[R] Installing GO 1.7.0

[Christian Lederer]

Hi,

is the announced solution for the GO 1.7.0 installation already
publicly available?
I am running into the same trouble as described in below, using
2.0.1 under Ubuntu Hoary.

Thanks,

Christian



 > Seth Falcon wrote:
> Hi Tom,
> 
> I'm cc'ing to Bioconductor as that is probably a better place for the
> discussion.
> 
> 
> "Tom 'spot' Callaway" <tcallawa at redhat.com> writes:
> 
> 
>>I'm in the process of packaging R (and R modules) for future inclusion
>>in Fedora Extras, and I've managed to get several hundred modules
>>installed without issue, however, the GO metadata package is refusing to
>>comply.
> 
> 
>>ERROR: installing package indices failed
>>
>>I let this run for over 6 hours, and it didn't seem to complete (or make
>>any changes).
> 
> 
> We have a solution for this and will send or make available an updated
> GO package shortly.  With the updated GO package you should be able to
> R CMD INSTALL without it taking much time.
> 
> Best,
> 
> + seth
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html


> I'm in the process of packaging R (and R modules) for future inclusion
> in Fedora Extras, and I've managed to get several hundred modules
> installed without issue, however, the GO metadata package is refusing to
> comply.
> 
> Since I'm packaging this in rpm format, I can't use any of the automated
> functions for build, I've got to do it locally through R.
> 
> The following steps work for other metadata packages (directory names
> changing, obviously), but not for GO:
> 
> With the GO tarball unpacked into R-GO-1.7.0/GO...
> 
> cd R-GO-1.7.0/
> rm -rf /var/tmp/R-GO-1.7.0-1-root-root
> mkdir -p /var/tmp/R-GO-1.7.0-1-root-root/usr/lib/R/library
> export R_LIBS=/var/tmp/R-GO-1.7.0-1-root-root/usr/lib/R/library
> /usr/bin/R CMD INSTALL \
> -l /var/tmp/R-GO-1.7.0-1-root-root/usr/lib/R/library GO
> 
> I get the following output:
> * Installing *source* package 'GO' ...
> ** R
> ** data
> ** preparing package for lazy loading
> 
> ** help
>  >>> Building/Updating help pages for package 'GO'
>      Formats: text html latex example
>   GO                                text    html    latex
>   GOALLLOCUSID                      text    html    latex   example
>   GOBPANCESTOR                      text    html    latex   example
>   GOBPCHILDREN                      text    html    latex   example
>   GOBPOFFSPRING                     text    html    latex   example
>   GOBPPARENTS                       text    html    latex   example
>   GOCCANCESTOR                      text    html    latex   example
>   GOCCCHILDREN                      text    html    latex   example
>   GOCCOFFSPRING                     text    html    latex   example
>   GOCCPARENTS                       text    html    latex   example
>   GOLOCUSID                         text    html    latex   example
>   GOLOCUSID2ALLGO                   text    html    latex   example
>   GOLOCUSID2GO                      text    html    latex   example
>   GOMFANCESTOR                      text    html    latex   example
>   GOMFCHILDREN                      text    html    latex   example
>   GOMFOFFSPRING                     text    html    latex   example
>   GOMFPARENTS                       text    html    latex   example
>   GOQC                              text    html    latex
>   GOTERM                            text    html    latex   example
> 
> But I never get the "* DONE (GO)" that I'm expecting. Instead, all of
> the memory on the machine allocates (512MB), it starts to swap out, and
> never completes.
> 
> When I look at the output from ps, I see:
>  8290 pts/5    S+     0:00 /bin/sh /usr/lib/R/bin/INSTALL
> -l /var/tmp/R-GO-1.7.0-1-root-root/us 8364 ?        S      0:00 
>  8421 pts/5    D+     1:11 /usr/lib/R/bin/exec/R --vanilla
> 
> When I kill the 8421 process, I get:
> 
> /usr/lib/R/bin/INSTALL: line 381:  8088 Done                    echo
> "invisible(.libPaths(c(\"${lib}\", .libPaths())));
> tools:::.install_package_indices(\".\", \"${R_PACKAGE_DIR}\")"
>       8089 Killed                  | R_DEFAULT_PACKAGES=NULL LANG=C
> "${R_EXE}" --vanilla >/dev/null
> ERROR: installing package indices failed
> 
> I let this run for over 6 hours, and it didn't seem to complete (or make
> any changes).
> 
> Unfortunately, lots of Bioconductor seems to depend on GO... so any help
> on getting this to install is appreciated.
> 
> Thanks,
> 
> ~spot
> -- Tom "spot" Callaway: Red Hat Sales Engineer || GPG Fingerprint: 93054260 Fedora Extras Steering Committee Member (RPM Standards and Practices) Aurora Linux Project Leader: http://auroralinux.org Lemurs, llamas, and sparcs, oh my! ______________________________________________ R-help at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html