Re: [Rd] R CMD config for R = 3.0.1
I need to build R on a Centos machine where I have no admin privileges. Believe I have to build from source, but cannot find the configure script in the source bundle. Am I missing something? -- View this message in context: http://r.789695.n4.nabble.com/R-CMD-config-for-R-3-0-1-tp4667399p4675813.html Sent from the R devel mailing list archive at Nabble.com. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD config for R = 3.0.1
Also have no cooperation from the admin of the machine, so can't ask for a yum install. -- View this message in context: http://r.789695.n4.nabble.com/R-CMD-config-for-R-3-0-1-tp4667399p4675814.html Sent from the R devel mailing list archive at Nabble.com. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD config for R = 3.0.1
On Sep 10, 2013, at 5:30 PM, crunch wrote: Also have no cooperation from the admin of the machine, so can't ask for a yum install. Please follow Brian's advice. If you don't have even Fortran on that machine, then you're really in a pickle: you can extract the gfortran rpm contents (and all dependencies you may need) by hand in any place that you have access to and adjust LD_LIBRARY_PATH for the runtime accordingly. However, it's not a trivial task - it particular if you're not very familiar with subtleties of Linux. (I had to do this fairly recently on a CentOS machine, so I know it's possible, but there are a few gotchas that may require a few symlinks created by hand). Cheers, Simon -- View this message in context: http://r.789695.n4.nabble.com/R-CMD-config-for-R-3-0-1-tp4667399p4675814.html Sent from the R devel mailing list archive at Nabble.com. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD config for R = 3.0.1
On 10/09/2013 22:24, crunch wrote: I need to build R on a Centos machine where I have no admin privileges. Believe I have to build from source, but cannot find the configure script in the source bundle. Am I missing something? Yes, as it is there. We can only guess that 'the source bundle' you have is not the correct file. As 3.0.2 is close, I would start with R-patched from ftp://ftp.stat.math.ethz.ch/Software/R/ (a link on the CRAN front page). It contains an installation manual, online at http://cran.r-project.org/doc/manuals/r-patched/R-admin.html [What may be more of a problem is installing the tools you need: does your box have a Fortran compiler, for example?] -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD config for R = 3.0.1
As an alternative, you might consider installing a virtual machine in your user space and installing R from there. That way you don't have to do a bunch of one-off gymnastics to get R compiled. On Sep 11, 2013, at 1:40 AM, Simon Urbanek simon.urba...@r-project.org wrote: On Sep 10, 2013, at 5:30 PM, crunch wrote: Also have no cooperation from the admin of the machine, so can't ask for a yum install. Please follow Brian's advice. If you don't have even Fortran on that machine, then you're really in a pickle: you can extract the gfortran rpm contents (and all dependencies you may need) by hand in any place that you have access to and adjust LD_LIBRARY_PATH for the runtime accordingly. However, it's not a trivial task - it particular if you're not very familiar with subtleties of Linux. (I had to do this fairly recently on a CentOS machine, so I know it's possible, but there are a few gotchas that may require a few symlinks created by hand). Cheers, Simon -- View this message in context: http://r.789695.n4.nabble.com/R-CMD-config-for-R-3-0-1-tp4667399p4675814.html Sent from the R devel mailing list archive at Nabble.com. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD config for R = 3.0.1
G'day Brian,
On Sat, 18 May 2013 10:28:43 +0100
Prof Brian Ripley rip...@stats.ox.ac.uk wrote:
[...]
Is it necessary for R = 3.0.1 to have one build as
main-architecture and the other one as sub-architecture? I could
not find anything in the NEWS file or the Admin manual that
indicated that this would now be necessary.
Not exclusively, but as the Mac build no longer uses this, we do need
people who do to test pre-releases. One of us needs to build such a
setup and test it
Either that, or amend the administration and installation manual to
state that one installation should not be a sub-architecture
installation. :)
But the latter solution also seems to have some problems. My usual
install script did the following:
1) Run ./configure with 'r_arch=32' (and a few other options) using a
config.site, configured for a 32bit build; followed by make
2) make check ; make install
3) `make distclean'; run ./configure with 'r_arch=64' (and a few other
options using a config.site configured for a 64 bit build; followed
by make
4) make check ; make install
5) make pdf info; make install-pdf install-info
When trying to install Rgraphviz afterwards (mmh, this is a
BioConductor package and not a CRAN package, so perhaps I should ask on
their lists?), Rgrahviz couldn't find the correct compiler settings as
R CMD config ... did not work (as reported originally).
So I changed my install script to remove the 'r_arch=64' in step 3.
