Hello Iam trying to install bioconductor 2.10 on my machine .Ruby script was written to call all the packages that are required for me . When I tried to execute I got the following error : checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking for gsl-config... /opt/users/swaroopa/LSBUILDBOX/trunk/depend encies/bioconductor210/build/srcLibs/../../../gsl-1_13/gsl/bin/gsl- config checking for GSL - version >= 1.6... yes configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -std=gnu99 -shared -L/usr/local/lib64 -o PICS.so background.o pics.o segment.o -lgsl -lgslcblas -lm /usr/bin/ld: cannot find -lgsl collect2: ld returned 1 exit status make: *** [PICS.so] Error 1 ERROR: compilation failed for package 'PICS' As part of troubleshooting I executed the highlighted command on the command prompt .It gave the same error .So I changed the highlighted statement and found that its working fine . Here is the command : gcc -std=gnu99 -shared -L/opt/users/swaroopa/LSBUILDBOX/trunk/dependencies/gsl-1_13/gsl/lib -o PICS.so src/background.o src/pics.o src/segment.o -lgsl -lgslcblas -lm This worked fine and able to get the PICS.so But the question in my mind is where exactly these values are modified . Thanks for your time Thanks, Swaroopa [[alternative HTML version deleted]]

On Thu, Apr 19, 2012 at 9:41 AM, Swaroopa Muppiri <swaroopa at="" appistry.com=""> wrote: > Hello > > Iam trying to install bioconductor 2.10 on my machine .Ruby script was written to call all the packages that are required for me . > > When I tried to execute I got the following error : > What command is being executed here? > checking whether gcc -std=gnu99 accepts -g... yes > checking for gcc -std=gnu99 option to accept ISO C89... none needed > checking for gsl-config... /opt/users/swaroopa/LSBUILDBOX/trunk/depe ndencies/bioconductor210/build/srcLibs/../../../gsl-1_13/gsl/bin/gsl- config > checking for GSL - version >= 1.6... yes > configure: creating ./config.status > config.status: creating src/Makevars > ** libs > gcc -std=gnu99 -shared -L/usr/local/lib64 -o PICS.so background.o pics.o segment.o -lgsl -lgslcblas -lm > /usr/bin/ld: cannot find -lgsl > collect2: ld returned 1 exit status > make: *** [PICS.so] Error 1 > ERROR: compilation failed for package 'PICS' > > As part of troubleshooting I executed the highlighted command on the command prompt .It gave the same error .So I changed the highlighted statement and found that its working fine . The mailing list strips off HTML versions of emails, so we can't see what you highlighted. > Here is the command : > > gcc -std=gnu99 -shared -L/opt/users/swaroopa/LSBUILDBOX/trunk/dependencies/gsl-1_13/gsl/lib -o PICS.so src/background.o src/pics.o src/segment.o -lgsl -lgslcblas -lm > > This worked fine and able to get the PICS.so > > But the question in my mind is where exactly these values are modified . > You could edit PICS/src/Makevars or (a better alternative) pass the appropriate values by passing the configure.args argument to install.packages(), biocLite(), or whatever you are using to install PICS (if you are using R CMD INSTALL, you can add the --configure-vars argument). Dan > Thanks for your time > > > Thanks, > Swaroopa > > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor