Installing GO 1.7.0

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
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

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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

Installing GO 1.7.0

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