I am forwarding the below message from our sys-admin because I don't
know what the problem is. We are getting a "No space left on device"
error when there is plenty of space. See below.
Mark Lyman
From: Palmer, Michael
Sent: Monday, April 27, 2009 12:09 PM
To: Lyman, Mark
Subject: Install of R 2.9.0
Mark -
I'm having trouble installing R-2.9.0. During "make install" it thinks
it's running out of space when there's actually lots of space available.
I'm installing this on the head node of a cluster running SLES 9 into a
common GPFS filesystem named /apps. Any ideas?
These are the basic steps I'm using to install R -
Create a directory - /apps/R/R290
Copy the tar file to /apps/R/R290
cd /apps/R/R290
tar -xzvf R-2.9.0.tar.gz
cd R-2.9.0
./configure prefix=/apps/R/R290
make
make check
make install
all appears to go well until well into "make install". The first
indication of errors is -
head:/apps/R/R290/R-2.9.0 # make install
mkdir -p -- /apps/R/R290/lib64/R
make[1]: Entering directory `/apps/R/R290/R-2.9.0/m4'
make[1]: Nothing to be done for `install'.
make[1]: Leaving directory `/apps/R/R290/R-2.9.0/m4'
make[1]: Entering directory `/apps/R/R290/R-2.9.0/tools'
make[1]: Nothing to be done for `install'.
make[1]: Leaving directory `/apps/R/R290/R-2.9.0/tools'
make[1]: Entering directory `/apps/R/R290/R-2.9.0/doc'
installing doc ...
mkdir -p -- /apps/R/R290/lib64/R/doc
mkdir -p -- /apps/R/R290/share/man/man1
/usr/bin/install -c -m 644 ../NEWS "/apps/R/R290/lib64/R/doc"
make[2]: Entering directory `/apps/R/R290/R-2.9.0/doc/html'
installing doc/html ...
mkdir -p -- /apps/R/R290/lib64/R/doc/html
make[3]: Entering directory `/apps/R/R290/R-2.9.0/doc/html/search'
installing doc/html/search ...
mkdir -p -- /apps/R/R290/lib64/R/doc/html/search
make[3]: Leaving directory `/apps/R/R290/R-2.9.0/doc/html/search'
make[2]: Leaving directory `/apps/R/R290/R-2.9.0/doc/html'
make[2]: Entering directory `/apps/R/R290/R-2.9.0/doc/manual'
installing doc/manual ...
mkdir -p -- /apps/R/R290/lib64/R/doc/manual
make[2]: Leaving directory `/apps/R/R290/R-2.9.0/doc/manual'
make[1]: Leaving directory `/apps/R/R290/R-2.9.0/doc'
make[1]: Entering directory `/apps/R/R290/R-2.9.0/etc'
mkdir -p -- /apps/R/R290/lib64/R/etc
installing etc ...
make[1]: Leaving directory `/apps/R/R290/R-2.9.0/etc'
make[1]: Entering directory `/apps/R/R290/R-2.9.0/share'
installing share ...
