Lyman, Mark wrote:
I have just received some additional information. After the "No space
left on device", there are many file not found error messages. Also, the
first time or two our admin ran the install process R would not start.
Now R can start up despite all of the error messages. Can these error
messages be ignored?
Well, I do not want to blame your admin ... but I fear I need to ...
if cp answer about a full file space, the admin should look if there is
really no space left or quotas may apply or network problems or whatever
may cause that problem. At least R won't.
Uwe Ligges
Mark Lyman
From: Lyman, Mark
Sent: Monday, April 27, 2009 12:49 PM
To: r-help@r-project.org
Subject: FW: Install of R 2.9.0
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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
