Kaspar Pflugshaupt
2002-Jan-31 15:32 UTC
[R] MacOS X: Packages KernSmooth and cluster won't compile
Hello, I'm using R 1.40 on MacOS X X.1.2 (installed via the fink package manager). To upgrade my installed packages, I tried to use update.packages() today. All went well for most packages, with the exception of KernSmooth and cluster. In both cases, libraries were not found although I think they are present. Here's what happened: ----------------------------------> update.packages()[snip] KernSmooth : Version 2.22-6 in /sw/lib/R/library Version 2.22-7 on CRAN Update (y/N)? y cluster : Version 1.3-6 in /sw/lib/R/library Version 1.4-0 on CRAN Update (y/N)? y [snip] Installing *source* package `KernSmooth' ... [snip] cc -I/sw/lib/R/include -I/sw/include -fno-common -g -O2 -c sstdiag.c -o sstdiag.o cc -bundle -bundle_loader /sw/lib/R/bin/R.bin -o KernSmooth.so blkest.o cp.o dgedi.o dgefa.o dgesl.o linbin.o linbin2D.o locpoly.o rlbin.o sdiag.o sstdiag.o -lf77blas -lcblas -latlas -L/usr/local/lib -lf2c -lm /usr/bin/ld: can't locate file for: -lf77blas make: *** [KernSmooth.so] Error 1 ERROR: compilation failed for package `KernSmooth' Installing *source* package `cluster' ... [snip] cc -bundle -bundle_loader /sw/lib/R/bin/R.bin -o cluster.so clara.o daisy.o fanny.o meet.o mona.o pam.o spannel.o twins.o -L/usr/local/lib -lf2c -lm /usr/bin/ld: can't locate file for: -lf2c make: *** [cluster.so] Error 1 ERROR: compilation failed for package `cluster' --------------------------------------- So, in the first case, library f77blas was not found. I do have /sw/lib/libf77blas.a, though. In the second case, library f2c is missed, but it's there at /sw/lib/libf2c.a. Is this a linking path problem, and how can I check? I had assumed that /sw/lib/ should be visible to the linker, since it's fink's standard lib directory and I've compiled many packages with fink. Thanks for any hint Kaspar -- Kaspar Pflugshaupt Geobotanisches Institut Zuerichbergstr. 38 CH-8044 Zuerich Tel. ++41 1 632 43 19 Fax ++41 1 632 12 15 mailto:pflugshaupt at geobot.umnw.ethz.ch privat:pflugshaupt at mails.ch http://www.geobot.umnw.ethz.ch -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
Jan de Leeuw
2002-Jan-31 16:45 UTC
[R] MacOS X: Packages KernSmooth and cluster won't compile
This is one disadvantage of using the fink version of R: although the maintainer (jsw at cdc.noaa.gov ) has patched and ported the base and recommended packages, there is no guarantee that other contributed packages must not be patched to fit into the fink hierarchy. The advantage of fink is that you get easy updating and the package manager keeps track of the libraries that are installed. But you do give up some control (and you lose some features such as gnome) compared to rolling your own or downloading from ftp://gifi.stat.ucla.edu/pub/R. Contact Jeff at the email address given above to see if he can help. On Thursday, January 31, 2002, at 07:32 AM, Kaspar Pflugshaupt wrote:> Hello, > > I'm using R 1.40 on MacOS X X.1.2 (installed via the fink package > manager). > > To upgrade my installed packages, I tried to use update.packages() > today. > All went well for most packages, with the exception of KernSmooth and > cluster. In both cases, libraries were not found although I think they > are > present. > > Here's what happened: > > ---------------------------------- >> update.packages() > > [snip] > > KernSmooth : > Version 2.22-6 in /sw/lib/R/library > Version 2.22-7 on CRAN > Update (y/N)? y > cluster : > Version 1.3-6 in /sw/lib/R/library > Version 1.4-0 on CRAN > Update (y/N)? y > > [snip] > > Installing *source* package `KernSmooth' ... > > [snip] > > cc -I/sw/lib/R/include -I/sw/include -fno-common -g -O2 -c > sstdiag.c -o > sstdiag.o > cc -bundle -bundle_loader /sw/lib/R/bin/R.bin -o KernSmooth.so blkest.o > cp.o dgedi.o dgefa.o dgesl.o linbin.o linbin2D.o locpoly.o rlbin.o > sdiag.o > sstdiag.o -lf77blas -lcblas -latlas -L/usr/local/lib -lf2c -lm > /usr/bin/ld: can't locate file for: -lf77blas > make: *** [KernSmooth.so] Error 1 > ERROR: compilation failed for package `KernSmooth' > Installing *source* package `cluster' ... > > [snip] > > cc -bundle -bundle_loader /sw/lib/R/bin/R.bin -o cluster.so clara.o > daisy.o > fanny.o meet.o mona.o pam.o spannel.o twins.o -L/usr/local/lib -lf2c > -lm > /usr/bin/ld: can't locate file for: -lf2c > make: *** [cluster.so] Error 1 > ERROR: compilation failed for package `cluster' > --------------------------------------- > > So, in the first case, library f77blas was not found. I do have > /sw/lib/libf77blas.a, though. In the second case, library f2c is > missed, but > it's there at /sw/lib/libf2c.a. > > Is this a linking path problem, and how can I check? I had assumed that > /sw/lib/ should be visible to the linker, since it's fink's standard lib > directory and I've compiled many packages with fink. > > Thanks for any hint > > Kaspar > > > > -- > > Kaspar Pflugshaupt > Geobotanisches Institut > Zuerichbergstr. 38 > CH-8044 Zuerich > > Tel. ++41 1 632 43 19 > Fax ++41 1 632 12 15 > > mailto:pflugshaupt at geobot.umnw.ethz.ch > privat:pflugshaupt at mails.ch > http://www.geobot.umnw.ethz.ch > > -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- > .-.-.- > r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R- > FAQ.html > Send "info", "help", or "[un]subscribe" > (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch > _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ > ._._._ > >==Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: deleeuw at stat.ucla.edu homepage: http://www.stat.ucla.edu/~deleeuw ======================================================= No matter where you go, there you are. --- Buckaroo Banzai http://www.stat.ucla.edu/~deleeuw/sounds/nomatter.au ======================================================= -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._