Re: [R] 2.0.1 compilation problem on Fedora Core 2
Thanks to Brian this was solved immediately without rebooting. The reason for /tmp being (rw,noexec,nosuid) was to avoid executing and suiding. This is probably more important in a networked environment which the machine is not really in at the moment. I may well change it as it has already caused two problems! On the other hand other programs have installed without a problem. Maybe there is a case for a tmp directory being set up in the source tree, then there will be no problem. JOhn John Logsdon Try to make things as simple Quantex Research Ltd, Manchester UK as possible but not simpler [EMAIL PROTECTED] [EMAIL PROTECTED] +44(0)161 445 4951/G:+44(0)7717758675 www.quantex-research.com On Wed, 1 Dec 2004, Prof Brian Ripley wrote: On Wed, 1 Dec 2004, John Logsdon wrote: A useful clue, Brian. Maybe this is the reason as foreign.ts.out contains: * Installing *source* package 'foreign' ... /usr/src/redhat/SOURCES/R-2.0.1/bin/INSTALL: ./configure: /bin/sh: bad interpreter: Permission denied ERROR: configuration failed for package 'foreign' Does this try and execute from /tmp by any chance? I had a similar Yes, it does, a configure script. I believe you can alter that by setting TMPDIR to point somewhere else. That's a pretty esoteric situation: why is /tmp so special to you? problem recently because /tmp is mounted (rw,noexec,nosuid) for security reasons. I had to alter /etc/fstab temporarily and reboot as /tmp is used by many things. The others installed so far have 0 size: -rw-r--r-- 1 root root 0 Dec 1 15:19 VR.ts -rw-r--r-- 1 root root 0 Dec 1 15:19 boot.ts -rw-r--r-- 1 root root196 Dec 1 15:20 foreign.ts.out -rw-r--r-- 1 root root 0 Dec 1 15:20 cluster.ts John John Logsdon Try to make things as simple Quantex Research Ltd, Manchester UK as possible but not simpler [EMAIL PROTECTED] [EMAIL PROTECTED] +44(0)161 445 4951/G:+44(0)7717758675 www.quantex-research.com On Wed, 1 Dec 2004, Prof Brian Ripley wrote: On Wed, 1 Dec 2004, John Logsdon wrote: I have a compilation problem on FC2, 2xXeon box. The following dialogue output from the end of the compilation illustrates: [very large snipping sound ...] * DONE (cluster) begin installing recommended package foreign make[2]: *** [foreign.ts] Error 1 make[2]: Leaving directory `/usr/src/redhat/SOURCES/R-2.0.1/src/library/Recommended' Take a look at the file foreign.out in that directory. (R-devel does this better, by cat-ing the file at that point.) -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] 2.0.1 compilation problem on Fedora Core 2
On Thu, 2 Dec 2004, John Logsdon wrote: Thanks to Brian this was solved immediately without rebooting. The reason for /tmp being (rw,noexec,nosuid) was to avoid executing and suiding. This is probably more important in a networked environment which the machine is not really in at the moment. I may well change it as it has already caused two problems! On the other hand other programs have installed without a problem. Maybe there is a case for a tmp directory being set up in the source tree, then there will be no problem. As I said, why is /tmp so special to you? If you can exec and suid from the source tree, what useful extra protection do you have? We definitely do not want to unpack in the source tree, which on my machine is on a readonly file system (unpacked on another machine). Perhaps in the build tree, but R CMD INSTALL is also used later. A note in the R-admin manual seems sufficient here, as this it the only time this has come up in literally thousands of installations. JOhn John Logsdon Try to make things as simple Quantex Research Ltd, Manchester UK as possible but not simpler [EMAIL PROTECTED] [EMAIL PROTECTED] +44(0)161 445 4951/G:+44(0)7717758675 www.quantex-research.com On Wed, 1 Dec 2004, Prof Brian Ripley wrote: On Wed, 1 Dec 2004, John Logsdon wrote: A