(The modified script is attached.) But now, trying to install
Rgraphviz falls over earlier when a dependencies of Rgraphviz,
BiocGenerics, is installed. Trying to install BiocGenerics fails with:
[...]
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - 32
*** arch - R
ERROR: sub-architecture 'R' is not installed
ERROR: loading failed for 'R'
* removing '/opt/R/R-3.0.1/lib/R/library/BiocGenerics'
I have no idea why the process tries to check for an 'arch - R'. But
this seems to be happening for packages that do not contain code that
needs to be compiled, another example is 'car' which is needed by 'AER'.
So I am bit puzzled how I should change my scripts. Does step 3 needs
something stronger than 'make distclean'? Or should the 'r_arch=32' be
dropped in step 1 but step 3 should use 'r_arch=64'?
Essentially, I would like to install 32bit and 64bit builds on my
machines, with one or both as sub-architectures (to save space) and
with the 64bit the 'default', i.e. the one that is run by
${R_HOME}/bin/R.
Cheers,
Berwin
#!/bin/bash -e
VERSION=3.0.1
part1a ()
{
cd /opt/src/R-$VERSION
echo **
echo *** configure (32bit)
echo **
cp ../R-config.site-32 config.site
./configure --prefix=/opt/R/R-$VERSION --with-blas --with-lapack
--enable-R-shlib r_arch=32 | tee CONFIGURE_32
echo *
echo *** make (32 bit)
echo *
make -j6
}
part2()
{
echo *
echo *** make check
echo *
make check
make install
}
part1b ()
{
echo **
echo *** configure (64bit)
echo **
make distclean
cp ../R-config.site-64 config.site
./configure --prefix=/opt/R/R-$VERSION --with-blas --with-lapack
--enable-R-shlib | tee CONFIGURE_64
echo *
echo *** make (64 bit)
echo *
make -j6
}
part3 ()
{
echo **
echo *** make documentation
echo **
make pdf info
make install-pdf install-info
}
export http_proxy=http://proxy.uwa.edu.au:
export LANG=en_AU.UTF-8
echo Installing R-$VERSION
part1a /opt/src/R-$VERSION-LOG 21
part2/opt/src/R-$VERSION-CheckLOG 21
part1b /opt/src/R-$VERSION-LOG 21
part2 /opt/src/R-$VERSION-CheckLOG 21
part3 /opt/src/R-$VERSION-LOG 21
echo Done
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Re: [Rd] R CMD config for R = 3.0.1
Could you try current R-patched or R-devel? Works in my tests at least.
On 19/05/2013 08:25, Berwin A Turlach wrote:
G'day Brian,
On Sat, 18 May 2013 10:28:43 +0100
Prof Brian Ripley rip...@stats.ox.ac.uk wrote:
[...]
Is it necessary for R = 3.0.1 to have one build as
main-architecture and the other one as sub-architecture? I could
not find anything in the NEWS file or the Admin manual that
indicated that this would now be necessary.
Not exclusively, but as the Mac build no longer uses this, we do need
people who do to test pre-releases. One of us needs to build such a
setup and test it
Either that, or amend the administration and installation manual to
state that one installation should not be a sub-architecture
installation. :)
That is not sufficient. AFAICS the issue only occurs after installation
(which is probably why no one else saw it), and the Renviron files for
the different sub-architectures will be different (in R_PLATFORM).
But the latter solution also seems to have some problems. My usual
install script did the following:
1) Run ./configure with 'r_arch=32' (and a few other options) using a
config.site, configured for a 32bit build; followed by make
2) make check ; make install
3) `make distclean'; run ./configure with 'r_arch=64' (and a few other
options using a config.site configured for a 64 bit build; followed
by make
4) make check ; make install
5) make pdf info; make install-pdf install-info
When trying to install Rgraphviz afterwards (mmh, this is a
BioConductor package and not a CRAN package, so perhaps I should ask on
their lists?), Rgrahviz couldn't find the correct compiler settings as
R CMD config ... did not work (as reported originally).
So I changed my install script to remove the 'r_arch=64' in step 3.
(The modified script is attached.) But now, trying to install
Rgraphviz falls over earlier when a dependencies of Rgraphviz,
BiocGenerics, is installed. Trying to install BiocGenerics fails with:
[...]
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - 32
*** arch - R
ERROR: sub-architecture 'R' is not installed
ERROR: loading failed for 'R'
* removing '/opt/R/R-3.0.1/lib/R/library/BiocGenerics'
I have no idea why the process tries to check for an 'arch - R'. But
this seems to be happening for packages that do not contain code that
needs to be compiled, another example is 'car' which is needed by 'AER'.
