Install of R 2.9.0
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]]
______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.