search for: 3gf

...folks, if you want to use MKL (the fast BLAS I have tested on my Thinkpad T410) with the R 2.14.0 built as Debian/Ubuntu packages available on CRAN mirror, the following tricks may works for without some known side-effects (likes openmp breaking issues), you may try to build your own libblas.so.3gf.0 with following command: $ gfortran -L/opt/intel/lib/intel64 -liomp5 -L/opt/intel/mkl/lib/intel64 -lmkl_rt -lmkl_core -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_gf_ilp64 -lgomp -lpthread -shared -Wl,-soname,libblas.so.3gf -o libblas.so.3gf. $ sudo mkdir /usr/local/lib/MKL $ sudo cp libblas.so.3gf.0 /...

...al/lib/R/site-library/lme4 ---------BUT [ 48 ] <wow> (ron) /usr/bin/R CMD config LAPACK_LIBS -llapack ---------AND <wow> (ron) dpkg -l | grep lapack ii liblapack-dev 3.2.1-8 library of linear algebra routines 3 - static version ii liblapack3gf 3.2.1-8 library of linear algebra routines 3 - shared version [ 44 ] <wow> (ron) --------I did see a message indicating "Also do 'ldd /usr/lib/R/bin/exec/R' and make sure you do _not_ have a depends on Rlapack.so. ....": [ 47...

...debug memory problems. Now I can't even install an old version of this package on a netbook running the Ubuntu 10.10 netbook remix because it can't find the libraries libf77blas and libatlas. I have even gone to the extent of removing the r-base-core package entirely and removing libatlas3gf-base then reinstalling everything. I still get bates at eeek:/var/tmp$ R CMD INSTALL lme4_0.999375-37.tar.gz * installing to library ?/home/bates/R/i686-pc-linux-gnu-library/2.12? * installing *source* package ?lme4? ... ** libs gcc -I/usr/share/R/include -I"/usr/lib/R/library/Matrix/inclu...

...libraries so it not an lme4 package problem. ---------BUT [ 48 ] <wow> (ron) /usr/bin/R CMD config LAPACK_LIBS -llapack ---------AND <wow> (ron) dpkg -l | grep lapack ii liblapack-dev 3.2.1-8 library of linear algebra routines 3 - static version ii liblapack3gf 3.2.1-8 library of linear algebra routines 3 - shared version [ 44 ] <wow> (ron) --------I did see a message indicating "Also do 'ldd /usr/lib/R/bin/exec/R' and make sure you do _not_ have a depends on Rlapack.so. ....": [ 47 ] <wow> (ron)...

Hi, Since upgrading to version 2.11.0~20100402-1, starting R fails with: /usr/lib64/R/bin/exec/R: error while loading shared libraries: libblas.so.3gf: cannot open shared object file: No such file or directory Is this occurring to others on sid? -- Seb

...g. I installed (from a CRAN mirror) the pre-built binaries of R (which, as far as I know, is compiled as a shared library) on Ubuntu 10.10 using apt-get install r-base r-base-dev I successfully built GotoBLAS2 from source, copied the library to /usr/lib and created s symbolic link from libblas.so.3gf to point to the new GotoBLAS2 library. I think the symbolic links and everything are set up correctly, because the BLAS itself works: I'm using Dirk Eddelbuettel's gbcd package to benchmark the difference, and I can still run the matrix multiplication benchmarks (I guess crossprod doesn...

My IT people have set up R on a a Kubuntu box with an RWkard front end.? I have OpenBLAS set up as a shared BLAS but I'm not sure how to get R to see it.? A.3.1 of the installation docs talks about it but I'm not clear if I need a option on my startup line or if I need to find a config file.? The BLAS is is in: ? /usr/lib/openblas-base ? on my machine. I'm not sure how to confirm that

Hello, After upgrading to 2.7.2 this morning via the cran repository, I get the following error when calling R via the command line: Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/home/jstumpf/R/i486-pc-linux-gnu-library/2.7/kernlab/libs/kernlab.so': libRlapack.so: cannot open shared object file: No such file or directory Fatal error: unable to

...agree? I could not find the presentation of R Bivand on this... Any other references on this question? Secondly, I am a little bit confused about how this is done on Ubuntu. First of all.... I am not sure of which BLAS is actually being used... a dpkg -l indicated me that both liblas (-dev and 3gf) and libatlas (3gf-base) are installed... Doing: $ ls -n /usr/lib/R/lib/ total 2528 -rw-r--r-- 1 0 0 2583076 2011-02-26 04:21 libR.so I don't see which one is used actually... how can I figure out? Thanks! Matthieu

...f3a5fe000) libRblas.so => not found libgfortran.so.2 => /usr/lib/libgfortran.so.2 (0x00007fb132100000) libm.so.6 => /lib/libm.so.6 (0x00007fb131e7e000) libR.so => /usr/lib/R/lib/libR.so (0x00007fb13195e000) libc.so.6 => /lib/libc.so.6 (0x00007fb1315fc000) libblas.so.3gf => /usr/lib/libblas.so.3gf (0x00007fb131381000) libreadline.so.5 => /lib/libreadline.so.5 (0x00007fb131141000) libpcre.so.3 => /usr/lib/libpcre.so.3 (0x00007fb130f1b000) libz.so.1 => /usr/lib/libz.so.1 (0x00007fb130d03000) libdl.so.2 => /lib/libdl.so.2 (0x00007fb130aff000...

