Re: [R] Installing GO 1.7.0

From: Christian Lederer <lederer_at_slcmsr.org>
Date: Wed 04 May 2005 - 06:59:16 EST

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@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@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



R-help@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 Received on Wed May 04 07:10:54 2005

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