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Package Details: r-mkl 3.6.1-1

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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 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=3.6.1
Submitter:	giniu
Maintainer:	alexanderp
Last Packager:	alexanderp
Votes:	19
Popularity:	0.82
First Submitted:	2010-05-06 00:10
Last Updated:	2019-07-11 20:06

Dependencies (26)

bzip2 (bzip2-git, bzip2-rustify-git, bzip2-with-lbzip2-symlinks)
curl (curl-http2-git, curl-git)
gcc-fortran (gcc-fortran-multilib-x32, gcc-fortran-multilib-git, gcc-fortran-git)
gcc-libs (gcc-libs-multilib-x32, gcc-libs-multilib-git, fastgcc, gcc-libs-git)
icu (icu-git)
intel-common-libs
intel-mkl (intel-mkl-slim)
libjpeg (libjpeg-droppatch, mozjpeg-git, mozjpeg, libjpeg-turbo)
libpng (libpng-git)
libtiff (libtiff-git)
libxmu
libxt
ncurses (ncurses-nohex)
openmp (openmp-svn)
pango (pango-ubuntu, pango-git)
pcre (pcre-svn)
perl (perl-git)
readline (readline-athame-git)
unzip (unzip-natspec, unzip-iconv)
xz (xz-git, xz-static-git)
zip (zip-natspec)
zlib (zlib-asm, zlib-static, zlib-git)
java-environment (jdk5, jdk9-openj9-bin, tuxjdk, jdk7-openjdk-infinality, java-8-openjdk-shenandoah, jdk8-openjdk-infinality, java-gcj-compat, jdk10-openjdk-openj9-bin, jdk9, zulu-10-bin, jdk-devel, jdk10, jdk-dcevm, jdk8-arm, jdk8-arm64, jdk8-openjdk-shenandoah, jdk8-openjdk-jetbrains, jdk8-j9-bin, jdk6, jdk-arm, jdk12-openj9-bin, zulu-12-bin, jdk7-j9-bin, jdk7r1-j9-bin, jetbrains-jre, jetbrains-jre8, java-openjdk-bin, jdk13-openj9-bin, java-openjdk-ea-bin, jdk8, jdk11, jdk8-openj9-bin, jdk7, jdk11-adoptopenjdk, zulu-embedded-jdk11, jdk, jdk-openj9-bin, jdk-adoptopenjdk, zulu-11-bin, graal-bin, jdk12, amazon-corretto-8, amazon-corretto-11, jdk8-jetbrains, jdk-jetbrains, jdk11-openj9-bin, jdk-openjdk, jdk10-openjdk, jdk11-openjdk, jdk7-openjdk, jdk8-openjdk) (make)
tk (tk85) (make)
texlive-bin (texlive-bin-svn, texlive-full, texlive-installer) (optional) – LaTeX sty files
tk (tk85) (optional) – tcl-tk interface

Required by (259)

