[R] FW: Install of R 2.9.0

[Uwe Ligges]

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 at 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
> 
> 
> 	[[alternative HTML version deleted]]
> 
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