[BioC] Compilation problem RBGL_1.26
Bernt Guldbrandtsen
Bernt.Guldbrandtsen at agrsci.dk
Tue Oct 19 20:30:25 CEST 2010
And then, apparently not; compiling with Intel's icc gives a very similar problem:
-------------------------------------------------
icc -I/opt/ghpc/R-2.12.0/lib64/R/include "-I/opt/ghpc/include" -IboostIncl -fpic -g -O2 -c incrConnComp.cpp -o incrConnComp.o
incrConnComp.cpp(65): error: name followed by "::" must be a class or namespace name
Components::value_type::iterator j;
^
incrConnComp.cpp(65): error: expected a ";"
Components::value_type::iterator j;
^
incrConnComp.cpp(71): error: identifier "j" is undefined
for (j = components[k].begin(); j != components[k].end(); j++ )
^
incrConnComp.cpp(71): error: class "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 "begin"
for (j = components[k].begin(); j != components[k].end(); j++ )
^
incrConnComp.cpp(71): error: class "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 "end"
for (j = components[k].begin(); j != components[k].end(); j++ )
^
incrConnComp.cpp(76): error: class "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 "begin"
for (j = components[k].begin(); j != components[k].end(); j++ )
^
incrConnComp.cpp(76): error: class "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 "end"
for (j = components[k].begin(); j != components[k].end(); j++ )
^
compilation aborted for incrConnComp.cpp (code 2)
make: *** [incrConnComp.o] Error 2
ERROR: compilation failed for package 'RBGL'
* removing '/opt/ghpc/R-2.12.0/lib64/R/library/RBGL'
* restoring previous '/opt/ghpc/R-2.12.0/lib64/R/library/RBGL'
The downloaded packages are in
'/tmp/RtmpFDel9f/downloaded_packages'
Updating HTML index of packages in '.Library'
Warning message:
In install.packages(pkgs = pkgs, repos = repos, ...) :
installation of package 'RBGL' had non-zero exit status
-------------------------------------------------
Best regards,
Bernt Guldbrandtsen
________________________________________
Fra: Vincent Carey [stvjc at channing.harvard.edu]
Sendt: 19. oktober 2010 19:59
Til: Bernt Guldbrandtsen
Cc: bioconductor at stat.math.ethz.ch
Emne: Re: [BioC] Compilation problem RBGL_1.26
I could not reproduce this on a 32-bit ubuntu 9.10 with gcc 4.4.1 --
biocLite gave a successful compilation and install.
On Tue, Oct 19, 2010 at 10:34 AM, Bernt Guldbrandtsen
<Bernt.Guldbrandtsen at agrsci.dk> wrote:
> 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:
> ---------------------------------------------------------------
> 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
> ---------------------------------------------------------------
> About gcc:
> ---------------------------------------------------------------
> [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)
> ---------------------------------------------------------------
> Session info is:
> ---------------------------------------------------------------
>> 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
> ---------------------------------------------------------------
>
> All other R packages are up to date.
>
> Am I missing something obvious here?
>
> Kind regards
>
>
> Bernt Guldbrandtsen
>
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