[R] Installing GO 1.7.0

From: Tom 'spot' Callaway <tcallawa_at_redhat.com>
Date: Thu 31 Mar 2005 - 03:10:06 EST

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

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.



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
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Received on Thu Mar 31 03:23:49 2005

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