So I am bit puzzled how I should change my scripts. Does step 3 needs
something stronger than 'make distclean'? Or should the 'r_arch=32' be
dropped in step 1 but step 3 should use 'r_arch=64'?
Essentially, I would like to install 32bit and 64bit builds on my
machines, with one or both as sub-architectures (to save space) and
with the 64bit the 'default', i.e. the one that is run by
${R_HOME}/bin/R.
Cheers,
Berwin
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
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Re: [Rd] R CMD config for R = 3.0.1
G'day Brian, On Sun, 19 May 2013 08:40:04 +0100 Prof Brian Ripley rip...@stats.ox.ac.uk wrote: Could you try current R-patched or R-devel? Works in my tests at least. Tried R-patched (2013-05-18 r62762) and R-devel (2013-05-18 r62762), installed with my original script. Things seem fine when I try to install my usual selection of packages in either of those versions. Loading under correct (and existing) architectures is tested and packages that query the configuration get the correct answers from `R CMD config'. Thank you very much for the help. Cheers, Berwin __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R CMD config for R = 3.0.1
Dear all,
When installing the usual packages that I use, after installing R
3.0.1, I noticed that the installation of some packages that query R about
its configuration did not succeed. The problem is exemplified by:
berwin@bossiaea:~$ R-3.0.1 CMD config CC
/opt/R/R-3.0.1/lib/R/bin/config: 222: .: Can't open
/opt/R/R-3.0.1/lib/R/etc/Renviron
Prior to R 3.0.1 such commands worked fine:
berwin@bossiaea:~$ R-3.0.0 CMD config CC
gcc -std=gnu99
I noticed now that my installations of the development and
patched version of R have the same problem (since I usually do not install
packages in those versions that query the configuration, I hadn't
noticed the issue earlier).
The problem seems to be line 222 of `R RHOME`/bin/config (when R is R
3.0.1) which reads:
. ${R_HOME}/etc/Renviron
The file ${R_HOME}/etc/Renviron does not necessarily exists if one has
opted for 32/64-bit builds and installed both as sub-architectures,
which I have. In my installation ${R_HOME}/etc/32/Renviron and
${R_HOME}/etc/64/Renviron exist, but no ${R_HOME}/etc/Renviron.
Is it necessary for R = 3.0.1 to have one build as
main-architecture and the other one as sub-architecture? I could not
find anything in the NEWS file or the Admin manual that indicated that
this would now be necessary.
Cheers,
Berwin
For completeness:
I am running an Ubuntu 12.04 system and:
berwin@bossiaea:~$ echo sessionInfo() | R-3.0.1 --slave
R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu/64 (64-bit)
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methodsbase
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Re: [Rd] R CMD config for R = 3.0.1
On 18/05/2013 07:54, Berwin A Turlach wrote:
Dear all,
When installing the usual packages that I use, after installing R
3.0.1, I noticed that the installation of some packages that query R about
its configuration did not succeed. The problem is exemplified by:
berwin@bossiaea:~$ R-3.0.1 CMD config CC
/opt/R/R-3.0.1/lib/R/bin/config: 222: .: Can't open
/opt/R/R-3.0.1/lib/R/etc/Renviron
Prior to R 3.0.1 such commands worked fine:
berwin@bossiaea:~$ R-3.0.0 CMD config CC
gcc -std=gnu99
I noticed now that my installations of the development and
patched version of R have the same problem (since I usually do not install
packages in those versions that query the configuration, I hadn't
noticed the issue earlier).
The problem seems to be line 222 of `R RHOME`/bin/config (when R is R
3.0.1) which reads:
. ${R_HOME}/etc/Renviron
The file ${R_HOME}/etc/Renviron does not necessarily exists if one has
opted for 32/64-bit builds and installed both as sub-architectures,
which I have. In my installation ${R_HOME}/etc/32/Renviron and
${R_HOME}/etc/64/Renviron exist, but no ${R_HOME}/etc/Renviron.
Is it necessary for R = 3.0.1 to have one build as
main-architecture and the other one as sub-architecture? I could not
find anything in the NEWS file or the Admin manual that indicated that
this would now be necessary.
Not exclusively, but as the Mac build no longer uses this, we do need
people who do to test pre-releases. One of us needs to build such a
setup and test it
Cheers,
Berwin
For completeness:
I am running an Ubuntu 12.04 system and:
berwin@bossiaea:~$ echo sessionInfo() | R-3.0.1 --slave
R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu/64 (64-bit)
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methodsbase
__
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--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
