On 12 May 2009 at 13:30, Agustin Lobo wrote: | Dirk, | > So on Ubuntu, uninstall r-cran-robustbase and re-install robustbase | from CRAN | > sources. And file a bug report with Ubuntu. | | That's the first thing I did: tried to install using | install.packages("robustbase"), which downloads the source and tries to | compile. But the gcc step fails: | gcc -std=gnu99 -shared -o robustbase.so R-rng4ftn.o init.o lmrob.o mc.o | qn_sn.o rf-common.o rffastmcd.o rfltsreg.o wgt_himed.o -L/usr/lib/R/lib | -lRlapack -lblas -L/usr/lib/gcc/i486-linux-gnu/4.2 -lgfortran -lm | -L/usr/lib/gcc/i486-linux-gnu/4.2 -lgfortran -lm -L/usr/lib/R/lib -lR | /usr/bin/ld: cannot find -lRlapack | collect2: ld returned 1 exit status
Where is your R from? Which Ubuntu release? Which R release? On a just-upgraded Ubuntu 9.04 which CRAN-port-for-Ubuntu packages thanks to Vincent and Michael, I have e...@joe:~$ ldd /usr/lib/R/bin/exec/R linux-gate.so.1 => (0xb7f07000) libR.so => /usr/lib/R/lib/libR.so (0xb7bd9000) libc.so.6 => /lib/tls/i686/cmov/libc.so.6 (0xb7a76000) libblas.so.3gf => /usr/lib/atlas/libblas.so.3gf (0xb76f9000) libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0xb7645000) libm.so.6 => /lib/tls/i686/cmov/libm.so.6 (0xb761f000) libreadline.so.5 => /lib/libreadline.so.5 (0xb75ed000) libpcre.so.3 => /lib/libpcre.so.3 (0xb75bb000) libbz2.so.1.0 => /lib/libbz2.so.1.0 (0xb75aa000) libz.so.1 => /lib/libz.so.1 (0xb7593000) libdl.so.2 => /lib/tls/i686/cmov/libdl.so.2 (0xb758f000) /lib/ld-linux.so.2 (0xb7f08000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xb7580000) libncurses.so.5 => /lib/libncurses.so.5 (0xb754e000) e...@joe:~$ As I recall, Rlapack.so disappeared from my system a long time ago. You may need to sort some things out on your system. And with that, here is the test I should have done earlier but didn't for lack of time: e...@joe:~$ wajig install r-cran-robustbase Reading package lists... Done Building dependency tree Reading state information... Done The following packages were automatically installed and are no longer required: [...] Use 'apt-get autoremove' to remove them. The following NEW packages will be installed: r-cran-robustbase 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 639kB of archives. After this operation, 2187kB of additional disk space will be used. Get:1 http://ron jaunty/universe r-cran-robustbase 0.4-3-1 [639kB] Fetched 639kB in 6s (94.9kB/s) Selecting previously deselected package r-cran-robustbase. (Reading database ... 345584 files and directories currently installed.) Unpacking r-cran-robustbase (from .../r-cran-robustbase_0.4-3-1_i386.deb) ... Setting up r-cran-robustbase (0.4-3-1) ... e...@joe:~$ echo 'library(robustbase);cat("Hi\n")' | R --silent --no-save > library(robustbase);cat("Hi\n") Hi > e...@joe:~$ So scratch Ubuntu too. The error is local to Augustin's system, and as per Martin, possibly other older Ubuntu sytems. Just upgrade. | Also, when you say "fill a bug with Ubuntu", is there an r-sig-ubuntu or | the Launchpad for general bug reports in Ubuntu? Launchpad. But first get your ducks in a row. You may just have done something to your system. Frankly, mails like your earlier Although I did remove the ln libRlapack.so -> ./lapack.so don't install a lot of confidence in me that your system is still standard enough for us to diagnose in a meaningful way. If you break it, you get to keep the pieces. Can you upgrade to 9.04 ? So to sum up: No bug on current Debian testing or Ubuntu jaunty. Dirk | | Thanks | | Agus | | | Dirk Eddelbuettel escribi : | > On 12 May 2009 at 11:45, Martin Maechler wrote: | > | Agustin, posted on R-help. | > | I think the problem is one of the debian/ubuntu package | > | 'r-cran-robustbase' and its setup or (missing?) dependencies. | > | | > | I can confirm Agustin's