Hello,
I'm trying to install RBGL 1.42 from bioconductor. I've tried the following as well as installing from source, but keep getting the same error messages. Anyone know a workaround?
I'm including the full output of my installation attempt with the error in bold at the bottom. Following this is the output of sessionInfo(). I'm working on a linux cluster, using R 3.0.2 and Bioconductor version 2.13
Thanks for your help!! Please let me know if I can be more precise!
A
> biocLite("RBGL")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2.
Installing package(s) 'RBGL'
trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/RBGL_1.38.0.tar.gz'
Content type 'application/x-gzip' length 2265926 bytes (2.2 Mb)
opened URL
==================================================
downloaded 2.2 Mb
* installing *source* package ‘RBGL’ ...
untarring boost include tree...
** libs
g++ -I/n/sw/centos6/R-3.0.2/lib64/R/include -DNDEBUG -I/usr/local/include -Irbgl_trimmed_boost_1_49_0 -fpic -g -O2 -c bbc.cpp -o bbc.o
In file included from /n/sw/gcc-4.6.1/lib/gcc/x86_64-unknown-linux-gnu/4.6.1/../../../../include/c++/4.6.1/bits/localefwd.h:42:0,
from /n/sw/gcc-4.6.1/lib/gcc/x86_64-unknown-linux-gnu/4.6.1/../../../../include/c++/4.6.1/ios:42,
from /n/sw/gcc-4.6.1/lib/gcc/x86_64-unknown-linux-gnu/4.6.1/../../../../include/c++/4.6.1/ostream:40,
from /n/sw/gcc-4.6.1/lib/gcc/x86_64-unknown-linux-gnu/4.6.1/../../../../include/c++/4.6.1/iostream:40,
from RBGL.hpp:7,
from bbc.cpp:1:
/n/sw/gcc-4.6.1/lib/gcc/x86_64-unknown-linux-gnu/4.6.1/../../../../include/c++/4.6.1/x86_64-unknown-linux-gnu/bits/c++locale.h:53:23: error: ‘uselocale’ was not declared in this scope
/n/sw/gcc-4.6.1/lib/gcc/x86_64-unknown-linux-gnu/4.6.1/../../../../include/c++/4.6.1/x86_64-unknown-linux-gnu/bits/c++locale.h:53:45: error: invalid type in declaration before ‘;’ token
/n/sw/gcc-4.6.1/lib/gcc/x86_64-unknown-linux-gnu/4.6.1/../../../../include/c++/4.6.1/x86_64-unknown-linux-gnu/bits/c++locale.h: In function ‘int std::__convert_from_v(__locale_struct* const&, char*, int, const char*, ...)’:
/n/sw/gcc-4.6.1/lib/gcc/x86_64-unknown-linux-gnu/4.6.1/../../../../include/c++/4.6.1/x86_64-unknown-linux-gnu/bits/c++locale.h:76:53: error: ‘__gnu_cxx::__uselocale’ cannot be used as a function
/n/sw/gcc-4.6.1/lib/gcc/x86_64-unknown-linux-gnu/4.6.1/../../../../include/c++/4.6.1/x86_64-unknown-linux-gnu/bits/c++locale.h:101:33: error: ‘__gnu_cxx::__uselocale’ cannot be used as a function
In file included from /usr/include/stdio.h:929:0,
from /n/sw/gcc-4.6.1/lib/gcc/x86_64-unknown-linux-gnu/4.6.1/../../../../include/c++/4.6.1/cstdio:44,
from RBGL.hpp:8,
from bbc.cpp:1:
/usr/include/bits/stdio.h: In function ‘__ssize_t getline(char**, size_t*, FILE*)’:
/usr/include/bits/stdio.h:118:52: error: ‘__getdelim’ was not declared in this scope
make: *** [bbc.o] Error 1
ERROR: compilation failed for package ‘RBGL’
sessionInfo():
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.12.1 graph_1.40.1
loaded via a namespace (and not attached):
[1] BiocGenerics_0.8.0 parallel_3.0.2 stats4_3.0.2 tools_3.0.2
Do you know if there has been trouble on this cluster compiling packages containing C++ code that uses
#include <iostream>? I think there's a mismatch in your version of gcc and libc or you have a bad install of gcc. More specifically, I think the gcc you get when you compile was built with an outdated version of c++locale.h. And I think all the errors in the output you included come from the same issue, not just the boldface one.As a shortcut to making a package to eliminate the RBGL package as the culprit, could you install the
inlinepackage, and runf = inline::cxxfunction(includes="#include <iostream>", body='printf("%d.%d.%d\\n", __GNUC__, __GNUC_MINOR__, __GNUC_PATCHLEVEL__); return R_NilValue;')and then call
f()? I predict it won't let you compile. That indicates something amiss with the gcc you get on your cluster. In that case:As a shot in the dark, before other shenanigans, get the RBGL source tarball, untar and try adding
PKG_CPPFLAGS=-D_GNU_SOURCEon a new line in RBGL/src/Makevars. Try runningR CMD INSTALLon that source directory. Note that unlike the HOME/.R/Makevars mentioned above you can't specify compilers in a package-level Makevars file, so don't try settingCC/CXXin the RBGL package.