[BioC] Installation of Bioconductor packages

[Martin Morgan]

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]]
>
>
>
>
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