[BioC] RBGL fails to compile / install

[Groot, Philip de]

Hello all,
 
When trying to install GOstats (via biocLite), this fails because of the RBGL library:
> biocLite("GOstats")
Using R version 2.10.1, biocinstall version 2.5.10.
Installing Bioconductor version 2.5 packages:
[1] "GOstats"
Please wait...
also installing the dependencies 'GSEABase', 'Category', 'RBGL'
trying URL 'http://www.bioconductor.org/packages/2.5/bioc/src/contrib/GSEABase_1.8.0.tar.gz'
Content type 'application/x-gzip' length 172840 bytes (168 Kb)
opened URL
==================================================
downloaded 168 Kb
trying URL 'http://www.bioconductor.org/packages/2.5/bioc/src/contrib/Category_2.12.0.tar.gz'
Content type 'application/x-gzip' length 472185 bytes (461 Kb)
opened URL
==================================================
downloaded 461 Kb
trying URL 'http://www.bioconductor.org/packages/2.5/bioc/src/contrib/RBGL_1.22.0.tar.gz'
Content type 'application/x-gzip' length 1895494 bytes (1.8 Mb)
opened URL
==================================================
downloaded 1.8 Mb
trying URL 'http://www.bioconductor.org/packages/2.5/bioc/src/contrib/GOstats_2.12.0.tar.gz'
Content type 'application/x-gzip' length 2510297 bytes (2.4 Mb)
opened URL
==================================================
downloaded 2.4 Mb
* installing *source* package 'GSEABase' ...
** R
** inst
** preparing package for lazy loading
Welcome to Bioconductor
  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: AnnotationDbi
** help
*** installing help indices
** building package indices ...
* DONE (GSEABase)
* installing *source* package 'RBGL' ...
untarring boost include tree...
** libs
/usr/bin/g++ -I/geninf/prog64/R/R-2.10.1/lib64/R/include  -I/geninf/prog64/R/curl-7.19.7/src   -IboostIncl  -fpic  -g -O2 -c bbc.cpp -o bbc.o
boostIncl/boost/graph/named_graph.hpp:485: sorry, unimplemented: use of `
   enumeral_type' in template type unification
boostIncl/boost/graph/named_graph.hpp:485: sorry, unimplemented: use of `
   enumeral_type' in template type unification
make: *** [bbc.o] Error 1
ERROR: compilation failed for package 'RBGL'
* removing '/mnt/geninf12/prog64/R/R-2.10.1/lib64/R/library/RBGL'

 

> sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

loaded via a namespace (and not attached):
[1] tools_2.10.1


gcc version:

gcc (GCC) 3.3.3 (SuSE Linux)
Copyright (C) 2003 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

It could be that the compiler is outdated, but I only have a problem with RBGL. For the moment, I fixed it by installing RBGL version 1.20 (from the previous Bioconductor release) and this compiles and installs fine. Loading GOstats works, but I am not sure whether I might run into problems later on.

Just to let you know.

Regards,

Dr. Philip de Groot Ph.D.
Bioinformatics Researcher

Wageningen University / TIFN
Nutrigenomics Consortium
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
PO Box 8129, 6700 EV Wageningen
Visiting Address: Erfelijkheidsleer: De Valk, Building 304
Dreijenweg 2, 6703 HA  Wageningen
Room: 0052a
T: +31-317-485786
F: +31-317-483342
E-mail:   Philip.deGroot at wur.nl <mailto:Philip.deGroot at wur.nl> 
Internet: http://www.nutrigenomicsconsortium.nl <http://www.nutrigenomicsconsortium.nl/> 
             http://humannutrition.wur.nl <http://humannutrition.wur.nl/> 
             https://madmax.bioinformatics.nl <https://madmax.bioinformatics.nl/>