Michael Friendly
2008-Dec-09 15:33 UTC
[R-sig-Debian] update.packages() for R 2.7.1: mgcv fails
Hi I just upgraded my debian/stable to R 2.7.1 via apt-get install r-base r-base-core r-base-dev, and then began to update.packages() > update.packages(lib.loc="/usr/local/lib/R/site-library") > update.packages(lib.loc="/usr/lib/R/library") but I get: .... * Installing *source* package 'mgcv' ... ** libs gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c gcv.c -o gcv.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c gdi.c -o gdi.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c init.c -o init.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c magic.c -o magic.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c mat.c -o mat.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c matrix.c -o matrix.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c mgcv.c -o mgcv.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c qp.c -o qp.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c tprs.c -o tprs.o gcc -std=gnu99 -shared -o mgcv.so gcv.o gdi.o init.o magic.o mat.o matrix.o mgcv.o qp.o tprs.o -llapack -lblas -lgfortran -lm -L/usr/lib/R/lib -lR /usr/bin/ld: cannot find -llapack collect2: ld returned 1 exit status make: *** [mgcv.so] Error 1 ERROR: compilation failed for package 'mgcv' ** Removing '/usr/lib/R/library/mgcv' ** Restoring previous '/usr/lib/R/library/mgcv' * I'm not sure which version of lapack is missing or where to find it. Also, for r-cran-* packages, whether update.packages(lib.loc="/usr/lib/R/library") is equivalent to apt-get install r-cran-mgcv etc. thanks, -Michael > sessionInfo() R version 2.7.1 (2008-06-23) i486-pc-linux-gnu locale: LC_CTYPE=en_CA;LC_NUMERIC=C;LC_TIME=en_CA;LC_COLLATE=en_CA;LC_MONETARY=C;LC_MESSAGES=en_CA;LC_PAPER=en_CA;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_CA;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.7.1 > -- 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
Dirk Eddelbuettel
2008-Dec-09 16:26 UTC
[R-sig-Debian] update.packages() for R 2.7.1: mgcv fails
Hi Michael, On 9 December 2008 at 10:33, Michael Friendly wrote: | Hi | I just upgraded my debian/stable to R 2.7.1 via apt-get install r-base | r-base-core r-base-dev, and then Did you get them from Debian, or from CRAN ? I presume it is CRAN? | began to update.packages() | | > update.packages(lib.loc="/usr/local/lib/R/site-library") | > update.packages(lib.loc="/usr/lib/R/library") | but I get: | .... | * Installing *source* package 'mgcv' ... | ** libs | gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c gcv.c -o gcv.o | gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c gdi.c -o gdi.o | gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c init.c -o init.o | gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c magic.c -o | magic.o | gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c mat.c -o mat.o | gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c matrix.c -o | matrix.o | gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c mgcv.c -o mgcv.o | gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c qp.c -o qp.o | gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c tprs.c -o tprs.o | gcc -std=gnu99 -shared -o mgcv.so gcv.o gdi.o init.o magic.o mat.o | matrix.o mgcv.o qp.o tprs.o -llapack -lblas -lgfortran -lm | -L/usr/lib/R/lib -lR | /usr/bin/ld: cannot find -llapack | collect2: ld returned 1 exit status | make: *** [mgcv.so] Error 1 | ERROR: compilation failed for package 'mgcv' | ** Removing '/usr/lib/R/library/mgcv' | ** Restoring previous '/usr/lib/R/library/mgcv' | * | | I'm not sure which version of lapack is missing or where to find it. You need liblapack-dev with a version of 3.1 or greater. You may need to point apt to backports.org -- not sure as I do not run Debian stable (but only testing). However the README on CRAN in the bin/linux/debian directory mentions pre-built packages for r-recommended, so for mgcv you could sudo apt-get install r-cran-mgcv to get working. You'd still need liblapack I suppose. | Also, for r-cran-* packages, whether | update.packages(lib.loc="/usr/lib/R/library") | is equivalent to apt-get install r-cran-mgcv etc. Versions can be different between the two. It is a tradeoff choice you need to make. 'apt-cache policy somepackage' will always tell you what version you'd get from the different (if any) repos you are lined up to. Doing R directly via install.packages() is completely independent to that though but should stay clear of trouble as non-overlapping directory trees are used. Hope this helps, Dirk | | thanks, | -Michael | | | > sessionInfo() | R version 2.7.1 (2008-06-23) | i486-pc-linux-gnu | | locale: | LC_CTYPE=en_CA;LC_NUMERIC=C;LC_TIME=en_CA;LC_COLLATE=en_CA;LC_MONETARY=C;LC_MESSAGES=en_CA;LC_PAPER=en_CA;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_CA;LC_IDENTIFICATION=C | | attached base packages: | [1] stats graphics grDevices utils datasets methods base | | loaded via a namespace (and not attached): | [1] tools_2.7.1 | > | | -- | 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 -- Three out of two people have difficulties with fractions.