If the problem persists, please give us some compiler specifics. I guess you are using GCC, but a version number would be nice. Also please check that R CMD config CC and R CMD config CXX points to the compiler you think you are using :) Kasper On Aug 7, 2007, at 9:02 AM, Nathan Haigh wrote: > Seth Falcon wrote: >> Nathan Haigh <n.haigh at="" sheffield.ac.uk=""> writes: >> >> >>> James MacDonald wrote: >>> >>>> Hi Nathan, >>>> >>>> What's your sessionInfo()? >>>> >>>> sessionInfo() >>>> >>> R version 2.4.0 Patched (2006-11-25 r39997) >>> i486-pc-linux-gnu >>> >> >> Can you try upgrading to the latest R release (2.5.1) and trying >> biocLite again? Are you really on a 486?! >> >> + seth >> >> > > I'm on a Debian machine, running the latest "stable" R version > according > to Debian. I can try installing 2.5.1 from unstable if you think > that's > gonna be required. I'll let you know if it's gonna cause problems with > updating loads of dependencies. > > No it's not a 486 it's a 686 - not sure why R reports that since > "uname-a" gives: > Linux bio5 2.6.18-4-686 #1 SMP Wed May 9 23:03:12 UTC 2007 i686 GNU/ > Linux > > _______________________________________________ > 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

Forgot this: because you are using R-2.4.0 you get an old(er) version of affxparser. That is essentially why Seth wants you to upgrade. As far as I can remember (and I am the maintainer after all), the 1.8.1 version of affxparser (the current stable one) is compatible with R-2.4.0, although I am not 100% sure. If you just want to get it working quickly, I suggest downloading the tarball from Bioconductor and install it manually. It might work. Kasper On Aug 7, 2007, at 9:02 AM, Nathan Haigh wrote: > Seth Falcon wrote: >> Nathan Haigh <n.haigh at="" sheffield.ac.uk=""> writes: >> >> >>> James MacDonald wrote: >>> >>>> Hi Nathan, >>>> >>>> What's your sessionInfo()? >>>> >>>> sessionInfo() >>>> >>> R version 2.4.0 Patched (2006-11-25 r39997) >>> i486-pc-linux-gnu >>> >> >> Can you try upgrading to the latest R release (2.5.1) and trying >> biocLite again? Are you really on a 486?! >> >> + seth >> >> > > I'm on a Debian machine, running the latest "stable" R version > according > to Debian. I can try installing 2.5.1 from unstable if you think > that's > gonna be required. I'll let you know if it's gonna cause problems with > updating loads of dependencies. > > No it's not a 486 it's a 686 - not sure why R reports that since > "uname-a" gives: > Linux bio5 2.6.18-4-686 #1 SMP Wed May 9 23:03:12 UTC 2007 i686 GNU/ > Linux > > _______________________________________________ > 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

Hi Nathan, What's your sessionInfo()? Nathan Haigh wrote: > James W. MacDonald wrote: >> Hi Nathan, >> >> Nathan Haigh wrote: >>> I have a need to calculate the median of probes across 4 reps and save >>> these medians to a single Affy ATH1 CEL file. Can this be done with >>> bioconductor? >>> >> I believe so. See the affxparser package, in particular the >> createCel() and updateCel() functions. >> >> Best, >> >> Jim >> > > Thanks for the head's up. > > I tried installing the package using: > source("http://bioconductor.org/biocLite.R") > biocLite(c("affxparser")) > > but get the following error: > > -- snip -- > g++ -I/usr/share/R/include -I/usr/share/R/include -imacros > R_affx_constants.h -Ifusion_sdk/calvin_files/array/src > -Ifusion_sdk/calvin_files/data/src > -Ifusion_sdk/calvin_files/exception/src > -Ifusion_sdk/calvin_files/fusion/src > -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter > -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter > -Ifusion_sdk/calvin_files/parameter/src > -Ifusion_sdk/calvin_files/parsers/src > -Ifusion_sdk/calvin_files/portability/src > -Ifusion_sdk/calvin_files/template/src > -Ifusion_sdk/calvin_files/utils/src > -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file > -Ifusion_sdk/portability -D_USE_MEM_MAPPING_ -fpic -g -O2 -O0 -c > fusion_sdk/calvin_files/data/src/CELData.cpp -o > fusion_sdk/calvin_files/data/src/CELData.o > fusion_sdk/calvin_files/data/src/CELData.h:188: error: extra > qualification 'affymetrix_calvin_io::CelFileData::' on member > 'GetAlgorithmVersion' > make: *** [fusion_sdk/calvin_files/data/src/CELData.o] Error 1 > ERROR: compilation failed for package 'affxparser' > ** Removing '/usr/local/lib/R/site-library/affxparser' > > The downloaded packages are in > /tmp/RtmpgblgWq/downloaded_packages > Warning message: > installation of package 'affxparser' had non-zero exit status in: > install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, > > -- end -- > > Any ideas if I'm doing something stupid!? > > Thanks > Nathan > > _______________________________________________ > 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, MS Biostatistician UMCCC cDNA and Affymetrix Core University of Michigan 1500 E Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623