Hi.
On all of my machines, except for a netbook cursed with the GMA500
chipset, the R packages are synced to lenny-cran.
I have been using rpy in a chroot using the official lenny
R packages (2.7.1) given that i have not been able to find
compatible rpy deb packages to work with lenny-cran.
I am able to build the rpy deb package from source in
a 32-bit lenny chroot (with the stock R packages) using
the following sequence
kolmogorov:/tmp$ sudo apt-get source python-rpy
kolmogorov:/tmp/rpy-1.0.3$ sudo apt-get build-dep python-rpy
kolmogorov:/tmp/rpy-1.0.3$ sudo dch -l local 'localrpy'
kolmogorov:/tmp/rpy-1.0.3$ sudo debuild -us -uc
I am running into problems when I am trying to build
the deb packages from source against the AMD64 lenny-cran
packages. Specifically the last step fails. It complains
about (among other things) not finding the R version.
This command seems to work
$ R --version
R version 2.11.0 (2010-04-22)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
I hope that this is an appropriate forum for seeking
help for building rpy against the lenny-cran R packages.
Sincerely,
Kouros
Kouros Owzar
Biostatistics and Bioinformatics
Duke University
kolmogorov:/tmp/rpy-1.0.3# debuild -us -uc
dpkg-buildpackage -rfakeroot -D -us -uc
dpkg-buildpackage: warning: using a gain-root-command while being root
dpkg-buildpackage: set CFLAGS to default value: -g -O2
dpkg-buildpackage: set CPPFLAGS to default value:
dpkg-buildpackage: set LDFLAGS to default value:
dpkg-buildpackage: set FFLAGS to default value: -g -O2
dpkg-buildpackage: set CXXFLAGS to default value: -g -O2
dpkg-buildpackage: source package rpy
dpkg-buildpackage: source version 1.0.3-2local1
dpkg-buildpackage: source changed by root <root at kolmogorov>
dpkg-buildpackage: host architecture amd64
fakeroot debian/rules clean
dh_testdir
dh_testroot
rm -f build-stamp configure-stamp
[ ! -f Makefile ] || /usr/bin/make distclean
(cd doc/ && make clean && rm -vf manual.pdf manual.info
manual.dvi \
&& rm -vfr manual_html manual_html.tgz)
make[1]: Entering directory `/tmp/rpy-1.0.3/doc'
rm -f rpy.cp rpy.cps rpy.fn rpy.fns rpy.ky
rm -f rpy.kys rpy.log rpy.pg rpy.pgs rpy.tmp
rm -f rpy.toc rpy.tp rpy.tps rpy.vr rpy.vrs
rm -f rpy.aux
make[1]: Leaving directory `/tmp/rpy-1.0.3/doc'
for python in python2.4 python2.5; \
do $python setup.py clean; \
done
RHOMES= []
DEBUG= True
Setting RHOMES to ['/usr/lib64/R']
Traceback (most recent call last):
File "setup.py", line 109, in ?
RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True)
File "/tmp/rpy-1.0.3/rpy_tools.py", line 103, in get_R_VERSION
raise RuntimeError("Couldn't obtain version number from
output\n"
RuntimeError: Couldn't obtain version number from output
of `R --version'.
RHOMES= []
DEBUG= True
Setting RHOMES to ['/usr/lib64/R']
Traceback (most recent call last):
File "setup.py", line 109, in <module>
RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True)
File "/tmp/rpy-1.0.3/rpy_tools.py", line 103, in get_R_VERSION
raise RuntimeError("Couldn't obtain version number from
output\n"
RuntimeError: Couldn't obtain version number from output
of `R --version'.
