Trying to automate some of the uni's CGH experiments. Have pretty much installed CGHweb. Stuck on cghFLasso. Anyone seen this error before. >>>>>>>>>>>>>>>error<<<<<<<<<<<<<<<<<<<<<<< Installing package(s) into '/home/chrisf/R/x86_64-unknown-linux-gnu-library/2.13' (as 'lib' is unspecified) trying URL 'http://cran.fhcrc.org/src/contrib/cghFLasso_0.2-1.tar.gz' Content type 'application/x-gzip' length 129919 bytes (126 Kb) opened URL ================================================== downloaded 126 Kb * installing *source* package 'cghFLasso' ... ** libs gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include -fpic -g -O2 -c L2L1VitExact.c -o L2L1VitExact.o g77 -fpic -g -O2 -c smooth.f90 -o smooth.o g77: smooth.f90: linker input file unused because linking not done g77 -shared -L/usr/local/lib64 -o cghFLasso.so L2L1VitExact.o smooth.o -L/usr/local/lib64/R/lib -lR g77: smooth.o: No such file or directory make: *** [cghFLasso.so] Error 1 ERROR: compilation failed for package 'cghFLasso' * removing '/home/chrisf/R/x86_64-unknown-linux-gnu-library/2.13/cghFLasso' The downloaded packages are in '/tmp/RtmpoTkkOD/downloaded_packages' Warning message: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'cghFLasso' had non-zero exit status >>>>>>>>>>>>>>>>version<<<<<<<<<<<<<<<<<<< Using R version 2.13.0, biocinstall version 2.8.4. platform x86_64-unknown-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 13.0 year 2011 month 04 day 13 svn rev 55427 language R version.string R version 2.13.0 (2011-04-13)

I had no problem installing this package (not a Bioc package AFAICT) with biocLite. My linux system has gfortran rex-bash-3.2$ gfortran -v Using built-in specs. Target: x86_64-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java- awt=gtk --disable-dssi --enable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with- cpu=generic --host=x86_64-redhat-linux Thread model: posix gcc version 4.1.2 20080704 (Red Hat 4.1.2-48) Your g77 doesn't seem up to the task of compiling F90. On Wed, Sep 21, 2011 at 3:57 AM, Chris Fenton <chrisf@fagmed.uit.no> wrote: > Trying to automate some of the uni's CGH experiments. > Have pretty much installed CGHweb. > Stuck on cghFLasso. > Anyone seen this error before. > > >>>>>>>>>>>>>>>error<<<<<<<<<<<<<<<<<<<<<<< > Installing package(s) into > '/home/chrisf/R/x86_64-unknown-linux-gnu-library/2.13' > (as 'lib' is unspecified) > trying URL 'http://cran.fhcrc.org/src/contrib/cghFLasso_0.2-1.tar.gz' > Content type 'application/x-gzip' length 129919 bytes (126 Kb) > opened URL > ================================================== > downloaded 126 Kb > > * installing *source* package 'cghFLasso' ... > ** libs > gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/include > -fpic -g -O2 -c L2L1VitExact.c -o L2L1VitExact.o > g77 -fpic -g -O2 -c smooth.f90 -o smooth.o > g77: smooth.f90: linker input file unused because linking not done > g77 -shared -L/usr/local/lib64 -o cghFLasso.so L2L1VitExact.o smooth.o > -L/usr/local/lib64/R/lib -lR > g77: smooth.o: No such file or directory > make: *** [cghFLasso.so] Error 1 > ERROR: compilation failed for package 'cghFLasso' > * removing > '/home/chrisf/R/x86_64-unknown-linux-gnu-library/2.13/cghFLasso' > > The downloaded packages are in > '/tmp/RtmpoTkkOD/downloaded_packages' > Warning message: > In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'cghFLasso' had non-zero exit status > > >>>>>>>>>>>>>>>>version<<<<<<<<<<<<<<<<<<< > Using R version 2.13.0, biocinstall version 2.8.4. > > platform x86_64-unknown-linux-gnu > arch x86_64 > os linux-gnu > system x86_64, linux-gnu > status > major 2 > minor 13.0 > year 2011 > month 04 > day 13 > svn rev 55427 > language R > version.string R version 2.13.0 (2011-04-13) > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]