Package Details: r-mkl 4.4.0-1

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
Submitter: giniu
Maintainer: alexanderp
Last Packager: alexanderp
Votes: 25
Popularity: 0.004410
First Submitted: 2010-05-06 00:10 (UTC)
Last Updated: 2024-04-29 17:06 (UTC)

Latest Comments

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burgerga commented on 2021-07-12 07:09 (UTC) (edited on 2021-07-12 07:10 (UTC) by burgerga)

@alexanderp Ah, yes you're right, however the contents of that file are:

#!/bin/sh
#
# This little script pretends to be mklvars.sh but actually just exports some variables
# to directories precisely where Arch installs them. No point shipping the original
# mklvars.sh which wrongly guesses all the paths.

export "LD_LIBRARY_PATH=/opt/intel/mkl/lib/intel64_lin:${LD_LIBRARY_PATH}"
export "LIBRARY_PATH=/opt/intel/mkl/lib/intel64_lin:${LIBRARY_PATH}"
export "NLSPATH=/opt/intel/mkl/lib/intel64_lin/locale/%l_%t/%N:${NLSPATH}"
export "CPATH=/opt/intel/mkl/include:${CPATH}"
export "PKG_CONFIG_PATH=/usr/lib/pkgconfig:${PKG_CONFIG_PATH}"

So it doesn't set MKLROOT (I don't know if the original did?), so how is MKLROOT set on your system?

EDIT: Maybe intel-mkl should set MKLROOT though, that would be more logical than setting it in r-mkl

alexanderp commented on 2021-07-11 10:50 (UTC)

@burgerga

Cannot reproduce this in my build system. In fact, mklvars.sh is still here:

pacman -Qo mklvars.sh
/usr/bin/mklvars.sh is owned by intel-mkl 2020.4.304-1

burgerga commented on 2021-07-06 23:01 (UTC) (edited on 2021-07-06 23:02 (UTC) by burgerga)

@alexanderp I'm getting the same issue as @jalapeno

/usr/bin/ld: cannot find -lmkl_gf_lp64
/usr/bin/ld: cannot find -lmkl_gnu_thread
/usr/bin/ld: cannot find -lmkl_core
collect2: error: ld returned 1 exit status

The problem in my case is that MKLROOT was not set during installation so ${MKLROOT}/lib/intel64 becomes /lib/intel64 which is used as -L flag in the BLAS_LIBS makevar in /usr/lib/R/etc/Makeconf, and then of course when we try to compile packages, the linker can't find the shared libraries.

I think the issue might be that intel-mkl does not come with mklvars.sh anymore. There is only mkl_link_tool in /opt/intel/mkl/bin and if you run it with either the -env or the -interactive option you can see that it assumes MKLROOT is already set...

sgrubsmyon commented on 2021-05-05 14:40 (UTC)

@Humble_Panda Yes, indeed. Removing and reinstalling (recompiling) the r-mkl package helped in my case.

Humble_Panda commented on 2021-02-08 08:27 (UTC)

Anyone else getting a broken R installation after one of the last updates? libicuuc.so.67 isn't on the system anymore...

alexanderp commented on 2021-01-20 14:22 (UTC)

@LuisDamiano, in my opinion, distributing a binary of this package defeats the purpose of the additional CPU performance optimizations obtained by compiling on a target system.

svenstaro commented on 2021-01-19 08:09 (UTC)

@LuisDamiano you could talk to the maintainers of the r package whether they'd be interested in pulling this in.

LuisDamiano commented on 2021-01-18 16:44 (UTC)

Thanks for the great work! It takes quite a bit to compile locally, would it be possible to get r-mkl added to the Extra official repo? Having the binaries would be quite useful.

k07k454n commented on 2020-11-24 18:30 (UTC) (edited on 2020-11-24 18:33 (UTC) by k07k454n)

Had issues for 4.0.2 and 4.0.3 like this during build:

Error: package or namespace load failed for ‘nnet’ in dyn.load(file, DLLpath = DLLpath, ...):                                                                                                                                                                                     
 unable to load shared object '/home/user/aur/r-mkl/src/R-4.0.3/library/nnet/libs/nnet.so':                                                                                                                                                                                       
  /home/user/aur/r-mkl/src/R-4.0.3/library/nnet/libs/nnet.so: undefined symbol: _ZGVbN2v_exp                                                                                                                                                                                      
Error: loading failed 
** testing if installed package can be loaded                                                                                            
Error: package or namespace load failed for ‘MASS’ in dyn.load(file, DLLpath = DLLpath, ...):                                                      
 unable to load shared object '/home/user/aur/r-mkl/src/R-4.0.3/library/MASS/libs/MASS.so':                                                        
  /home/user/aur/r-mkl/src/R-4.0.3/library/MASS/libs/MASS.so: undefined symbol: _ZGVbN2v_log                                                       
Error: loading failed

..so to build and install successfully had to first do 'export SHLIB_LDFLAGS=-lmvec' before makepkg

alexanderp commented on 2020-08-24 19:12 (UTC)

@jalapeno, if intel-mkl was updated, try recompiling the package.

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