mkdir -p -- /apps/R/R290/lib64/R/share
mkdir -p -- /apps/R/R290/lib64/R/share/R
mkdir -p -- /apps/R/R290/lib64/R/share/encodings
mkdir -p -- /apps/R/R290/lib64/R/share/java
mkdir -p -- /apps/R/R290/lib64/R/share/licenses
mkdir -p -- /apps/R/R290/lib64/R/share/make
mkdir -p -- /apps/R/R290/lib64/R/share/perl
mkdir -p -- /apps/R/R290/lib64/R/share/perl/R
mkdir -p -- /apps/R/R290/lib64/R/share/perl/File/Copy
mkdir -p -- /apps/R/R290/lib64/R/share/perl/Text
mkdir -p -- /apps/R/R290/lib64/R/share/sh
mkdir -p -- /apps/R/R290/lib64/R/share/texmf
make[1]: Leaving directory `/apps/R/R290/R-2.9.0/share'
make[1]: Entering directory `/apps/R/R290/R-2.9.0/src'
make[2]: Entering directory `/apps/R/R290/R-2.9.0/src/scripts'
mkdir -p -- /apps/R/R290/bin
mkdir -p -- /apps/R/R290/lib64/R/bin
make[2]: Leaving directory `/apps/R/R290/R-2.9.0/src/scripts'
make[2]: Entering directory `/apps/R/R290/R-2.9.0/src/include'
mkdir -p -- /apps/R/R290/lib64/R/include
make[3]: Entering directory `/apps/R/R290/R-2.9.0/src/include/R_ext'
mkdir -p -- /apps/R/R290/lib64/R/include/R_ext
make[3]: Leaving directory `/apps/R/R290/R-2.9.0/src/include/R_ext'
make[2]: Leaving directory `/apps/R/R290/R-2.9.0/src/include'
make[2]: Entering directory `/apps/R/R290/R-2.9.0/src/extra'
make[3]: Entering directory `/apps/R/R290/R-2.9.0/src/extra/blas'
mkdir -p -- /apps/R/R290/lib64/R/lib
make[3]: Leaving directory `/apps/R/R290/R-2.9.0/src/extra/blas'
make[3]: Entering directory `/apps/R/R290/R-2.9.0/src/extra/bzip2'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/apps/R/R290/R-2.9.0/src/extra/bzip2'
make[3]: Entering directory `/apps/R/R290/R-2.9.0/src/extra/pcre'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/apps/R/R290/R-2.9.0/src/extra/pcre'
make[3]: Entering directory `/apps/R/R290/R-2.9.0/src/extra/xdr'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/apps/R/R290/R-2.9.0/src/extra/xdr'
make[3]: Entering directory `/apps/R/R290/R-2.9.0/src/extra/zlib'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/apps/R/R290/R-2.9.0/src/extra/zlib'
make[3]: Entering directory `/apps/R/R290/R-2.9.0/src/extra/intl'
make[3]: Nothing to be done for `install'.
make[3]: Leaving directory `/apps/R/R290/R-2.9.0/src/extra/intl'
make[2]: Leaving directory `/apps/R/R290/R-2.9.0/src/extra'
make[2]: Entering directory `/apps/R/R290/R-2.9.0/src/appl'
make[2]: Nothing to be done for `install'.
make[2]: Leaving directory `/apps/R/R290/R-2.9.0/src/appl'
make[2]: Entering directory `/apps/R/R290/R-2.9.0/src/nmath'
make[2]: Nothing to be done for `install'.
make[2]: Leaving directory `/apps/R/R290/R-2.9.0/src/nmath'
make[2]: Entering directory `/apps/R/R290/R-2.9.0/src/unix'
gcc -std=gnu99 -I. -I../../src/include -I../../src/include
-I/usr/X11R6/include -I/usr/local/include -DHAVE_CONFIG_H -g -O2
-DR_HOME='"/apps/R/R290/lib64/R"' -o Rscript \
./Rscript.c
make[2]: Leaving directory `/apps/R/R290/R-2.9.0/src/unix'
make[2]: Entering directory `/apps/R/R290/R-2.9.0/src/main'
mkdir -p -- /apps/R/R290/lib64/R/bin/exec
make[3]: Entering directory `/apps/R/R290/R-2.9.0/src/main'
make[3]: Leaving directory `/apps/R/R290/R-2.9.0/src/main'
make[2]: Leaving directory `/apps/R/R290/R-2.9.0/src/main'
make[2]: Entering directory `/apps/R/R290/R-2.9.0/src/modules'
make[3]: Entering directory `/apps/R/R290/R-2.9.0/src/modules/X11'
mkdir -p -- /apps/R/R290/lib64/R/modules
make[3]: Leaving directory `/apps/R/R290/R-2.9.0/src/modules/X11'
make[3]: Entering directory `/apps/R/R290/R-2.9.0/src/modules/internet'
make[3]: Leaving directory `/apps/R/R290/R-2.9.0/src/modules/internet'
make[3]: Entering directory `/apps/R/R290/R-2.9.0/src/modules/lapack'
make[3]: Leaving directory `/apps/R/R290/R-2.9.0/src/modules/lapack'
make[3]: Entering directory `/apps/R/R290/R-2.9.0/src/modules/vfonts'
make[3]: Leaving directory `/apps/R/R290/R-2.9.0/src/modules/vfonts'
make[2]: Leaving directory `/apps/R/R290/R-2.9.0/src/modules'
make[2]: Entering directory `/apps/R/R290/R-2.9.0/src/library'
mkdir -p -- /apps/R/R290/lib64/R/library
installing packages ...