useful clue, Brian. Maybe this is the reason as foreign.ts.out contains: * Installing *source* package 'foreign' ... /usr/src/redhat/SOURCES/R-2.0.1/bin/INSTALL: ./configure: /bin/sh: bad interpreter: Permission denied ERROR: configuration failed for package 'foreign' Does this try and execute from /tmp by any chance? I had a similar Yes, it does, a configure script. I believe you can alter that by setting TMPDIR to point somewhere else. That's a pretty esoteric situation: why is /tmp so special to you? problem recently because /tmp is mounted (rw,noexec,nosuid) for security reasons. I had to alter /etc/fstab temporarily and reboot as /tmp is used by many things. The others installed so far have 0 size: -rw-r--r-- 1 root root 0 Dec 1 15:19 VR.ts -rw-r--r-- 1 root root 0 Dec 1 15:19 boot.ts -rw-r--r-- 1 root root196 Dec 1 15:20 foreign.ts.out -rw-r--r-- 1 root root 0 Dec 1 15:20 cluster.ts John John Logsdon Try to make things as simple Quantex Research Ltd, Manchester UK as possible but not simpler [EMAIL PROTECTED] [EMAIL PROTECTED] +44(0)161 445 4951/G:+44(0)7717758675 www.quantex-research.com On Wed, 1 Dec 2004, Prof Brian Ripley wrote: On Wed, 1 Dec 2004, John Logsdon wrote: I have a compilation problem on FC2, 2xXeon box. The following dialogue output from the end of the compilation illustrates: [very large snipping sound ...] * DONE (cluster) begin installing recommended package foreign make[2]: *** [foreign.ts] Error 1 make[2]: Leaving directory `/usr/src/redhat/SOURCES/R-2.0.1/src/library/Recommended' Take a look at the file foreign.out in that directory. (R-devel does this better, by cat-ing the file at that point.) -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] 2.0.1 compilation problem on Fedora Core 2
On Wed, 1 Dec 2004, John Logsdon wrote: I have a compilation problem on FC2, 2xXeon box. The following dialogue output from the end of the compilation illustrates: [very large snipping sound ...] * DONE (cluster) begin installing recommended package foreign make[2]: *** [foreign.ts] Error 1 make[2]: Leaving directory `/usr/src/redhat/SOURCES/R-2.0.1/src/library/Recommended' Take a look at the file foreign.out in that directory. (R-devel does this better, by cat-ing the file at that point.) -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] 2.0.1 compilation problem on Fedora Core 2
A useful clue, Brian. Maybe this is the reason as foreign.ts.out contains: * Installing *source* package 'foreign' ... /usr/src/redhat/SOURCES/R-2.0.1/bin/INSTALL: ./configure: /bin/sh: bad interpreter: Permission denied ERROR: configuration failed for package 'foreign' Does this try and execute from /tmp by any chance? I had a similar problem recently because /tmp is mounted (rw,noexec,nosuid) for security reasons. I had to alter /etc/fstab temporarily and reboot as /tmp is used by many things. The others installed so far have 0 size: -rw-r--r-- 1 root root 0 Dec 1 15:19 VR.ts -rw-r--r-- 1 root root 0 Dec 1 15:19 boot.ts -rw-r--r-- 1 root root196 Dec 1 15:20 foreign.ts.out -rw-r--r-- 1 root root 0 Dec 1 15:20 cluster.ts John John Logsdon Try to make things as simple Quantex Research Ltd, Manchester UK as possible but not simpler [EMAIL PROTECTED] [EMAIL PROTECTED] +44(0)161 445 4951/G:+44(0)7717758675 www.quantex-research.com On Wed, 1 Dec 2004, Prof Brian Ripley wrote: On Wed, 1 Dec 2004, John Logsdon wrote: I have a compilation problem on FC2, 2xXeon box. The following dialogue output from the end of the compilation illustrates: [very large snipping sound ...] * DONE (cluster) begin installing recommended package foreign make[2]: *** [foreign.ts] Error 1 make[2]: Leaving directory `/usr/src/redhat/SOURCES/R-2.0.1/src/library/Recommended' Take a look at the file foreign.out in that directory. (R-devel does this better, by cat-ing the file at that point.) -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
