Question: Installation error RBGL 1.42
gravatar for agroff
3.7 years ago by
United States
agroff0 wrote:


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!


> biocLite("RBGL")
Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2.
Installing package(s) 'RBGL'
trying URL ''
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()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=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    

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by agroff0

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 inline package, and run

f = 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:

  1. Talk to your sysadmin
  2. If that doesn't work, see if you can find an alternative gcc on the system, and use a personal Makevars to point to it; see 6.3.3 in R Installation and Administration (and note in the section above that where you use CC and CXX to point to your C and C++ compilers, respectively).

As a shot in the dark, before other shenanigans, get the RBGL source tarball, untar and try adding PKG_CPPFLAGS=-D_GNU_SOURCE on a new line in RBGL/src/Makevars. Try running R CMD INSTALL on 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 setting CC/CXX in the RBGL package.

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by Nathaniel Hayden ♦♦ 180
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