Hi all, I'm following the directions at: http://www.bioconductor.org/repository/devel/vignette/makecdfenv.pdf to try to make a CDF for the RAE230A chip, and running into some troubles. Running make.cdf.env itself works fine, but when I try to install it with rcmd INSTALL rae230acdf from a DOS prompt I get the error: 'make' is not recognized as an internal or external command, operable program or batch file. *** Installation of rae230acdf failed *** That's a reasonable error, as I do not have a C-compiler available to me. Do I have any work-arounds or other options to get this working, or am I pretty well stuck? Paul OS: win2k (SP3) R: 1.7.0 BioConductor 1.2 ---------------------------------------- This mail sent through www.mywaterloo.ca

You would need some additional tools to get it working. One is "http://www.stats.ox.ac.uk/pub/Rtools/tools.zip". Another one is "http://prdownloads.sourceforge.net/mingw/MinGW-2.0.0-3.exe" and this is the correct compiler we are supposed to use. Follow the instruction at http://www.stats.ox.ac.uk/pub/Rtools/. I got it working successfully with our custom cdf files. In case it is a mistypo, the command in DOS should be Rcmd INSTALL rae230acdf. This first R should be capitalized. wenqiong -----Original Message----- From: Paul Boutros [mailto:pcboutro@engmail.uwaterloo.ca] Sent: Tuesday, June 10, 2003 2:35 PM To: bioconductor@stat.math.ethz.ch Subject: [BioC] Problem using make.cdf.env Hi all, I'm following the directions at: http://www.bioconductor.org/repository/devel/vignette/makecdfenv.pdf to try to make a CDF for the RAE230A chip, and running into some troubles. Running make.cdf.env itself works fine, but when I try to install it with rcmd INSTALL rae230acdf from a DOS prompt I get the error: 'make' is not recognized as an internal or external command, operable program or batch file. *** Installation of rae230acdf failed *** That's a reasonable error, as I do not have a C-compiler available to me. Do I have any work-arounds or other options to get this working, or am I pretty well stuck? Paul OS: win2k (SP3) R: 1.7.0 BioConductor 1.2 ---------------------------------------- This mail sent through www.mywaterloo.ca _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

I contributed the envs to Bioconductor yesterday, so they will probably be on the website soon. I also emailed the win env to Paul. Anybody else who needs the env in the meantime can send me an email. Also, note that DOS is case insensitive, so it doesn't matter if you capitalize or not. Jim James W. MacDonald UMCCC Microarray Core Facility 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> ririzarr@jhsph.edu 06/10/03 10:40PM >>> another alternative is to contribute the package to bioconductor and they will automatically make the windows binary. On Tue, 10 Jun 2003, Wenqiong Chen wrote: > You would need some additional tools to get it working. One is > "http://www.stats.ox.ac.uk/pub/Rtools/tools.zip". Another one is > "http://prdownloads.sourceforge.net/mingw/MinGW-2.0.0-3.exe" and this is the > correct compiler we are supposed to use. > Follow the instruction at http://www.stats.ox.ac.uk/pub/Rtools/. I got it > working successfully with our custom cdf files. > In case it is a mistypo, the command in DOS should be Rcmd INSTALL > rae230acdf. This first R should be capitalized. > wenqiong > > -----Original Message----- > From: Paul Boutros [mailto:pcboutro@engmail.uwaterloo.ca] > Sent: Tuesday, June 10, 2003 2:35 PM > To: bioconductor@stat.math.ethz.ch > Subject: [BioC] Problem using make.cdf.env > > > Hi all, > > I'm following the directions at: > http://www.bioconductor.org/repository/devel/vignette/makecdfenv.pdf > to try to make a CDF for the RAE230A chip, and running into some troubles. > Running make.cdf.env itself works fine, but when I try to install it with > rcmd INSTALL rae230acdf > from a DOS prompt I get the error: > > 'make' is not recognized as an internal or external command, > operable program or batch file. > *** Installation of rae230acdf failed *** > > That's a reasonable error, as I do not have a C-compiler available to me. > Do I > have any work-arounds or other options to get this working, or am I pretty > well > stuck? > > Paul > > OS: win2k (SP3) > R: 1.7.0 > BioConductor 1.2 > > ---------------------------------------- > This mail sent through www.mywaterloo.ca > > _______________________________________________ > 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 > _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

Hello Jim, I received your email from the Bioconductor mailing list. Can you email me the win env? I am having the same difficulty in creating the makecdfenv for our propriety chip. Thank you Lisa Lisa Devereaux B.App Sci (Hons) Biotechnician GENETRAKS PTY LTD Email: <mailto:lisa.d@genetraks.com> lisa.d@genetraks.com Website: <http: www.genetraks.com=""/> www.genetraks.com Level 1, 80 Jephson Street PO Box 2060 Toowong QLD 4006 Australia Tel: 61 7 3327 9822 Fax: 61 7 3719 5499 Confidentiality: The contents of this email are confidential and are intended only for the named recipient. If the reader of this e-mail is not the intended recipient you are hereby notified that any use, reproduction, disclosure or distribution of the information contained in the e-mail is prohibited. If you have received this e-mail in error, please reply to us immediately and delete the document and any attachments. [[alternative HTML version deleted]]

Which win env do you need? If you are using a proprietary chip designed for you by Affymetrix, then none of the envs that I have contributed will work. You need to make the env using the cdf file that Affy has given you. If you are having troubles making the env, then run make.cdf.package("name of cdf here") and email the entire folder that is produced directly to me (don't use the Bioconductor list). Preferably zipped. I will email a zipped package back to you that you can install using 'Install package from local zip file...'. Jim James W. MacDonald UMCCC Microarray Core Facility 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "Lisa Devereaux" <lisa.d@genetraks.com> 06/18/03 09:11PM >>> Hello Jim, I received your email from the Bioconductor mailing list. Can you email me the win env? I am having the same difficulty in creating the makecdfenv for our propriety chip. Thank you Lisa Lisa Devereaux B.App Sci (Hons) Biotechnician GENETRAKS PTY LTD Email: <mailto:lisa.d@genetraks.com> lisa.d@genetraks.com Website: <http: www.genetraks.com=""/> www.genetraks.com Level 1, 80 Jephson Street PO Box 2060 Toowong QLD 4006 Australia Tel: 61 7 3327 9822 Fax: 61 7 3719 5499 Confidentiality: The contents of this email are confidential and are intended only for the named recipient. If the reader of this e-mail is not the intended recipient you are hereby notified that any use, reproduction, disclosure or distribution of the information contained in the e-mail is prohibited. If you have received this e-mail in error, please reply to us immediately and delete the document and any attachments. [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor