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Package Details: r-mkl 4.0.2-1

Package Actions

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=4.0.2
Submitter:	giniu
Maintainer:	alexanderp
Last Packager:	alexanderp
Votes:	19
Popularity:	0.010618
First Submitted:	2010-05-06 00:10
Last Updated:	2020-06-29 23:36

Dependencies (25)

bzip2 (bzip2-git, bzip2-rustify-git, bzip2-with-lbzip2-symlinks)
curl (curl-git)
icu (icu-git, icu-git-static)
intel-mkl
libjpeg (libjpeg-droppatch, mozjpeg-git, mozjpeg, libjpeg-turbo-git, libjpeg-turbo)
libpng (libpng-git, libpng-apng)
libtiff (libtiff-git)
libxmu
libxt
ncurses (ncurses-nohex, ncurses-git)
openmp (openmp-svn, openmp-nvptx)
pango (pango-ubuntu, pango-git)
pcre2 (pcre2-svn)
perl (perl-git)
readline (readline-athame-git, readline-git)
unzip (unzip-natspec, unzip-iconv)
xz (xz-git, xz-static-git)
zip (zip-natspec)
zlib (zlib-static, zlib-git, zlib-asm, minizip-asm, zlib-ng-git)
gcc-fortran (gcc-fortran-multilib-x32, gcc-fortran-multilib-git, gcc-fortran-git) (make)
java-environment (jdk5, tuxjdk, jdk7-openjdk-infinality, java-8-openjdk-shenandoah, jdk8-openjdk-infinality, java-gcj-compat, jdk9, zulu-10-bin, jdk-devel, jdk8-arm64, jdk6, jdk12-openj9-bin, zulu-12-bin, jdk12, jdk8-openjdk-dcevm, jdk11-graalvm-ee-bin, zulu-13-bin, jdk8-jetbrains, jdk8-arm, jdk13-openj9-bin, jdk9-openj9-bin, jdk10, jdk11-openjdk-dcevm, jdk8-openjdk-jetbrains, jdk8-openjdk-shenandoah, jdk10-openj9-bin, jetbrains-jre8, liberica-jdk-11-bin, liberica-jdk-11-full-bin, liberica-jdk-11-lite-bin, liberica-jre-11-bin, liberica-jre-11-full-bin, jdk11-adoptopenjdk, zulu-11-bin, amazon-corretto-11, jdk14-openj9-bin, jdk11-openj9-bin, sapmachine-jdk-bin, jdk11, jdk7, jdk8, liberica-jdk-8-full-bin, amazon-corretto-8, jdk-openj9, jdk7-j9-bin, jdk7r1-j9-bin, zulu-embedded-jdk8, jdk8-graalvm-bin, jdk11-graalvm-bin, jdk8-openj9-bin, jdk-arm, jdk8-adoptopenjdk, jdk, jdk-adoptopenjdk, zulu-8-bin, jdk8-j9-bin, zulu-15-bin, zulu-14-bin, liberica-jdk-full-bin, zulu-embedded-jdk11, jetbrains-jre, jdk-openj9-bin, java-openjdk-loom-ea-bin, java-openjdk-bin, jdk-jetbrains, java-openjdk-ea-bin, jdk-openjdk, jdk11-openjdk, jdk7-openjdk, jdk8-openjdk) (make)
tk (tk85) (make)
gcc-fortran (gcc-fortran-multilib-x32, gcc-fortran-multilib-git, gcc-fortran-git) (optional) – needed to compile some CRAN packages
texlive-bin (texlive-bin-svn, texlive-installer, texlive-full) (optional) – LaTeX sty files
tk (tk85) (optional) – tcl-tk interface

Required by (365)

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Sources (5)

Latest Comments

1 2 3 4 5 6 ... Next › Last »

alexanderp commented on 2020-08-24 19:12

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

jalapeno commented on 2020-08-20 19:55

When attempting to install a package in r-mkl, I get this error:

install.packages("mnormt")
[truncated]
/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
make: *** [/usr/share/R//make/shlib.mk:6: tmvnsim.so] Error 1
ERROR: compilation failed for package ‘tmvnsim’

I was unable to find a solution here, but managed to just copy lmkl_gf_lp64.so lmkl_gf_thread and lmkl_core.so' from/opt/intel/mkl/lib/intel64to/usr/lib/R/lib`.