...000 r-xp 00000000 08:01 5243815 /lib/i386-linux-gnu/ld-2.13.so00374000-00375000 r--p 0001d000 08:01 5243815 /lib/i386-linux-gnu/ld-2.13.so00375000-00376000 rw-p 0001e000 08:01 5243815 /lib/i386-linux-gnu/ld-2.13.so00376000-003f1000 r-xp 00000000 08:01 1840896 /usr/lib/libblas/libblas.so.3gf.0003f1000-003f2000 r--p 0007a000 08:01 1840896 /usr/lib/libblas/libblas.so.3gf.0003f2000-003f3000 rw-p 0007b000 08:01 1840896 /usr/lib/libblas/libblas.so.3gf.0003f3000-00430000 r-xp 00000000 08:01 5243775 /lib/i386-linux-gnu/libpcre.so.3.12.100430000-00431000 r--p 0003c000 08:01 5243775...

...08:01 5243815 /lib/i386-linux-gnu/ld-2.13.so00374000-00375000 r--p > 0001d000 08:01 5243815 /lib/i386-linux-gnu/ld-2.13.so00375000-00376000 > rw-p 0001e000 08:01 5243815 > /lib/i386-linux-gnu/ld-2.13.so00376000-003f1000 r-xp 00000000 08:01 > 1840896 /usr/lib/libblas/libblas.so.3gf.0003f1000-003f2000 r--p 0007a000 > 08:01 1840896 /usr/lib/libblas/libblas.so.3gf.0003f2000-003f3000 rw-p > 0007b000 08:01 1840896 > /usr/lib/libblas/libblas.so.3gf.0003f3000-00430000 r-xp 00000000 08:01 > 5243775 /lib/i386-linux-gnu/libpcre.so.3.12.100430000-00431000 r--p > 00...

....0 b5c8c000-b5c8d000 r--p 000fe000 08:01 8653389 /usr/lib/i386-linux-gnu/libgfortran.so.3.0.0 b5c8d000-b5c8e000 rw-p 000ff000 08:01 8653389 /usr/lib/i386-linux-gnu/libgfortran.so.3.0.0 b5c8e000-b5c8f000 rw-p 00000000 00:00 0 b5c8f000-b642c000 r-xp 00000000 08:01 9310128 /usr/lib/lapack/liblapack.so.3gf.0 b642c000-b642d000 r--p 0079c000 08:01 9310128 /usr/lib/lapack/liblapack.so.3gf.0 b642d000-b6430000 rw-p 0079d000 08:01 9310128 /usr/lib/lapack/liblapack.so.3gf.0 b6430000-b653d000 rw-p 00000000 00:00 0 b654a000-b654e000 r-xp 00000000 08:01 656077 /usr/lib/R/library/tools/libs/tools.so b654e000-b6...

Rhelpers: I recently installed the 64-bit version of R on my Debian system, and afterwards was asked if it was compiled using ATLAS. Is there a way to test to see if R is using ATLAS? --j

...-f /var/spool/atlas39/libatlas39_3.9.25-1_amd64.deb Package: libatlas39 Source: atlas39 Version: 3.9.25-1 Architecture: amd64 Maintainer: Dirk Eddelbuettel <edd at debian.org> Installed-Size: 22656 Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libgfortran3 (>= 4.3) Suggests: libblas3gf, liblapack3gf Provides: libatlas.so.3gf, libblas.so.3gf, liblapack.so.3gf Section: libs Priority: optional Homepage: http://math-atlas.sourceforge.net/ Description: Automatically Tuned Linear Algebra Software, version 3.9.25 ATLAS is an approach for the automatic generation and optimization of nu...

today i upgraded from 2.12 to 2.15.2 on ubuntu 12.04 and now i get this message whenever i try to start R. Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/usr/lib/R/library/stats/libs/stats.so': /usr/lib/liblapack.so.3gf: undefined symbol: ATL_chemv any suggestions as to how to fix this? [[alternative HTML version deleted]]

I've attempted to use the optimized GotoBLAS2 library with a freshly compiled R-2.11.1 patched on 64-bit Ubuntu 10.4. (See details below). When I run this version of R, the timings are not different than the original install, and only one core is used in test computations. Can someone point out my error? Thanks. --Dale Details ... I'm running the 64-bit version of Ubuntu 10.04 on my 2

...t; I have checked which libraries R is pointing to: --- busta at temisto:~$ ldd /usr/lib/R/bin/exec/R linux-vdso.so.1 => (0x00007fff1e100000) libR.so => /usr/lib/R/lib/libR.so (0x00007f9157c54000) libc.so.6 => /lib/libc.so.6 (0x00007f91578f2000) libblas.so.3gf => /usr/lib/atlas/libblas.so.3gf (0x00007f9156f42000) libgfortran.so.2 => /usr/lib/libgfortran.so.2 (0x00007f9156c83000) libm.so.6 => /lib/libm.so.6 (0x00007f9156a02000) libreadline.so.5 => /lib/libreadline.so.5 (0x00007f91567c2000) libpcre.so.3 => /us...

I just upgraded to Ubuntu 8.10 (i386) from 8.04. After the upgrade, I ran update.packages(.libPaths()[1]) in R to get the packages installed from source up to date too. Unfortunately, two packages could not be updated: mclust and mboost. In both cases, the error I got mentioned lf77blas. Here's the output for mboost: * Installing *source* package 'mboost' ... ** libs gcc -std=gnu99

Hello, Recently updated Ubuntu to 10.04, I have installed the r-base and r-base-dev packages from CRAN with sudo apt-get install r-base But now when I want to start R I get the following error: gpetris at definetti:~$ R /usr/lib/R/bin/exec/R: symbol lookup error: /usr/local/lib/libreadline.so.6: undefined symbol: PC Any clue??? Has anybody seen that before? I have tried to reinstall the