Package Details: r-mkl 3.6.2-1

Git Clone URL: https://aur.archlinux.org/r-mkl.git (read-only, click to copy)
Package Base: r-mkl
Description: Language and environment for statistical computing and graphics, linked to the Intel(R) MKL.
Upstream URL: http://www.r-project.org/
Keywords: hpc mathematics modelling r statistics
Licenses: GPL
Conflicts: microsoft-r-open, r
Provides: r=3.6.2
Submitter: giniu
Maintainer: alexanderp
Last Packager: alexanderp
Votes: 19
Popularity: 0.23
First Submitted: 2010-05-06 00:10
Last Updated: 2020-01-07 12:22

Dependencies (26)

Required by (265)

Sources (4)

Latest Comments

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GeorgeChao commented on 2016-09-09 06:47

I found my config.log. As follows,

---
configure:5690: result: /usr/bin/pkg-config
configure:5750: checking for gcc
configure:5777: result: icc -std=c99
configure:6006: checking for C compiler version
configure:6015: icc -std=c99 --version >&5

Error: A license for Comp-CL could not be obtained (-1,359,2).

Is your license file in the right location and readable?
The location of your license file should be specified via
the $INTEL_LICENSE_FILE environment variable.

License file(s) used were (in this order):
1. Trusted Storage
** 2. /opt/intel/composerxe/linux/licenses
... rest of stderr output deleted ...
configure:6026: $? = 1
configure:6015: icc -std=c99 -v >&5

Error: A license for Comp-CL could not be obtained (-1,359,2).

Is your license file in the right location and readable?
The location of your license file should be specified via
the $INTEL_LICENSE_FILE environment variable.

License file(s) used were (in this order):
1. Trusted Storage
** 2. /opt/intel/composerxe/linux/licenses

GeorgeChao commented on 2016-09-09 06:47

I found my config.log. As follows,

---
configure:5690: result: /usr/bin/pkg-config
configure:5750: checking for gcc
configure:5777: result: icc -std=c99
configure:6006: checking for C compiler version
configure:6015: icc -std=c99 --version >&5

Error: A license for Comp-CL could not be obtained (-1,359,2).

Is your license file in the right location and readable?
The location of your license file should be specified via
the $INTEL_LICENSE_FILE environment variable.

License file(s) used were (in this order):
1. Trusted Storage
** 2. /opt/intel/composerxe/linux/licenses
... rest of stderr output deleted ...
configure:6026: $? = 1
configure:6015: icc -std=c99 -v >&5

Error: A license for Comp-CL could not be obtained (-1,359,2).

Is your license file in the right location and readable?
The location of your license file should be specified via
the $INTEL_LICENSE_FILE environment variable.

License file(s) used were (in this order):
1. Trusted Storage
** 2. /opt/intel/composerxe/linux/licenses

GeorgeChao commented on 2016-09-09 06:31

my C compiler got some error.
---
gcc -version
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-pc-linux-gnu/6.2.1/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /build/gcc/src/gcc/configure --prefix=/usr --libdir=/usr/lib --libexecdir=/usr/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=https://bugs.archlinux.org/ --enable-languages=c,c++,ada,fortran,go,lto,objc,obj-c++ --enable-shared --enable-threads=posix --enable-libmpx --with-system-zlib --with-isl --enable-__cxa_atexit --disable-libunwind-exceptions --enable-clocale=gnu --disable-libstdcxx-pch --disable-libssp --enable-gnu-unique-object --enable-linker-build-id --enable-lto --enable-plugin --enable-install-libiberty --with-linker-hash-style=gnu --enable-gnu-indirect-function --disable-multilib --disable-werror --enable-checking=release
Thread model: posix
gcc version 6.2.1 20160830 (GCC)


Error output
---
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 `/home/gg/softwares/r-mkl_R-3.3.1/src/R-3.3.1':
configure: error: C compiler cannot create executables
See `config.log' for more details
==> ERROR: A failure occurred in build().
Aborting...

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