Is there some other way that this ought to be done? Or, is this the only work-around?

tealeaf commented on 2020-07-26 19:51

As a follow-up to my previous comment: downgrading to intel-mkl-2020.1.217-6 resolved this for the moment.

tealeaf commented on 2020-07-26 15:28

Not sure if this belongs here, in intel-mkl, or elsewhere, but I'm having a problem running R-INLA under this on a new machine. I can install with:

install.packages("INLA", repos=c(getOption("repos"), INLA="https://inla.r-inla-download.org/R/testing"), dep=TRUE)

as normal, but running:

library(INLA)
inla.pardiso.check()

I get:

/home/joss/.R/packages/INLA/bin/linux/64bit/inla: symbol lookup error: /opt/intel/mkl/lib/intel64/libmkl_gf_lp64.so: undefined symbol: mkl_lapack_scombssq
Error in system(paste(shQuote(inla.call.no.remote()), "-m pardiso"), intern = TRUE) : error in running command

The strange thing is that this is working on my old machine with an almost identical setup.

sxyzy1016 commented on 2020-06-26 10:32

using icc to build it by uncomment the line # _CC="icc" and get:

...
icc -I../../src/extra -I/usr/include/tirpc -I. -I../../src/include -I../../src/include  -D_FORTIFY_SOURCE=2 -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O3 -fPIC -m64 -march=native -fp-model precise -fp-model source -I/opt/intel/mkl/include  -c arithmetic.c -o arithmetic.o
arithmetic.c(61): warning #274: declaration is not visible outside of function
  int matherr(struct exception *exc)
                     ^

arithmetic.c(63): error: pointer to incomplete class type is not allowed
      switch (exc->type) {
              ^

arithmetic.c(64): error: identifier "DOMAIN" is undefined
      case DOMAIN:
           ^

arithmetic.c(65): error: identifier "SING" is undefined
      case SING:
           ^

arithmetic.c(68): error: identifier "OVERFLOW" is undefined
      case OVERFLOW:
           ^

arithmetic.c(71): error: identifier "UNDERFLOW" is undefined
      case UNDERFLOW:
           ^

arithmetic.c(72): error: pointer to incomplete class type is not allowed
    exc->retval = 0.0;
    ^

compilation aborted for arithmetic.c (code 2)
...

in build(). EDIT: according to this, use

sed -i '/^#define HAVE_MATHERR 1/d' src/include/config.h

between configure and make will make it work.

Svenstaro commented on 2020-06-15 17:22

Alright but can you check the new intel-mkl that blue includes a shim script for mklvars.sh? It should work.

alexanderp commented on 2020-06-15 10:51

Hi @Svenstaro. No reason, other than wanting to fix r-mkl as quickly as possible after the move of intel-mkl to [Community]. I read the discussions on not including the original MKL scripts on the basis of standardization, so I made the decision to maintain compatibility locally.

Anyway, I copied the mklvars.sh script from upstream, therefore it should work for any package that depends on it.

Also, thank you for bringing intel-mkl to [Community]. Hopefully we'll get smoother upgrades and less incompatibilities this way.

Svenstaro commented on 2020-06-14 22:51

Hey, I'm the maintainer of the intel-mkl package and I just stumbled upon this pacakage right here. I'm trying to add a mklvars.sh to the [community] package that works for most people.

I'm curious: Why didn't you provide a patch for this on our bug tracker? Currently, your patch only works for this package but maybe other people would also be happy to benefit from the added mklvars.sh.

alexanderp commented on 2020-04-07 21:43

Update: I've added logic that allows this package to compile with both the AUR and Community versions of intel-mkl.

alexanderp commented on 2020-04-07 20:29

@mys_721tx, the intel-mkl package in Community is a mess. It's trying to force some rules/opinions which have obviously broken the software which depend on it. It's missing a lot of setup scripts from the original package on AUR and has rearranged most libraries and files.

I suggest to keep using intel-mkl from AUR, until the Community version is fixed.

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