Package Details: r-mkl 3.3.1-3

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: 0.094356
First Submitted: 2010-05-06 00:10
Last Updated: 2016-09-10 20:48

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

leonardof commented on 2016-09-17 20:42

Thank you, alexanderp!

alexanderp commented on 2016-09-17 10:16

leonardof, I suggest you follow up your problem with the intel forums. You've probably got the wrong license and this page is not the place for these kinds of issues.
Once you've got the intel compilers working, try using r-mkl again.

leonardof commented on 2016-09-17 03:51

I can't compile r-mkl despite having got the community license and having put the LIC file at /opt/intel/licenses/. Reading r-mkl/src/R-3.3.1/config.log (see excerpt below), I gather that somehow my license isn't valid... How can it be?

configure:5750: checking for gcc
configure:5777: result: icc
configure:6006: checking for C compiler version
configure:6015: icc --version >&5

Error: A license for (Comp-CL) could not be found.
License file(s) used were (in this order):
1. Trusted Storage
** 2. /opt/intel/composerxe/linux/licenses
** 3. /opt/intel/licenses/NCOM____XXXX-XXXXXXXX_1.lic
** 4. /opt/intel/licenses/NCOM____XXXX-XXXXXXXX_2.lic
** 5. /home/leonardof/intel/licenses
** 6. /opt/intel/compilers_and_libraries_2017.0.098/linux/bin/intel64/../../Licenses
** 7. /home/leonardof/Licenses
... rest of stderr output deleted ...
configure:6026: $? = 1
configure:6015: icc -v >&5

Error: A license for (Comp-CL) could not be found.
License file(s) used were (in this order):
1. Trusted Storage
** 2. /opt/intel/composerxe/linux/licenses
** 3. /opt/intel/licenses/NCOM____XXXX-XXXXXXXX_1.lic
** 4. /opt/intel/licenses/NCOM____XXXX-XXXXXXXX_2.lic
** 5. /home/leonardof/intel/licenses
** 6. /opt/intel/compilers_and_libraries_2017.0.098/linux/bin/intel64/../../Licenses
** 7. /home/leonardof/Licenses
... rest of stderr output deleted ...
configure:6026: $? = 1
configure:6015: icc -V >&5

Error: A license for (Comp-CL) could not be found.
License file(s) used were (in this order):
1. Trusted Storage
** 2. /opt/intel/composerxe/linux/licenses
** 3. /opt/intel/licenses/NCOM____XXXX-XXXXXXXX_1.lic
** 4. /opt/intel/licenses/NCOM____XXXX-XXXXXXXX_2.lic
** 5. /home/leonardof/intel/licenses
** 6. /opt/intel/compilers_and_libraries_2017.0.098/linux/bin/intel64/../../Licenses
** 7. /home/leonardof/Licenses
... rest of stderr output deleted ...
configure:6026: $? = 1
configure:6015: icc -qversion >&5

Error: A license for (Comp-CL) could not be found.
License file(s) used were (in this order):
1. Trusted Storage
** 2. /opt/intel/composerxe/linux/licenses
** 3. /opt/intel/licenses/NCOM____XXXX-XXXXXXXX_1.lic
** 4. /opt/intel/licenses/NCOM____XXXX-XXXXXXXX_2.lic
** 5. /home/leonardof/intel/licenses
** 6. /opt/intel/compilers_and_libraries_2017.0.098/linux/bin/intel64/../../Licenses
** 7. /home/leonardof/Licenses
... rest of stderr output deleted ...
configure:6026: $? = 1
configure:6046: checking whether the C compiler works
configure:6068: icc -O3 -qno-opt-matmul -xHost -m64 -parallel -mkl=parallel -qopenmp -ipo -fp-model precise -fp-model source -qopt-mem-layout-trans=2 -diag-disable=188,308 -I/opt/intel/composerxe/linux/mkl/include -D_FORTIFY_SOURCE=2 -Wl,-O1,--sort-common,--as-needed,-z,relro conftest.c >&5

Error: A license for (Comp-CL) could not be found.
License file(s) used were (in this order):
1. Trusted Storage
** 2. /opt/intel/composerxe/linux/licenses
** 3. /opt/intel/licenses/NCOM____XXXX-XXXXXXXX_1.lic
** 4. /opt/intel/licenses/NCOM____XXXX-XXXXXXXX_2.lic
** 5. /home/leonardof/intel/licenses
** 6. /opt/intel/compilers_and_libraries_2017.0.098/linux/bin/intel64/../../Licenses
** 7. /home/leonardof/Licenses
** 8. /Users/Shared/Library/Application Support/Intel/Licenses
** 9. /opt/intel/compilers_and_libraries_2017.0.098/linux/bin/intel64/*.lic

Please refer https://software.intel.com/en-us/faq/licensing#invalid-license-error for more information..

icc: error #10052: could not checkout FLEXlm license


The second LIC file was an attempted workaround, using the MAC address of the wifi instead of the ethernet.

alexanderp commented on 2016-09-09 07:14

You should get a license to use Intel MKL. See https://wiki.archlinux.org/index.php/Intel_C%2B%2B

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

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