Dear all, thank's again for all your constructive tips ! After all carefully checked the list of changes from R-2.14.x to R-2.15.0 and saw this note "C/C++ code in packages is now compiled with -NDEBUG against the C/C++ function assert being called in production use. Developers can turn this off during package development with PKG_CPPFLAGS = -UNDEBUG."
So I did setenv PKG_CPPFLAGS -UNDEBUG before launching my R-script to install some 280 libraries and this did resolve my problem ! Before this I tried something similar to Dirks suggestion, I unpacked the tar.gz by hand, ran the config, but among a lots of stuff running over my screen I didn't find any helpful clues... Wolfgang 2012/4/19 Dirk Eddelbuettel <[email protected]> > > On 19 April 2012 at 11:14, Wolfgang Raffelsberger wrote: > | Dear Michael, > | > | thank's for your quick answer. Yes, I've thought about the sudo option > | which should work with RODBC as you stated, but probably it won't with a > > a) For RODBC, just do 'apt-get install r-cran-rodbc'. Similar for many > other > packages on the repos, and if you got to Michael's PPA (for Ubuntu) or > Don's > site (for Debian) you get almost all of CRAN as a binary .deb. > > | bunch of other R-libraries suffering the same problem. > | Anyway, this is the installation on a bigger system and the system > | adminstrator doesn't think giving me the rights for sudo is a good > solution > | - in particular, if similar installations didn't require this in the > past. > > b) What you do with is entirely your local issue, as is your current error > of > being unable to replicate what you once had. Based on the limited info you > had, we cannot help you. > > | Somehow I was hoping to find a way to see the content of the `config.log' > | for more details, but if it really gets written to disk it seems to > | disappear within milliseconds thereafter. I'll try the R-devel list to > | suggest an argument allowing to display or keep this file. > > c) Untangle the steps that R CMD INSTALL does. Unpack the tar.gz by hand, > run configure by hand. Nobody will delete the file under you. > > Dirk > > | Wolfgang > | > | 2012/4/18 Michael Rutter <[email protected]> > | > | > On 04/18/2012 12:24 PM, Wolfgang Raffelsberger wrote: > | > > | >> Dear list, > | >> > | >> as I started installing R-2.15.0 on a Red Hat 4.5.1-4 as well a Ubuntu > | >> 10.04.3 systems. > | >> While the basic installation went fine (like the previous R-2.14.2), > now > | >> I'm having trouble installing almost one third of the additional > libraries > | >> I want (which installed flawlessly with R-2.14.2), among them RODBC > for > | >> which I show the message below (obtained on Ubuntu) : > | >> > | >> surf_forInstallation_> R CMD INSTALL RODBC_1.3-5.tar.gz > | >> * installing to library > '/linux/biolo/R_surf/R-2.15.0/**lib64/R/library' > | >> * installing *source* package 'RODBC' ... > | >> ** package 'RODBC' successfully unpacked and MD5 sums checked > | >> checking for gcc... > | >> gcc -std=gnu99 > | >> checking for C compiler default output file name... configure: error: > C > | >> compiler cannot create executables > | >> See `config.log' for more details. > | >> ERROR: configuration failed for package 'RODBC' > | >> * removing '/linux/biolo/R_surf/R-2.15.0/**lib64/R/library/RODBC' > | >> > | >> > | >> In fact, I get identical messages on our Red Hat 4.5.1-4 and the > Ubuntu > | >> 10.04.3 systems mentioned above. > | >> Obviously something with our C compiler(s) didn't work out. > | >> In order to learn more about the problem I tried to look at config.log > | >> mentioned in the installation-message above, however, I cannot find > | >> the file, neither in my current path nor in > | >> /linux/biolo/R_surf/R-2.15.0/**lib64/R/library . > | >> Obviously the RODBC directory doesn't exist any more when the > installation > | >> attempt ends. > | >> > | >> Any hints ? > | >> I'm new to the Debian-list, but at least I haven't seen similar > (recent) > | >> posts on R-help or the bioconductor lists. > | >> > | > > | > Wolfgang, > | > > | > For the Ubuntu box, I would start by using my R PPA found here: > | > > | > https://launchpad.net/~**marutter/+archive/rrutter< > https://launchpad.net/~marutter/+archive/rrutter> > | > > | > I would also suggest using apt and/or synaptic to install as many > packages > | > as possible from the repositories (sudo apt-get install r-cran-rodbc, > for > | > example). > | > > | > The error you received indicates to me you do not have any development > | > packages or a c++ complier installed. Have you installed "r-base-dev"? > | > That should install the needed compilers. > | > > | > Michael > | > > | > -- > | > Dr. Michael A. Rutter > | > School of Science > | > Penn State Erie, The Behrend College > | > Station Road > | > Erie, PA 16563 > | > http://math.bd.psu.edu/**faculty/rutter< > http://math.bd.psu.edu/faculty/rutter> > | > > | > ______________________________**_________________ > | > R-SIG-Debian mailing list > | > [email protected] > | > https://stat.ethz.ch/mailman/**listinfo/r-sig-debian< > https://stat.ethz.ch/mailman/listinfo/r-sig-debian> > | > > | > | [[alternative HTML version deleted]] > | > | _______________________________________________ > | R-SIG-Debian mailing list > | [email protected] > | https://stat.ethz.ch/mailman/listinfo/r-sig-debian > > -- > R/Finance 2012 Conference on May 11 and 12, 2012 at UIC in Chicago, IL > See agenda, registration details and more at http://www.RinFinance.com > [[alternative HTML version deleted]] _______________________________________________ R-SIG-Debian mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-debian
