I feel like Marlon Brando in "On the Waterfront" where he's told "It's not your night, kid", except for me it has been the last two months trying to debug memory problems. Now I can't even install an old version of this package on a netbook running the Ubuntu 10.10 netbook remix because it can't find the libraries libf77blas and libatlas. I have even gone to the extent of removing the r-base-core package entirely and removing libatlas3gf-base then reinstalling everything. I still get bates at eeek:/var/tmp$ R CMD INSTALL lme4_0.999375-37.tar.gz * installing to library ?/home/bates/R/i686-pc-linux-gnu-library/2.12? * installing *source* package ?lme4? ... ** libs gcc -I/usr/share/R/include -I"/usr/lib/R/library/Matrix/include" -I"/usr/lib/R/library/stats/include" -fpic -std=gnu99 -O3 -pipe -g -c init.c -o init.o gcc -I/usr/share/R/include -I"/usr/lib/R/library/Matrix/include" -I"/usr/lib/R/library/stats/include" -fpic -std=gnu99 -O3 -pipe -g -c lmer.c -o lmer.o gcc -I/usr/share/R/include -I"/usr/lib/R/library/Matrix/include" -I"/usr/lib/R/library/stats/include" -fpic -std=gnu99 -O3 -pipe -g -c local_stubs.c -o local_stubs.o gcc -shared -o lme4.so init.o lmer.o local_stubs.o -llapack -lf77blas -latlas -lgfortran -lm -L/usr/lib/R/lib -lR /usr/bin/ld: cannot find -lf77blas /usr/bin/ld: cannot find -latlas collect2: ld returned 1 exit status make: *** [lme4.so] Error 1 ERROR: compilation failed for package ?lme4? * removing ?/home/bates/R/i686-pc-linux-gnu-library/2.12/lme4? The thing that seems to be missing in /usr/lib/ is a symbolic link from libatlas.so.3gf to libatlas.so. All I have is lrwxrwxrwx 1 root root 33 2011-01-28 09:37 libatlas.so.3gf -> /etc/alternatives/libatlas.so.3gf Can someone tell me if I should see a link from libatlas.so.3gf to libatlas.so?
Dirk Eddelbuettel
2011-Jan-28 16:15 UTC
[R-sig-Debian] R CMD INSTALL cannot find libf77blas
On 28 January 2011 at 09:49, Douglas Bates wrote:
| I feel like Marlon Brando in "On the Waterfront" where he's told
"It's
| not your night, kid", except for me it has been the last two months
| trying to debug memory problems. Now I can't even install an old
| version of this package on a netbook running the Ubuntu 10.10 netbook
| remix because it can't find the libraries libf77blas and libatlas.
|
| I have even gone to the extent of removing the r-base-core package
| entirely and removing libatlas3gf-base then reinstalling everything.
| I still get
|
|
| bates at eeek:/var/tmp$ R CMD INSTALL lme4_0.999375-37.tar.gz
| * installing to library ?/home/bates/R/i686-pc-linux-gnu-library/2.12?
| * installing *source* package ?lme4? ...
| ** libs
| gcc -I/usr/share/R/include -I"/usr/lib/R/library/Matrix/include"
| -I"/usr/lib/R/library/stats/include" -fpic -std=gnu99 -O3 -pipe
-g
| -c init.c -o init.o
| gcc -I/usr/share/R/include -I"/usr/lib/R/library/Matrix/include"
| -I"/usr/lib/R/library/stats/include" -fpic -std=gnu99 -O3 -pipe
-g
| -c lmer.c -o lmer.o
| gcc -I/usr/share/R/include -I"/usr/lib/R/library/Matrix/include"
| -I"/usr/lib/R/library/stats/include" -fpic -std=gnu99 -O3 -pipe
-g
| -c local_stubs.c -o local_stubs.o
| gcc -shared -o lme4.so init.o lmer.o local_stubs.o -llapack -lf77blas
| -latlas -lgfortran -lm -L/usr/lib/R/lib -lR
| /usr/bin/ld: cannot find -lf77blas
| /usr/bin/ld: cannot find -latlas
| collect2: ld returned 1 exit status
| make: *** [lme4.so] Error 1
| ERROR: compilation failed for package ?lme4?
| * removing ?/home/bates/R/i686-pc-linux-gnu-library/2.12/lme4?
|
| The thing that seems to be missing in /usr/lib/ is a symbolic link
| from libatlas.so.3gf to libatlas.so. All I have is
|
|
| lrwxrwxrwx 1 root root 33 2011-01-28 09:37
| libatlas.so.3gf -> /etc/alternatives/libatlas.so.3gf
|
| Can someone tell me if I should see a link from libatlas.so.3gf to
libatlas.so?
Weird. This all works so reliably ... that I even wrote a CRAN package /
paper exploiting all this mechanically --- see 'gcbd'. (Did I ever send
you
the paper for comments?)
