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!