[Fedora-r-devel-list] Re: Any feedback? any at all?
Tom Moertel <tom-RKvYLT2W2Q9BDgjK7y7TUQ(a)public.gmane.org> writes:
I am interested in seeing your script. It sounds like it embodies a
lot of knowledge about building a bunch of R packages, and that
knowledge is valuable. I'd hope we can make some use of it. :-)
http://nersp.osg.ufl.edu/~asr/media/R2spec-2.6.2-asr.src.rpm
It depends now on python-cheetah (available from EPEL).
Updated instructions:
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for me to get the dependencies to build and install all (most) of
ggplot2's broad depgraph, I must:
yum install openmpi openmpi-devel openmpi-libs unixODBC-devel pvm tcl tcl-devel
perl-DateManip perl-Date-Calc perl-version
and then install from EPEL:
environment-modules-3.2.6-4.el5.x86_64.rpm
mpich2-1.1.1-1.el5.x86_64.rpm
perl-IO-stringy-2.110-5.el5.noarch.rpm
perl-Jcode-2.06-6.el5.noarch.rpm
perl-OLE-Storage_Lite-0.14-9.el5.noarch.rpm
perl-Parse-RecDescent-1.96-1.el5.noarch.rpm
perl-Spreadsheet-WriteExcel-2.18-1.el5.noarch.rpm
perl-Unicode-Map-0.112-12.el5.x86_64.rpm
and then install from the graphviz people:
graphviz-2.24.0-1.el5.x86_64.rpm
graphviz-devel-2.24.0-1.el5.x86_64.rpm
After installing the r2spec and the sysdeps, I made a temp directory,
/var/tmp/Rbuild. I've got every script running happily from '.'; so
there's no specialness about the tempdir any more.
There, I ran (as root): [...]
I heard the 'prefer not running as root' from earlier: since step N
below is to install all these packages, is that really practical? In
any case, the below can be run as a normal user, but the install steps
below can't.
# clear; R2spec -n "Allen S. Rout" -e
"asr-hnhdhkBXzx8(a)public.gmane.org" -c --force --suggests --verbose
--package ggplot2
This downloaded the CRAN-like lists of packages, downloaded source
tarballs, and built (and copied) the specfiles and source.
It also generated a few dot files, including the broad and narrow
dependency graphs for the requested package.
It also generates a 'buildorderlist'; a path through the depgraph such
that each package is attempted only after its dependencies are
processed.
Then I stripped out the packages I knew would not complete their RPM
build (mentioned below)
# mv buildorderlist buildorderlist.orig
# egrep -v
"R-Rmpi|R-rsprng|R-multcomp|R-flexmix|R-RandomFields|R-MCMCpack|R-tcltk2"
buildorderlist.orig > buildorderlist
Then I ran
/usr/lib/python2.4/site-packages/r2spec/buildfromlist.sh
Is it evil for me to have put the script in there? This is certainly
not general-purpose; putting it in the default bin would be silly.
This will build and install all of the RPMs in the broad graph. ... If
the individual builds work.
This script uses '.' or environment variable 'RBUILDLOG' as a tempdir
extensively; it drops a build log and an install log for every package
addressed. That way when things eventually bust you can see where
they went wrong.
Then I ran
/usr/lib/python2.4/site-packages/r2spec/checkfromlist.sh
which runs 'R CMD check' on every package, again logging, and
summarizing success or failure in 'checkresults'.
The check step took about 5.5 hours for me.
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I still fail to build (and haven't investigated much yet):
tcltk2: Fails to install: need tclsh8.3, not 8.4 ?
multcomp: requires Survival >= 2.35.7 ? ...
flexmix: dep on multcomp
R-RandomFields, R-MCMCpack: uncaught debug files in the build tree.
MPI, sprng
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- Allen S. Rout