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Robert DeLisle
▴
10
@robert-delisle-4707
Last seen 10.1 years ago
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]]