make: *** [clean] Error 1
dpkg-buildpackage: failure: fakeroot debian/rules clean gave error exit
status 2
debuild: fatal error at line 1319:
dpkg-buildpackage -rfakeroot -D -us -uc failed
Hi Kouros, I can not tell you why building rpy on amd64 did not work in your case. Anyway, I have reincluded rpy into the list of supported packages for the factory fresh backport of R 2.11.1 to lenny. The packages should arrive at CRAN tomorrow. Kind regards, Johannes Am Montag, 31. Mai 2010, um 08:26:02 schrieb owzar001:> Hi. > > On all of my machines, except for a netbook cursed with the GMA500 > chipset, the R packages are synced to lenny-cran. > > I have been using rpy in a chroot using the official lenny > R packages (2.7.1) given that i have not been able to find > compatible rpy deb packages to work with lenny-cran. > > I am able to build the rpy deb package from source in > a 32-bit lenny chroot (with the stock R packages) using > the following sequence > > kolmogorov:/tmp$ sudo apt-get source python-rpy > kolmogorov:/tmp/rpy-1.0.3$ sudo apt-get build-dep python-rpy > kolmogorov:/tmp/rpy-1.0.3$ sudo dch -l local 'localrpy' > kolmogorov:/tmp/rpy-1.0.3$ sudo debuild -us -uc > > I am running into problems when I am trying to build > the deb packages from source against the AMD64 lenny-cran > packages. Specifically the last step fails. It complains > about (among other things) not finding the R version. > > This command seems to work > $ R --version > R version 2.11.0 (2010-04-22) > Copyright (C) 2010 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > > > I hope that this is an appropriate forum for seeking > help for building rpy against the lenny-cran R packages. > > Sincerely, > > Kouros > > > Kouros Owzar > Biostatistics and Bioinformatics > Duke University > > kolmogorov:/tmp/rpy-1.0.3# debuild -us -uc > dpkg-buildpackage -rfakeroot -D -us -uc > dpkg-buildpackage: warning: using a gain-root-command while being root > dpkg-buildpackage: set CFLAGS to default value: -g -O2 > dpkg-buildpackage: set CPPFLAGS to default value: > dpkg-buildpackage: set LDFLAGS to default value: > dpkg-buildpackage: set FFLAGS to default value: -g -O2 > dpkg-buildpackage: set CXXFLAGS to default value: -g -O2 > dpkg-buildpackage: source package rpy > dpkg-buildpackage: source version 1.0.3-2local1 > dpkg-buildpackage: source changed by root <root at kolmogorov> > dpkg-buildpackage: host architecture amd64 > fakeroot debian/rules clean > dh_testdir > dh_testroot > rm -f build-stamp configure-stamp > [ ! -f Makefile ] || /usr/bin/make distclean > (cd doc/ && make clean && rm -vf manual.pdf manual.info manual.dvi \ > && rm -vfr manual_html manual_html.tgz) > make[1]: Entering directory `/tmp/rpy-1.0.3/doc' > rm -f rpy.cp rpy.cps rpy.fn rpy.fns rpy.ky > rm -f rpy.kys rpy.log rpy.pg rpy.pgs rpy.tmp > rm -f rpy.toc rpy.tp rpy.tps rpy.vr rpy.vrs > rm -f rpy.aux > make[1]: Leaving directory `/tmp/rpy-1.0.3/doc' > for python in python2.4 python2.5; \ > do $python setup.py clean; \ > done > RHOMES= [] > DEBUG= True > Setting RHOMES to ['/usr/lib64/R'] > Traceback (most recent call last): > File "setup.py", line 109, in ? > RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True) > File "/tmp/rpy-1.0.3/rpy_tools.py", line 103, in get_R_VERSION > raise RuntimeError("Couldn't obtain version number from output\n" > RuntimeError: Couldn't obtain version number from output > of `R --version'. > > RHOMES= [] > DEBUG= True > Setting RHOMES to ['/usr/lib64/R'] > Traceback (most recent call last): > File "setup.py", line 109, in <module> > RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True) > File "/tmp/rpy-1.0.3/rpy_tools.py", line 103, in get_R_VERSION > raise RuntimeError("Couldn't obtain version number from output\n" > RuntimeError: Couldn't obtain version number from output > of `R --version'. > > make: *** [clean] Error 1 > dpkg-buildpackage: failure: fakeroot debian/rules clean gave error exit > status 2 > debuild: fatal error at line 1319: > dpkg-buildpackage -rfakeroot -D -us -uc failed > > _______________________________________________ > R-SIG-Debian mailing list > R-SIG-Debian at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-debian
On 31 May 2010 at 02:26, owzar001 wrote:
| Hi.
