I'm working to install Bioconductor packages on a CentOS 5.6 system with R 2.13.0 (and GCC 4.4.5) installed. When I issue biocLite("BioBase") from within R (after setting the source location correctly), all the object files seem to build but at the link step I get a number of errors of this sort: anyMissing.o: In function `fgets': /usr/include/bits/stdio2.h:109: multiple definition of `fgets' Rinit.o:/usr/include/bits/stdio2.h:109: first defined here It seems to me that each object file was built with the same version of stdio2.h and there seems to be a dual inclusion error happening, but I cannot seem to resolve it. Any ideas on how to resolve this error? -Kirk Complete output: > biocLite("Biobase") Using R version 2.13.0, biocinstall version 2.8.4. Installing Bioconductor version 2.8 packages: [1] "Biobase" Please wait... Installing package(s) into ‘/usr/lib64/R/library’ (as ‘lib’ is unspecified) trying URL ' http://bioconductor.org/packages/2.8/bioc/src/contrib/Biobase_2.12.1.t ar.gz' Content type 'application/x-gzip' length 2222976 bytes (2.1 Mb) opened URL ================================================== downloaded 2.1 Mb * installing *source* package ‘Biobase’ ... ** libs gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c Rinit.c -o Rinit.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c anyMissing.c -o anyMissing.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c envir.c -o envir.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c matchpt.c -o matchpt.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c rowMedians.c -o rowMedians.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c sublist_extract.c -o sublist_extract.o gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/usr/lib64/R/lib -lR anyMissing.o: In function `fgets': /usr/include/bits/stdio2.h:109: multiple definition of `fgets' Rinit.o:/usr/include/bits/stdio2.h:109: first defined here anyMissing.o: In function `gets': /usr/include/bits/stdio2.h:94: multiple definition of `gets' Rinit.o:/usr/include/bits/stdio2.h:94: first defined here anyMissing.o: In function `stpncpy': /usr/include/bits/string3.h:160: multiple definition of `stpncpy' Rinit.o:/usr/include/bits/string3.h:160: first defined here envir.o: In function `stpncpy': /usr/include/bits/string3.h:160: multiple definition of `stpncpy' Rinit.o:/usr/include/bits/string3.h:160: first defined here envir.o: In function `fgets': /usr/include/bits/stdio2.h:109: multiple definition of `fgets' Rinit.o:/usr/include/bits/stdio2.h:109: first defined here envir.o: In function `gets': /usr/include/bits/stdio2.h:94: multiple definition of `gets' Rinit.o:/usr/include/bits/stdio2.h:94: first defined here matchpt.o: In function `stpncpy': /usr/include/bits/string3.h:160: multiple definition of `stpncpy' Rinit.o:/usr/include/bits/string3.h:160: first defined here matchpt.o: In function `fgets': /usr/include/bits/stdio2.h:109: multiple definition of `fgets' Rinit.o:/usr/include/bits/stdio2.h:109: first defined here matchpt.o: In function `gets': /usr/include/bits/stdio2.h:94: multiple definition of `gets' Rinit.o:/usr/include/bits/stdio2.h:94: first defined here rowMedians.o: In function `stpncpy': /usr/include/bits/string3.h:160: multiple definition of `stpncpy' Rinit.o:/usr/include/bits/string3.h:160: first defined here rowMedians.o: In function `fgets': /usr/include/bits/stdio2.h:109: multiple definition of `fgets' Rinit.o:/usr/include/bits/stdio2.h:109: first defined here rowMedians.o: In function `gets': /usr/include/bits/stdio2.h:94: multiple definition of `gets' Rinit.o:/usr/include/bits/stdio2.h:94: first defined here sublist_extract.o: In function `fgets': /usr/include/bits/stdio2.h:109: multiple definition of `fgets' Rinit.o:/usr/include/bits/stdio2.h:109: first defined here sublist_extract.o: In function `gets': /usr/include/bits/stdio2.h:94: multiple definition of `gets' Rinit.o:/usr/include/bits/stdio2.h:94: first defined here sublist_extract.o: In function `stpncpy': /usr/include/bits/string3.h:160: multiple definition of `stpncpy' Rinit.o:/usr/include/bits/string3.h:160: first defined here collect2: ld returned 1 exit status make: *** [Biobase.so] Error 1 ERROR: compilation failed for package ‘Biobase’ * removing ‘/usr/lib64/R/library/Biobase’ The downloaded packages are in ‘/tmp/RtmpiEGg4g/downloaded_packages’ Updating HTML index of packages in '.Library' Making packages.html ... done Warning message: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package 'Biobase' had non-zero exit status [[alternative HTML version deleted]]

