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Groot, Philip de
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630
@groot-philip-de-1307
Last seen 10.0 years ago
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=""/>