|
| On all of my machines, except for a netbook cursed with the GMA500
| chipset, the R packages are synced to lenny-cran.
|
| I have been using rpy in a chroot using the official lenny
| R packages (2.7.1) given that i have not been able to find
| compatible rpy deb packages to work with lenny-cran.
|
| I am able to build the rpy deb package from source in
| a 32-bit lenny chroot (with the stock R packages) using
| the following sequence
|
| kolmogorov:/tmp$ sudo apt-get source python-rpy
| kolmogorov:/tmp/rpy-1.0.3$ sudo apt-get build-dep python-rpy
| kolmogorov:/tmp/rpy-1.0.3$ sudo dch -l local 'localrpy'
| kolmogorov:/tmp/rpy-1.0.3$ sudo debuild -us -uc
|
| I am running into problems when I am trying to build
| the deb packages from source against the AMD64 lenny-cran
| packages. Specifically the last step fails. It complains
| about (among other things) not finding the R version.
That may be a clue as there is an oooooold bug in rpy -- each R triggers a
need for new build as the R version gets hardcoded into the library name.
Worse, the regexp assume single digits for each of a.b.c which started to
break with R 2.10.0 (as 10 has two digits). The patch I once committed is
simple, so try rpy from svn, or from a more recent Debian package. IIRC the
fix was
# edd 05 Apr 2006 version = re.search("R +([0-9]\.[0-9]\.[0-9])",
output)
# edd 16 Oct 2009 version = re.search("R
+([0-9]\.[0-9]+\.[0-9])", output)
version = re.search(" +([0-9]\.[0-9]+\.[0-9])", output)
this in rpy_tools.py. See if that helps.
Dirk
| This command seems to work
| $ R --version
| R version 2.11.0 (2010-04-22)
| Copyright (C) 2010 The R Foundation for Statistical Computing
| ISBN 3-900051-07-0
|
|
| I hope that this is an appropriate forum for seeking
| help for building rpy against the lenny-cran R packages.
|
| Sincerely,
|
| Kouros
|
|
| Kouros Owzar
| Biostatistics and Bioinformatics
| Duke University
|
| kolmogorov:/tmp/rpy-1.0.3# debuild -us -uc
| dpkg-buildpackage -rfakeroot -D -us -uc
| dpkg-buildpackage: warning: using a gain-root-command while being root
| dpkg-buildpackage: set CFLAGS to default value: -g -O2
| dpkg-buildpackage: set CPPFLAGS to default value:
| dpkg-buildpackage: set LDFLAGS to default value:
| dpkg-buildpackage: set FFLAGS to default value: -g -O2
| dpkg-buildpackage: set CXXFLAGS to default value: -g -O2
| dpkg-buildpackage: source package rpy
| dpkg-buildpackage: source version 1.0.3-2local1
| dpkg-buildpackage: source changed by root <root at kolmogorov>
| dpkg-buildpackage: host architecture amd64
| fakeroot debian/rules clean
| dh_testdir
| dh_testroot
| rm -f build-stamp configure-stamp
| [ ! -f Makefile ] || /usr/bin/make distclean
| (cd doc/ && make clean && rm -vf manual.pdf manual.info
manual.dvi \
| && rm -vfr manual_html manual_html.tgz)
| make[1]: Entering directory `/tmp/rpy-1.0.3/doc'
| rm -f rpy.cp rpy.cps rpy.fn rpy.fns rpy.ky
| rm -f rpy.kys rpy.log rpy.pg rpy.pgs rpy.tmp
| rm -f rpy.toc rpy.tp rpy.tps rpy.vr rpy.vrs
| rm -f rpy.aux
| make[1]: Leaving directory `/tmp/rpy-1.0.3/doc'
| for python in python2.4 python2.5; \
| do $python setup.py clean; \
| done
| RHOMES= []
| DEBUG= True
| Setting RHOMES to ['/usr/lib64/R']
| Traceback (most recent call last):
| File "setup.py", line 109, in ?
| RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True)
| File "/tmp/rpy-1.0.3/rpy_tools.py", line 103, in get_R_VERSION
| raise RuntimeError("Couldn't obtain version number from
output\n"
| RuntimeError: Couldn't obtain version number from output
| of `R --version'.
|
| RHOMES= []
| DEBUG= True
| Setting RHOMES to ['/usr/lib64/R']
| Traceback (most recent call last):
| File "setup.py", line 109, in <module>
| RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True)
| File "/tmp/rpy-1.0.3/rpy_tools.py", line 103, in get_R_VERSION
| raise RuntimeError("Couldn't obtain version number from
output\n"
| RuntimeError: Couldn't obtain version number from output
| of `R --version'.
|
| make: *** [clean] Error 1
| dpkg-buildpackage: failure: fakeroot debian/rules clean gave error exit
| status 2
| debuild: fatal error at line 1319:
| dpkg-buildpackage -rfakeroot -D -us -uc failed
|
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian
--
Regards, Dirk
> ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 1 Jun 2010 00:58:30 +0200 > From: Johannes Ranke <jranke at uni-bremen.de> > To: r-sig-debian at r-project.org > Subject: Re: [R-sig-Debian] building rpy against lenny-cran > Message-ID: <201006010058.31443.jranke at uni-bremen.de> > Content-Type: Text/Plain; charset="iso-8859-1" > > Hi Kouros, > > I can not tell you why building rpy on amd64 did not work in your case. > Anyway, I have reincluded rpy into the list of supported packages for > the factory fresh backport of R 2.11.1 to lenny. The packages should arrive at > CRAN tomorrow.Hi Johannes. I hope that you are well (I thought about you two weeks ago as I was driving past Cedar Cliff enroute to my parents). I was able to build the rpy package against lenny-cran thanks to two suggestions by Dirk (documented in my reply to Dirk). Thanks for contributing rpy deb packages to CRAN. These will be very helpful. Take care, Kouros
Hi Kouros, mhm, did we go to Cedar Cliff together? Did we go to model UN together? In this case I remember you as both intelligent and ambitious :) I am doing fine, working in an commercial environment since almost two years, but trying to keep up good science as well as possible. What have you been up to? Im am sure you know Ken Gehosky who was my best friend at Cedar Cliff is now teaching there - I thought this was kind of funny... Sincerely, Johannes Am Dienstag, 1. Juni 2010, um 14:50:14 schrieb owzar001:> > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 1 Jun 2010 00:58:30 +0200 > > From: Johannes Ranke <jranke at uni-bremen.de> > > To: r-sig-debian at r-project.org > > Subject: Re: [R-sig-Debian] building rpy against lenny-cran > > Message-ID: <201006010058.31443.jranke at uni-bremen.de> > > Content-Type: Text/Plain; charset="iso-8859-1" > > > > Hi Kouros, > > > > I can not tell you why building rpy on amd64 did not work in your case. > > Anyway, I have reincluded rpy into the list of supported packages for > > the factory fresh backport of R 2.11.1 to lenny. The packages should > > arrive at CRAN tomorrow. > > Hi Johannes. > > I hope that you are well (I thought about you two weeks ago as I was > driving past Cedar Cliff enroute to my parents). > > I was able to build the rpy package against lenny-cran thanks to two > suggestions by Dirk (documented in my reply to Dirk). > > Thanks for contributing rpy deb packages to CRAN. These will be very > helpful. > > Take care, Kouros > > _______________________________________________ > R-SIG-Debian mailing list > R-SIG-Debian at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-debian