Michael Friendly
2008-Apr-09 19:57 UTC
[R-sig-Debian] Updating packages after install of r-base 2.6.2: cant update rgl
Hi I just upgraded my R from stabel/etch from 2.4.x to 2.6.2 via sudo apt-get install r-base which worked fine, installing all dependencies From R, as root, I did update.packages() but a number of packages packages failed to install, either for missing gfortran or missing dependencies. Warning messages: 1: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package 'maptools' had non-zero exit status 2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package 'mvtnorm' had non-zero exit status 3: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package 'lmtest' had non-zero exit status 4: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package 'multcomp' had non-zero exit status 5: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package 'cluster' had non-zero exit status 6: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package 'KernSmooth' had non-zero exit status 7: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package 'mgcv' had non-zero exit status ... OK, I installed r-base-dev to get gfortran and other dependencies, then tried update.packages() again. This time only rgl failed, complaining about missing X11: trying URL 'http://probability.ca/cran/src/contrib/rgl_0.77.tar.gz' Content type 'application/x-tar' length 803692 bytes (784 Kb) opened URL =================================================downloaded 784 Kb * Installing *source* package 'rgl' ... checking for gcc... gcc -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -std=gnu99 -E checking for gcc... (cached) gcc -std=gnu99 checking whether we are using the GNU C compiler... (cached) yes checking whether gcc -std=gnu99 accepts -g... (cached) yes checking for gcc -std=gnu99 option to accept ANSI C... (cached) none needed checking for libpng-config... yes configure: using libpng-config configure: using libpng dynamic linkage checking for X... no configure: error: X11 not found but required, configure aborted. ERROR: configuration failed for package 'rgl' ** Removing '/usr/lib/R/site-library/rgl' ** Restoring previous '/usr/lib/R/site-library/rgl' The downloaded packages are in /tmp/RtmpSFCuUT/downloaded_packages Warning message: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package 'rgl' had non-zero exit status Finally, I tried to install r-cran-rgl, but with no joy: euclid:~# apt-get install r-cran-rgl Reading package lists... Done Building dependency tree... Done r-cran-rgl is already the newest version. 0 upgraded, 0 newly installed, 0 to remove and 267 not upgraded. Can anyone suggest what is wrong and how to fix it? thanks, -Michael -- Michael Friendly Email: friendly at yorku.ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele Street http://www.math.yorku.ca/SCS/friendly.html Toronto, ONT M3J 1P3 CANADA
Johannes Ranke
2008-Apr-10 06:43 UTC
[R-sig-Debian] Updating packages after install of r-base 2.6.2: cant update rgl
Hi Michael, * Michael Friendly <friendly at yorku.ca> [080409 22:00]:> Hi > > I just upgraded my R from stabel/etch from 2.4.x to 2.6.2 via > > sudo apt-get install r-base > which worked fine, installing all dependenciesI suppose you put some CRAN mirror into your /etc/apt/sources.list?> From R, as root, I did > > update.packages() > > but a number of packages packages failed to install, either for missing > gfortran > or missing dependencies.Yes, you need to explicitly upgrade r-base-dev, too, if you want to install packages from CRAN. ...> ... > > OK, I installed r-base-dev to get gfortran and other dependencies, then > tried > update.packages() again. This time only rgl failed, complaining about > missing X11: > > trying URL 'http://probability.ca/cran/src/contrib/rgl_0.77.tar.gz' > Content type 'application/x-tar' length 803692 bytes (784 Kb) > opened URL > =================================================> downloaded 784 Kb > > * Installing *source* package 'rgl' ... > checking for gcc... gcc -std=gnu99 > checking for C compiler default output file name... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc -std=gnu99 accepts -g... yes > checking for gcc -std=gnu99 option to accept ANSI C... none needed > checking how to run the C preprocessor... gcc -std=gnu99 -E > checking for gcc... (cached) gcc -std=gnu99 > checking whether we are using the GNU C compiler... (cached) yes > checking whether gcc -std=gnu99 accepts -g... (cached) yes > checking for gcc -std=gnu99 option to accept ANSI C... (cached) none needed > checking for libpng-config... yes > configure: using libpng-config > configure: using libpng dynamic linkage > checking for X... no > configure: error: X11 not found but required, configure aborted. > ERROR: configuration failed for package 'rgl' > ** Removing '/usr/lib/R/site-library/rgl' > ** Restoring previous '/usr/lib/R/site-library/rgl'Ok, I just did this on one of my etch boxes with CRAN R (and X installed): cecking for X... libraries , headers checking GL/gl.h usability... yes checking GL/gl.h presence... yes checking for GL/gl.h... yes checking GL/glu.h usability... yes checking GL/glu.h presence... yes checking for GL/glu.h... yes checking for glEnd in -lGL... yes checking for gluProject in -lGLU... yes configure: creating ./config.status config.status: creating src/Makevars So it works over here... On another box, without OpenGL, it fails, as one would expect. On a third box, where I have no X installed, it fails, too, with exactly the error message you quoted above. Could you give us the output of apt-cache policy xserver-xorg-core or just tell us if you have Xorg installed? Best regards, Johannes> Finally, I tried to install r-cran-rgl, but with no joy: > > euclid:~# apt-get install r-cran-rgl > Reading package lists... Done > Building dependency tree... Done > r-cran-rgl is already the newest version. > 0 upgraded, 0 newly installed, 0 to remove and 267 not upgraded. > > Can anyone suggest what is wrong and how to fix it? > > thanks, > -Michael > > -- > Michael Friendly Email: friendly at yorku.ca > Professor, Psychology Dept. > York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 > 4700 Keele Street http://www.math.yorku.ca/SCS/friendly.html > Toronto, ONT M3J 1P3 CANADA > > _______________________________________________ > R-SIG-Debian mailing list > R-SIG-Debian at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-debian-- Dr. Johannes Ranke jranke at uni-bremen.de Key ID: F649AF90 UFT Bremen, Leobenerstr. 1 +49 421 218 63373 D-28359 Bremen http://www.uft.uni-bremen.de/chemie/ranke