problem, working on Ubuntu 8.04.2 | > | (8.04 is a "LTS" = long time support version). | > | | > | apt-get install r-cran-robustbase | > | | > | works fine, but when trying to load the package, | > | there's a DLL - dependency on libRlapack.so | > | which is not fulfilled (and not fulfillable: There's *no* | > | libRlapack.so). | > | | > | For me, | > | | > | $ /usr/bin/R CMD config LAPACK_LIBS | > | -llapack | > | | > | and lapack.so is found inside /usr/lib/R/modules/ | > | and liblapack.so from the 'lapack3' Debian/Ubuntu package | > | is simply in /usr/lib/libpack.so | > | | > | Could it be that this is caused by an Ubuntu / Debian | > | mismatch? | > | > Scratch Debian here. It works there: | > | > e...@ron:~> echo 'library(robustbase);cat("Hi\n")' | R --silent --no-save | > R> library(robustbase);cat("Hi\n") | > Hi | > R> | > e...@ron:~> | > | > It looks like Ubuntu failed to rebuild the package. The Rlapack.so vs | > lapack.so is an old one from the Atlas 3.6 / gfortran transition well over a | > year ago and had affected other package. | > | > So on Ubuntu, uninstall r-cran-robustbase and re-install robustbase from CRAN | > sources. And file a bug report with Ubuntu. | > | > Dirk | > | > | > | Thank you in advance, | > | | > | Martin Maechler, ETH Zurich | > | | > | ------- start of forwarded message ------- | > | From: Agustin Lobo <aloboa...@gmail.com> | > | To: "r-h...@r-project.org" <r-h...@r-project.org> | > | Subject: [R] robustbase: cannot install | > | Date: Mon, 11 May 2009 18:20:14 +0200 | > | | > | This is really odd, | > | I've installed the binary of robustbase through synaptic on an ubuntu | > | 8.04 machine and get: | > | > library(robustbase) | > | Error in dyn.load(file, DLLpath = DLLpath, ...) : | > | unable to load shared library | > | '/usr/lib/R/site-library/robustbase/libs/robustbase.so': | > | libRlapack.so: cannot open shared object file: No such file or directory | > | Error: package/namespace load failed for 'robustbase' | > | > | > | | > | The package is where it is suposed to be: | > | /usr/lib/R/site-library/robustbase | > | | > | is this not a problem at compiling? | > | | > | The problem is that if I try to install the source with | > | install.packages("robustbase"), I get: | > | gcc -std=gnu99 -shared -o robustbase.so R-rng4ftn.o init.o lmrob.o mc.o | > | qn_sn.o rf-common.o rffastmcd.o rfltsreg.o wgt_himed.o -L/usr/lib/R/lib | > | -lRlapack -lblas -L/usr/lib/gcc/i486-linux-gnu/4.2 -lgfortran -lm | > | -L/usr/lib/gcc/i486-linux-gnu/4.2 -lgfortran -lm -L/usr/lib/R/lib -lR | > | /usr/bin/ld: cannot find -lRlapack | > | collect2: ld returned 1 exit status | > | | > | Despite the fact that I do have Rlapack: | > | ~$ R CMD config LAPACK_LIBS | > | -L/usr/lib/R/lib -lRlapack | > | | > | Am I doing something wrong? | > | | > | Thanks | > | | > | Agus | > | -- | > | Dr. Agustin Lobo | > | Institut de Ciencies de la Terra "Jaume Almera" (CSIC) | > | LLuis Sole Sabaris s/n | > | 08028 Barcelona | > | Spain | > | Tel. 34 934095410 | > | Fax. 34 934110012 | > | email: agustin.l...@ija.csic.es | > | http://www.ija.csic.es/gt/obster | > | | > | ______________________________________________ | > | r-h...@r-project.org mailing list | > | https://stat.ethz.ch/mailman/listinfo/r-help | > | PLEASE do read the posting guide http://www.R-project.org/posting-guide.html | > | and provide commented, minimal, self-contained, reproducible code. | > | ------- end of forwarded message ------- | > | | > | _______________________________________________ | > | R-SIG-Debian mailing list | > | R-SIG-Debian@r-project.org | > | https://stat.ethz.ch/mailman/listinfo/r-sig-debian | > -- Three out of two people have difficulties with fractions. _______________________________________________ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian