Package Details: r-mkl 3.3.1-2

Git Clone URL: https://aur.archlinux.org/r-mkl.git (read-only)
Package Base: r-mkl
Description: Language and environment for statistical computing and graphics, linked with Intel's MKL.
Upstream URL: http://www.r-project.org/
Keywords: hpc mathematics modelling r statistics
Licenses: GPL
Conflicts: r
Provides: r=3.3.1,r-mkl=3.3.1
Submitter: giniu
Maintainer: alexanderp
Last Packager: alexanderp
Votes: 14
Popularity: 0.173269
First Submitted: 2010-05-06 00:10
Last Updated: 2016-07-05 16:56

Required by (102)

Sources (4)

Pinned Comments

alexanderp commented on 2016-06-17 00:20

The latest update (3.3.0-2):
- fixes compilation with icc/ifort
- icc/ifort are enabled by default now
- adds floating point precision options to icc
- removes i686 build options

You'll notice an error while checking the Matrix package. This is due to the LAPACK functions which error out on zero size matrices.

Latest Comments

AnRe005 commented on 2016-08-07 09:22

Maybe a little late but,

--------------------------------------------------------------------------------------
The package compiles and runs well, however I can't install anything from within R, as there are always undefined symbols associated with intel compilers. For instance, if I try install.package("igraph"), the compilation runs well, but the package fails to load with:

Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/lib/R/library/igraph/libs/igraph.so':
/usr/lib/R/library/igraph/libs/igraph.so: undefined symbol: for_cpstr
--------------------------------------------------------------------------------------

**This error disappears when 'lifcore' is added to 'BLAS_LIBS' in the Makeconf file**

--------------------------------------------------------------------------------------
Rcmdr fails with:

unable to load shared object '/usr/lib/R/library/quantreg/libs/quantreg.so':
/usr/lib/R/library/quantreg/libs/quantreg.so: undefined symbol: etime_
--------------------------------------------------------------------------------------

**This error disappears when 'lifport' is added to 'BLAS_LIBS' in the Makeconf file**

So I was able to compile and install the 'igraph' package with icc.

The 'quantreg' package still doesn't compile fine and throws the following error message:

/opt/intel/composerxe/linux/compiler/lib/intel64/libifport.so.5: undefined symbol: __FFfrand

greenisagoodcolo commented on 2016-07-12 20:50

Thank you Lennartv. That was a big help :-D

AnRe005 commented on 2016-07-05 07:09

The md5sum and md512sum for r.png have changed.

New md5sum: 8e0c51650b8a63f110fa7b09e699e9c4

New md512sum: 1491b01d3d14b86d26c383e00e2305858a52ddd498158c9f7f6b33026ee01f246408b1676cffea73f7783c8c4cf546285705c43c0286adbd75ad77706918b5fe

lennartv commented on 2016-06-25 19:49

[SOLVED]: Following your solution proposal to compile packages where icc fails...

My .R/Makevars is:
CC=gcc
CXX=g++
CXX1X=g++
CFLAGS=-mtune=native -g -O3 -Wall
CXXFLAGS=-mtune=native -g -O3 -Wall
______________________________________
Installing "quantreg" I get:

Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/lennartv/R/x86_64-pc-linux-gnu-library/3.3/quantreg/libs/quantreg.so':
/home/lennartv/R/x86_64-pc-linux-gnu-library/3.3/quantreg/libs/quantreg.so: undefined symbol: __must_be_linked_with_icc_or_xild
Error: loading failed

Thanks in advance for your help. I highly appreciate your package in general.

____________
Never mind. This solved the issue for me:

CC=gcc
CXX=g++
CXX1X=g++
CFLAGS=-mtune=native -g -O3 -Wall
CPPFLAGS=
CXXFLAGS=-mtune=native -g -O3 -Wall
FC=gfortran
FCFLAGS=-O3 -fopenmp
F77=gfortran
FFLAGS=-O3 -fopenmp

alexanderp commented on 2016-06-22 20:27

Hello wast3,

yes, some packages fail to compile with icc. You can switch to gcc temporarily by creating a .R/Makevars file.

Or, you can build the package with gcc.

wast3 commented on 2016-06-22 19:57

The package compiles and runs well, however I can't install anything from within R, as there are always undefined symbols associated with intel compilers. For instance, if I try install.package("igraph"), the compilation runs well, but the package fails to load with:

Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/lib/R/library/igraph/libs/igraph.so':
/usr/lib/R/library/igraph/libs/igraph.so: undefined symbol: for_cpstr


Rcmdr fails with:

unable to load shared object '/usr/lib/R/library/quantreg/libs/quantreg.so':
/usr/lib/R/library/quantreg/libs/quantreg.so: undefined symbol: etime_

Guess something must be missing either from this package or intel-mkl

chendaniely commented on 2016-06-19 03:34

I'm having a problem with the update (used pacaur and yaourt):


==> Extracting sources...
-> Extracting R-3.3.0.tar.gz with bsdtar
==> Starting prepare()...
==> Starting build()...
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
loading site script './config.site'
loading build-specific script './config.site'
checking for pwd... /usr/bin/pwd
checking whether builddir is srcdir... yes
checking for working aclocal... found
checking for working autoconf... found
checking for working automake... found
checking for working autoheader... found
checking whether ln -s works... yes
checking for bison... bison -y
checking for xiar... xiar
checking for a BSD-compatible install... /usr/bin/install -c
checking for sed... /usr/bin/sed
checking for which... /usr/bin/which
checking for less... /usr/bin/less
checking for gtar... no
checking for gnutar... no
checking for tar... /usr/bin/tar
checking for tex... /usr/bin/tex
checking for pdftex... /usr/bin/pdftex
checking for pdflatex... /usr/bin/pdflatex
checking for makeindex... /usr/bin/makeindex
checking for texi2any... /usr/bin/texi2any
checking whether texi2any version is at least 5.1... yes
checking for ginstall-info... no
checking for install-info... /usr/bin/install-info
checking for texi2dvi... /usr/bin/texi2dvi
checking for kpsewhich... /usr/bin/kpsewhich
checking for latex inconsolata package... found zi4.sty
checking for unzip... /usr/bin/unzip
checking for zip... /usr/bin/zip
checking for gzip... /usr/bin/gzip
checking for bzip2... /usr/bin/bzip2
checking for firefox... /usr/bin/firefox
using default browser ... /usr/bin/firefox
checking for acroread... no
checking for acroread4... no
checking for xdg-open... /usr/bin/xdg-open
checking for notangle... false
checking for realpath... /usr/bin/realpath
checking for pkg-config... /usr/bin/pkg-config
checking for gcc... icc -std=c99
checking whether the C compiler works... no
configure: error: in `/tmp/yaourt-tmp-dchen/aur-r-mkl/src/R-3.3.0':
configure: error: C compiler cannot create executables



greenisagoodcolo commented on 2016-06-17 18:25

Thank you Alexanderp!

AnRe005 commented on 2016-06-17 11:28

Thanks for the fix. :-)

alexanderp commented on 2016-06-17 09:28

I pushed another update to fix errors due to missing dependencies.

All comments