[BioC] RBGL fails to compile / install

[Vincent Carey]

I just had an absolutely clean compile/install with g++ 4.1.2 on
x86_64 with R 2.10.1

We can see from
http://bioconductor.org/checkResults/2.5/bioc-LATEST/wilson2-NodeInfo.html
and related pages

that the build machines are using g++ 4.0.1 or greater.  It is
probably time to upgrade your compiler if you want to
build from source.

On Tue, Jan 5, 2010 at 4:24 AM, Groot, Philip de <philip.degroot at wur.nl> wrote:
> 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/>
>
>
>
>
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