It has a utilies.R in which I define purge and install wrapper to get atlas
(3.6 from Ubuntu), MKL (via REvo in Ubuntu 9.10), Atlas39 (local package) and
Goto (local package via the wondeful helper package from Tokyo). For Atlas
these do
installAtlas <- function() {
res <- system("sudo apt-get -y --force-yes install
libatlas3gf-base", intern=TRUE, ignore.stderr=TRUE)
invisible(res)
}
purgeAtlas <- function() {
##-- old local build wajig purge libatlas-base-dev libatlas-dev
libatlas3gf-amd64sse3 libatlas3gf-base
res <- system("sudo apt-get -y --force-yes purge
libatlas3gf-base", intern=TRUE, ignore.stderr=TRUE)
invisible(res)
}
I'd be more than happy to compare notes with you. My netbook has
libatlas3gf-base installed, it has
edd at dexter:~$ ls -l /usr/lib/libf77blas.so* /etc/alternatives/libf77blas.so*
lrwxrwxrwx 1 root root 33 2010-11-04 10:50 /etc/alternatives/libf77blas.so ->
/usr/lib/atlas-base/libf77blas.so
lrwxrwxrwx 1 root root 37 2010-10-29 14:00 /etc/alternatives/libf77blas.so.3gf
-> /usr/lib/atlas-base/libf77blas.so.3gf
lrwxrwxrwx 1 root root 31 2010-11-04 10:50 /usr/lib/libf77blas.so ->
/etc/alternatives/libf77blas.so
lrwxrwxrwx 1 root root 35 2010-10-29 14:00 /usr/lib/libf77blas.so.3gf ->
/etc/alternatives/libf77blas.so.3gf
edd at dexter:~$
The actual links are in /usr/lib/atlas-base/ which gets added to ld.so's
list
of directories.
AFAICT this mechanism hasn't really changed in years.
Dirk
|
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--
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
use synaptic , search using fortran77 and blas and atlas (separately) and install all those libs- not an exact answer but thats what worked for my ubuntu 10.10 couple of days back specifically ubuntu packages 4.0-2 (libcnf-dev) 3.0.0-1ubuntu1 (revolution-mkl) 1:4.1.1-5 (libnetcdf6) 3.8.3-22ubuntu2 (libatlas-base-dev) I am not sure but I these were the packages that finally got the job done- using synaptic Websites- http://decisionstats.com On Fri, Jan 28, 2011 at 9:19 PM, Douglas Bates <bates@stat.wisc.edu> wrote:> I feel like Marlon Brando in "On the Waterfront" where he's told "It's > not your night, kid", except for me it has been the last two months > trying to debug memory problems. Now I can't even install an old > version of this package on a netbook running the Ubuntu 10.10 netbook > remix because it can't find the libraries libf77blas and libatlas. > > I have even gone to the extent of removing the r-base-core package > entirely and removing libatlas3gf-base then reinstalling everything. > I still get > > > bates@eeek:/var/tmp$ R CMD INSTALL lme4_0.999375-37.tar.gz > * installing to library ‘/home/bates/R/i686-pc-linux-gnu-library/2.12’ > * installing *source* package ‘lme4’ ... > ** libs > gcc -I/usr/share/R/include -I"/usr/lib/R/library/Matrix/include" > -I"/usr/lib/R/library/stats/include" -fpic -std=gnu99 -O3 -pipe -g > -c init.c -o init.o > gcc -I/usr/share/R/include -I"/usr/lib/R/library/Matrix/include" > -I"/usr/lib/R/library/stats/include" -fpic -std=gnu99 -O3 -pipe -g > -c lmer.c -o lmer.o > gcc -I/usr/share/R/include -I"/usr/lib/R/library/Matrix/include" > -I"/usr/lib/R/library/stats/include" -fpic -std=gnu99 -O3 -pipe -g > -c local_stubs.c -o local_stubs.o > gcc -shared -o lme4.so init.o lmer.o local_stubs.o -llapack -lf77blas > -latlas -lgfortran -lm -L/usr/lib/R/lib -lR > /usr/bin/ld: cannot find -lf77blas > /usr/bin/ld: cannot find -latlas > collect2: ld returned 1 exit status > make: *** [lme4.so] Error 1 > ERROR: compilation failed for package ‘lme4’ > * removing ‘/home/bates/R/i686-pc-linux-gnu-library/2.12/lme4’ > > The thing that seems to be missing in /usr/lib/ is a symbolic link > from libatlas.so.3gf to libatlas.so. All I have is > > > lrwxrwxrwx 1 root root 33 2011-01-28 09:37 > libatlas.so.3gf -> /etc/alternatives/libatlas.so.3gf > > Can someone tell me if I should see a link from libatlas.so.3gf to > libatlas.so? > > _______________________________________________ > R-SIG-Debian mailing list > R-SIG-Debian@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-debian >[[alternative HTML version deleted]]