Feature-Level > Analyses for Microarray Data" workshop[1] while at BioC2006, so I > thought I'd try to work from the slides. However, I'm running into > some issues, which is not surprising given that I'm new to R and > BioConductor. As an example of one issue, I'd like to try out the > makePlatformDesign package as explained on slide 56 of the tutorial- > slides using our own data. Here is the transcript of the results, > where R's working directory is C:/tmp: > > <quote> > 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. > > > library(makePlatformDesign) > Loading required package: affyio > Loading required package: oligo > Loading required package: Biobase > Loading required package: tools > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()' or start with 'help(Biobase)'. For details > on reading vignettes, see the openVignette help page. > > Warning messages: > 1: package 'makePlatformDesign' was built under R version 2.4.0 > 2: package 'affyio' was built under R version 2.4.0 > 3: package 'oligo' was built under R version 2.4.0 > > > > makePDpackage("d:/2006-01-30_Orion_ogha2.ndf", > + "d:/77786_532.xys", > + manufacturer="nimblegen", type="tiling") > nimblegen tiling > The package will be called pd20060130orionogha2 > Reading d:/2006-01-30_Orion_ogha2.ndf > Assuming a simple design (NOT multiple-wells). > Creating package in C:/tmp/pd20060130orionogha2 > [1] "pd20060130orionogha2" > > > > install.packages("C:/tmp/pd20060130orionogha2", repos=NULL) > Error in gzfile(file, "r") : unable to open connection > In addition: Warning messages: > 1: error 1 in extracting from zip file > 2: cannot open compressed file 'pd20060130orionogha2/DESCRIPTION' > > > <quote> > > We've googled for the error message "Error in gzfile ..." without > any fruitful hits. Any ideas why we are getting this error? Wrong > version of R? Wrong version of BioConductor? Wrong > configuration? Wrong sequence of commands? Wrong data format? > Something else? > > Trying to install the package from the command line yielded these > results: > > <quote> > C:\tmp>R CMD INSTALL pd20060130orionogha2 > 'R' is not recognized as an internal or external command, > operable program or batch file. > > C:\tmp>path > PATH=D:\oracle\ora92\bin;C:\Program Files\Oracle\jre\1.3.1\bin;C: > \Program Files\Oracle\jre\1.1.8\bin;C:\WINDOWS\system32;C: > \WINDOWS;C:\WINDOWS\System32\Wbem;D:\j2sdk1.4.2_05\bin; > </quote> > > I suspect this is because the path to R needs to specified in the > PATH variable. When we explicitly used the path to R, we then got > errors about requiring perl. Before we go down the path of missing > dependencies (e.g. perl, gcc, and who knows what else) I thought > I'd post here to make sure that we were not overlooking the obvious. > > This is for R running on Windows 2003 server. > > [1] http://www.bioconductor.org/workshops/2006/BioC2006/labs/ > bcarvalho/ > > Regards, > - Robert Citek <rwcitek at="" oriongenomics.com="">