Thanks, Uwe. It seems that the filesystem did not have enough inodes. Mark Lyman
-----Original Message----- From: Uwe Ligges [mailto:lig...@statistik.tu-dortmund.de] Sent: Tuesday, April 28, 2009 5:58 AM To: Lyman, Mark Cc: r-help@r-project.org Subject: Re: [R] FW: 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@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@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. ______________________________________________ R-help@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.