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?

 

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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