On 06/21/2011 04:38 PM, Robert DeLisle wrote: > I'm working to install Bioconductor packages on a CentOS 5.6 system with R > 2.13.0 (and GCC 4.4.5) installed. When I issue biocLite("BioBase") from > within R (after setting the source location correctly), all the object files > seem to build but at the link step I get a number of errors of this sort: > > anyMissing.o: In function `fgets': > /usr/include/bits/stdio2.h:109: multiple definition of `fgets' > Rinit.o:/usr/include/bits/stdio2.h:109: first defined here > > It seems to me that each object file was built with the same version of > stdio2.h and there seems to be a dual inclusion error happening, but I > cannot seem to resolve it. > > Any ideas on how to resolve this error? > > -Kirk > > Complete output: > > >> biocLite("Biobase") > Using R version 2.13.0, biocinstall version 2.8.4. > Installing Bioconductor version 2.8 packages: > [1] "Biobase" > Please wait... > > Installing package(s) into ?/usr/lib64/R/library? > (as ?lib? is unspecified) > trying URL ' > http://bioconductor.org/packages/2.8/bioc/src/contrib/Biobase_2.12.1 .tar.gz' > Content type 'application/x-gzip' length 2222976 bytes (2.1 Mb) > opened URL > ================================================== > downloaded 2.1 Mb > > * installing *source* package ?Biobase? ... > ** libs > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g > -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector > --param=ssp-buffer-size=4 -m64 -mtune=generic -c Rinit.c -o Rinit.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g > -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector > --param=ssp-buffer-size=4 -m64 -mtune=generic -c anyMissing.c -o > anyMissing.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g > -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector > --param=ssp-buffer-size=4 -m64 -mtune=generic -c envir.c -o envir.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g > -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector > --param=ssp-buffer-size=4 -m64 -mtune=generic -c matchpt.c -o matchpt.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g > -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector > --param=ssp-buffer-size=4 -m64 -mtune=generic -c rowMedians.c -o > rowMedians.o > gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g > -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector > --param=ssp-buffer-size=4 -m64 -mtune=generic -c sublist_extract.c -o > sublist_extract.o > gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o Biobase.so Rinit.o > anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o > -L/usr/lib64/R/lib -lR > anyMissing.o: In function `fgets': > /usr/include/bits/stdio2.h:109: multiple definition of `fgets' > Rinit.o:/usr/include/bits/stdio2.h:109: first defined here Hi Robert -- Can you reproduce this with a more minimal example, e.g., tmp.c: #include <rdefines.h> void foo() {} and then R CMD SHLIB tmp.c ? There seems to be a relevant bug report at https://bugs.gentoo.org/show_bug.cgi?id=289757 Any luck relating your problem to that? Have there been compiler / other system upgrades since R was installed? Martin > anyMissing.o: In function `gets': > /usr/include/bits/stdio2.h:94: multiple definition of `gets' > Rinit.o:/usr/include/bits/stdio2.h:94: first defined here > anyMissing.o: In function `stpncpy': > /usr/include/bits/string3.h:160: multiple definition of `stpncpy' > Rinit.o:/usr/include/bits/string3.h:160: first defined here > envir.o: In function `stpncpy': > /usr/include/bits/string3.h:160: multiple definition of `stpncpy' > Rinit.o:/usr/include/bits/string3.h:160: first defined here > envir.o: In function `fgets': > /usr/include/bits/stdio2.h:109: multiple definition of `fgets' > Rinit.o:/usr/include/bits/stdio2.h:109: first defined here > envir.o: In function `gets': > /usr/include/bits/stdio2.h:94: multiple definition of `gets' > Rinit.o:/usr/include/bits/stdio2.h:94: first defined here > matchpt.o: In function `stpncpy': > /usr/include/bits/string3.h:160: multiple definition of `stpncpy' > Rinit.o:/usr/include/bits/string3.h:160: first defined here > matchpt.o: In function `fgets': > /usr/include/bits/stdio2.h:109: multiple definition of `fgets' > Rinit.o:/usr/include/bits/stdio2.h:109: first defined here > matchpt.o: In function `gets': > /usr/include/bits/stdio2.h:94: multiple definition of `gets' > Rinit.o:/usr/include/bits/stdio2.h:94: first defined here > rowMedians.o: In function `stpncpy': > /usr/include/bits/string3.h:160: multiple definition of `stpncpy' > Rinit.o:/usr/include/bits/string3.h:160: first defined here > rowMedians.o: In function `fgets': > /usr/include/bits/stdio2.h:109: multiple definition of `fgets' > Rinit.o:/usr/include/bits/stdio2.h:109: first defined here > rowMedians.o: In function `gets': > /usr/include/bits/stdio2.h:94: multiple definition of `gets' > Rinit.o:/usr/include/bits/stdio2.h:94: first defined here > sublist_extract.o: In function `fgets': > /usr/include/bits/stdio2.h:109: multiple definition of `fgets' > Rinit.o:/usr/include/bits/stdio2.h:109: first defined here > sublist_extract.o: In function `gets': > /usr/include/bits/stdio2.h:94: multiple definition of `gets' > Rinit.o:/usr/include/bits/stdio2.h:94: first defined here > sublist_extract.o: In function `stpncpy': > /usr/include/bits/string3.h:160: multiple definition of `stpncpy' > Rinit.o:/usr/include/bits/string3.h:160: first defined here > collect2: ld returned 1 exit status > make: *** [Biobase.so] Error 1 > ERROR: compilation failed for package ?Biobase? > * removing ?/usr/lib64/R/library/Biobase? > > The downloaded packages are in > ?/tmp/RtmpiEGg4g/downloaded_packages? > Updating HTML index of packages in '.Library' > Making packages.html ... done > Warning message: > In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package 'Biobase' had non-zero exit status > > [[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 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. 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