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
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]]

