[BioC] Compilation problem RBGL_1.26

[Bernt Guldbrandtsen]

Dear Bioconductor,

I was trying to update to the new release of Bioconductor under R-2.12.0 and ran into the following compilation problem when building RBGL_1.26 during compilation of incrConnComp.cpp under Fedora 10:
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g++ -I/opt/ghpc/R-2.12.0/lib/R/include  "-I/opt/ghpc/include"   -IboostIncl  -fpic  -g -O2 -c incrConnComp.cpp -o incrConnComp.o
incrConnComp.cpp: In function 'SEXPREC* BGL_incr_comp_internal(SEXPREC*, SEXPREC*, SEXPREC*, E_IC_METHOD)':
incrConnComp.cpp:65: error: expected initializer before 'j'
incrConnComp.cpp:71: error: 'j' was not declared in this scope
incrConnComp.cpp:71: error: 'struct std::pair<boost::detail::component_index_iterator<__gnu_cxx::__normal_iterator<unsigned int*, std::vector<unsigned int, std::allocator<unsigned int> > > >, boost::detail::component_index_iterator<__gnu_cxx::__normal_iterator<unsigned int*, std::vector<unsigned int, std::allocator<unsigned int> > > > >' has no member named 'begin'
incrConnComp.cpp:71: error: 'struct std::pair<boost::detail::component_index_iterator<__gnu_cxx::__normal_iterator<unsigned int*, std::vector<unsigned int, std::allocator<unsigned int> > > >, boost::detail::component_index_iterator<__gnu_cxx::__normal_iterator<unsigned int*, std::vector<unsigned int, std::allocator<unsigned int> > > > >' has no member named 'end'
incrConnComp.cpp:76: error: 'struct std::pair<boost::detail::component_index_iterator<__gnu_cxx::__normal_iterator<unsigned int*, std::vector<unsigned int, std::allocator<unsigned int> > > >, boost::detail::component_index_iterator<__gnu_cxx::__normal_iterator<unsigned int*, std::vector<unsigned int, std::allocator<unsigned int> > > > >' has no member named 'begin'
incrConnComp.cpp:76: error: 'struct std::pair<boost::detail::component_index_iterator<__gnu_cxx::__normal_iterator<unsigned int*, std::vector<unsigned int, std::allocator<unsigned int> > > >, boost::detail::component_index_iterator<__gnu_cxx::__normal_iterator<unsigned int*, std::vector<unsigned int, std::allocator<unsigned int> > > > >' has no member named 'end'
make: *** [incrConnComp.o] Error 1
ERROR: compilation failed for package 'RBGL'
* removing '/opt/ghpc/R-2.12.0/lib/R/library/RBGL'
* restoring previous '/opt/ghpc/R-2.12.0/lib/R/library/RBGL'

The downloaded packages are in
        '/tmp/RtmpwPfL9j/downloaded_packages'
Updating HTML index of packages in '.Library'
Warning message:
In install.packages("RBGL", rep = biocinstallRepos()) :
  installation of package 'RBGL' had non-zero exit status
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About gcc:
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[root at pn01 ~]# gcc -v
Using built-in specs.
Target: i386-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --with-cpu=generic --host=i386-redhat-linux
Thread model: posix
gcc version 4.1.2 20070925 (Red Hat 4.1.2-27)
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Session info is:
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> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i686-pc-linux-gnu (32-bit)

locale:
 [1] LC_CTYPE=en_US       LC_NUMERIC=C         LC_TIME=en_US
 [4] LC_COLLATE=en_US     LC_MONETARY=C        LC_MESSAGES=en_US
 [7] LC_PAPER=en_US       LC_NAME=C            LC_ADDRESS=C
[10] LC_TELEPHONE=C       LC_MEASUREMENT=en_US LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] tools_2.12.0
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All other R packages are up to date.

Am I missing something obvious here?

Kind regards 


Bernt Guldbrandtsen