[R] package install error in CentOS
I am trying to install package Cairo on CentOS 5.2, but I keep getting this error: * Installing *source* package 'Cairo' ... /usr/lib64/R/bin/INSTALL: ./configure: /bin/sh: bad interpreter: Permission denied ERROR: configuration failed for package 'Cairo' ** Removing '/usr/lib64/R/library/Cairo' The downloaded packages are in /tmp/Rtmp8ML568/downloaded_packages Updating HTML index of packages in '.Library' Warning message: In install.packages(Cairo) : installation of package 'Cairo' had non-zero exit status I tried to do it manually but with no luck: [jer...@138 shizzle]$ sudo R CMD INSTALL Cairo_1.4-4.tar.gz * Installing to library '/usr/lib64/R/library' * Installing *source* package 'Cairo' ... /usr/lib64/R/bin/INSTALL: ./configure: /bin/sh: bad interpreter: Permission denied ERROR: configuration failed for package 'Cairo' ** Removing '/usr/lib64/R/library/Cairo' I have tried to changing the $TMPDIR to another dir, and giving it 777 permissions, but I keep getting the error. Some info: sessionInfo() R version 2.8.0 (2008-10-20) x86_64-redhat-linux-gnu locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base [jer...@138 shizzle]$ gcc --version gcc (GCC) 4.1.2 20071124 (Red Hat 4.1.2-42) Copyright (C) 2006 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -- View this message in context: http://www.nabble.com/package-install-error-in-CentOS-tp21094790p21094790.html Sent from the R help mailing list archive at Nabble.com. __ 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.
Re: [R] package install error in CentOS
Check that your data partitions have the 'exec' flag set in /etc/fstab, particulary the /tmp partition: http://www.centos.org/modules/newbb/viewtopic.php?topic_id=1687forum=31 Jeff Jeroen Ooms wrote: I am trying to install package Cairo on CentOS 5.2, but I keep getting this error: * Installing *source* package 'Cairo' ... /usr/lib64/R/bin/INSTALL: ./configure: /bin/sh: bad interpreter: Permission denied ERROR: configuration failed for package 'Cairo' ** Removing '/usr/lib64/R/library/Cairo' The downloaded packages are in /tmp/Rtmp8ML568/downloaded_packages Updating HTML index of packages in '.Library' Warning message: In install.packages(Cairo) : installation of package 'Cairo' had non-zero exit status I tried to do it manually but with no luck: [jer...@138 shizzle]$ sudo R CMD INSTALL Cairo_1.4-4.tar.gz * Installing to library '/usr/lib64/R/library' * Installing *source* package 'Cairo' ... /usr/lib64/R/bin/INSTALL: ./configure: /bin/sh: bad interpreter: Permission denied ERROR: configuration failed for package 'Cairo' ** Removing '/usr/lib64/R/library/Cairo' I have tried to changing the $TMPDIR to another dir, and giving it 777 permissions, but I keep getting the error. Some info: sessionInfo() R version 2.8.0 (2008-10-20) x86_64-redhat-linux-gnu locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base [jer...@138 shizzle]$ gcc --version gcc (GCC) 4.1.2 20071124 (Red Hat 4.1.2-42) Copyright (C) 2006 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. __ 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.
Re: [R] package install error in CentOS
solved: There was indeed a problem with exec rights in the /tmp dir as they were set by my VPS host. I fixed it by creating a dir 'tempdir' in my homedir, and giving it 777 rights. Then set the environment variable TMPDIR in R: Sys.setenv(TMPDIR=/home/jeroen/tempdir); install.packages(Cairo); thank you :) Jeffrey Horner wrote: Check that your data partitions have the 'exec' flag set in /etc/fstab, particulary the /tmp partition: http://www.centos.org/modules/newbb/viewtopic.php?topic_id=1687forum=31 Jeff Jeroen Ooms wrote: I am trying to install package Cairo on CentOS 5.2, but I keep getting this error: * Installing *source* package 'Cairo' ... /usr/lib64/R/bin/INSTALL: ./configure: /bin/sh: bad interpreter: Permission denied ERROR: configuration failed for package 'Cairo' ** Removing '/usr/lib64/R/library/Cairo' The downloaded packages are in /tmp/Rtmp8ML568/downloaded_packages Updating HTML index of packages in '.Library' Warning message: In install.packages(Cairo) : installation of package 'Cairo' had non-zero exit status I tried to do it manually but with no luck: [jer...@138 shizzle]$ sudo R CMD INSTALL Cairo_1.4-4.tar.gz * Installing to library '/usr/lib64/R/library' * Installing *source* package 'Cairo' ... /usr/lib64/R/bin/INSTALL: ./configure: /bin/sh: bad interpreter: Permission denied ERROR: configuration failed for package 'Cairo' ** Removing '/usr/lib64/R/library/Cairo' I have tried to changing the $TMPDIR to another dir, and giving it 777 permissions, but I keep getting the error. Some info: sessionInfo() R version 2.8.0 (2008-10-20) x86_64-redhat-linux-gnu locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base [jer...@138 shizzle]$ gcc --version gcc (GCC) 4.1.2 20071124 (Red Hat 4.1.2-42) Copyright (C) 2006 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. __ 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. -- View this message in context: http://www.nabble.com/package-install-error-in-CentOS-tp21094790p21097936.html Sent from the R help mailing list archive at Nabble.com. __ 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.