cp: cannot create regular file
`/apps/R/R290/lib64/R/library/tcltk/po/it/LC_MESSAGES/R-tcltk.mo': No
space left on device
cp: cannot create directory `/apps/R/R290/lib64/R/library/tcltk/po/ja':
No space left on device
cp: cannot create directory `/apps/R/R290/lib64/R/library/tcltk/po/ko':
No space left on device
cp: cannot create directory
`/apps/R/R290/lib64/R/library/tcltk/po/pt_BR': No space left on device
cp: cannot create directory `/apps/R/R290/lib64/R/library/tcltk/po/ru':
No space left on device
cp: cannot create directory
`/apps/R/R290/lib64/R/library/tcltk/po/zh_CN': No space left on device
cp: cannot create directory `/apps/R/R290/lib64/R/library/tcltk/man': No
space left on device
cp: cannot create directory `/apps/R/R290/lib64/R/library/tcltk/libs':
No space left on device
cp: cannot create regular file
`/apps/R/R290/lib64/R/library/tcltk/CONTENTS': No space left on device
cp: cannot create regular file
`/apps/R/R290/lib64/R/library/tcltk/INDEX': No space left on device
cp: cannot create directory `/apps/R/R290/lib64/R/library/tcltk/help':
No space left on device
cp: cannot create directory `/apps/R/R290/lib64/R/library/tcltk/html':
No space left on device
cp: cannot create directory `/apps/R/R290/lib64/R/library/tcltk/latex':
No space left on device
cp: cannot create directory `/apps/R/R290/lib64/R/library/tcltk/R-ex':
No space left on device
cp: cannot create regular file `/apps/R/R290/lib64/R/library/R.css': No
space left on device
cp: cannot create directory `/apps/R/R290/lib64/R/library/MASS': No
space left on device
cp: cannot create directory `/apps/R/R290/lib64/R/library/class': No
space left on device
cp: cannot create directory `/apps/R/R290/lib64/R/library/nnet': No
space left on device
cp: cannot create directory `/apps/R/R290/lib64/R/library/spatial': No
space left on device
cp: cannot create directory `/apps/R/R290/lib64/R/library/boot': No
space left on device
cp: cannot create directory `/apps/R/R290/lib64/R/library/cluster': No
space left on device
cp: cannot create directory `/apps/R/R290/lib64/R/library/codetools': No
space left on device
cp: cannot create directory `/apps/R/R290/lib64/R/library/foreign': No
space left on device
cp: cannot create directory `/apps/R/R290/lib64/R/library/KernSmooth':
No space left on device
cp: cannot create directory `/apps/R/R290/lib64/R/library/lattice': No
space left on device
cp: cannot create directory `/apps/R/R290/lib64/R/library/nlme': No
space left on device
cp: cannot create directory `/apps/R/R290/lib64/R/library/mgcv': No
space left on device
cp: cannot create directory `/apps/R/R290/lib64/R/library/rpart': No
space left on device
cp: cannot create directory `/apps/R/R290/lib64/R/library/survival': No
space left on device
cp: cannot create directory `/apps/R/R290/lib64/R/library/Matrix': No
space left on device
tar: ./base/R/Rprofile: Cannot open: No space left on device
There's actually a lot of space on the filesystem -
head:/apps/R/R290/R-2.9.0 # df -h
Filesystem Size Used Avail Use% Mounted on
/dev/hdi2 15G 11G 3.4G 76% /
tmpfs 3.9G 4.0K 3.9G 1% /dev/shm
/dev/hdi1 958M 25M 885M 3% /boot
/dev/hdi5 15G 7.6G 5.9G 57% /opt
/dev/hdi6 28G 129M 27G 1% /scratch
/dev/gpfs_apps 400G 94G 307G 24% /apps
/dev/gpfs_home 5.5T 5.2T 263G 96% /home
head:/apps/R/R290/R-2.9.0 #
-MJP
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