apache-spark (requires r) (optional)
apache-spark-git (requires r) (optional)
data-science-languages-meta (requires r)
data-science-mkl-meta
diffoscope-git (requires r) (optional)
diffoscope-git (requires r) (check)
dnaa (requires r)
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emacs-ess-git (requires r)
fgbio-git (requires r) (check)
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gatk-bin (requires r) (optional)
grass6 (requires r) (optional)
iramuteq-bin (requires r)
jamovi-rbundle (requires r) (make)
jamovi-rbundle (requires r)
jasp-desktop-git (requires r)
jasp-desktop-git (requires r) (make)
jasp-rbundle (requires r)
jasp-rbundle (requires r) (make)
knime-desktop (requires r) (optional)
ledger-plots-git (requires r)
libcorkipset-git (requires r)
littler (requires r) (make)
littler (requires r)
littler-git (requires r) (make)
littler-git (requires r)
mange (requires r) (optional)
mapdamage (requires r) (optional)
mathematica (requires r) (optional)
mathematica-09 (requires r) (optional)
monetdb (requires r)
monetdb (requires r) (make)
nteract-bin (requires r) (optional)
nvim-r (requires r) (optional)
phantompeakqualtools (requires r)
plink (requires r)
pp-git (requires r) (optional)
python-rchitect (requires r)
python-rpy2-hg (requires r)
python2-rchitect (requires r)
qtltools-git (requires r)
quake-bio (requires r)
qualimap (requires r)
quine-relay (requires r)
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r-askpass (requires r)
r-assertthat (requires r)
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r-zoo (requires r)
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rsem (requires r)
rserve-sandbox-docker (requires r)
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rstudio-desktop (requires r)
rstudio-desktop-bin (requires r)
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rstudio-desktop-preview-bin (requires r)
rstudio-server-bin (requires r)
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shiny-server-git (requires r) (make)
shiny-server-git (requires r)
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simpleitk (requires r) (make)
simpleitk (requires r) (optional)
taverna (requires r) (optional)
zim-git (requires r) (optional)

Sources (4)

Latest Comments

1 2 3 4 5 6 ... Next › Last »

petronny commented on 2019-10-17 05:21

@xia0er R uses R-package/src/Makevars instead of the system Makevars when building packages. I find this when I try to build r-mxnet.

I can't recall exactly but I think there is a way to set the Makevars in userspace by editing something like ~/.R/Makevars.

Also someone filed an issue on arch4edu about that the prebuilt binary needs rebuild against the latest mkl. I'm working on it.

xia0er commented on 2019-10-16 20:09

My issue is fixed by editing /etc/R/Makeconf: FCLIBS_XTRA = -L/opt/intel/lib

Not sure why this is still needed, as I can see that /etc/ld.so.conf.d/intel-common-libs.conf has /opt/intel/lib included. I have also tried to set the environment variable export LD_LIBRARY_PATH=-L/opt/intel/lib before starting R, but it doesn't fix the issue.

Hope this helps others with similar issues.

alexanderp commented on 2019-10-15 21:58

@xia0er, looks like your system (container) might be broken. It's considered bad practice to manually manage software inside the container. Instead, recreate your base image.

xia0er commented on 2019-10-15 18:52

@alexanderp The docker image is based on archlinux/base and I update all packages to the latest version with pacman -Syyu before download and install r-mkl with this PKGBUILD (also tried @petronny's binary package) in my own Dockerfile. After building the image and run it in a container, r-mkl works fine as far as I can see, but fails when installing classInt (as a dependency for the package sf). I also tried installing the r packages in the Dockerfile, but it fails in the building process with the same error. Thanks for your help!

alexanderp commented on 2019-10-15 07:52

@xia0er, I guess the first question is how long ago the docker container was built and whether you updated software inside the container.

xia0er commented on 2019-10-15 05:24

Anyone experiencing issue when installing the classInt package on r-mkl? I am getting a strange error on an otherwise fully functional r-mkl installation:

... gcc -shared -L/usr/lib64/R/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o classInt.so fish1.o init.o -lgfortran -limf -lm -lquadmath -L/usr/lib64/R/lib -lR /usr/sbin/ld: cannot find -limf collect2: error: ld returned 1 exit status make: *** [/usr/share/R//make/shlib.mk:6: classInt.so] Error 1 ERROR: compilation failed for package ‘classInt’ ...

But libimf.so is present in the /opt/intel/lib directory.

Besides, it also complains missing include dirs in a warning message, but, oddly, pointing to 2019.4.243

gfortran -fno-optimize-sibling-calls -fpic -m64 -I/opt/intel/compilers_and_libraries_2019.4.243/linux/mkl/include -c fish1.f -o fish1.o f951: Warning: Nonexistent include directory ‘/opt/intel/compilers_and_libraries_2019.4.243/linux/mkl/include’ [-Wmissing-include-dirs] fish1.f:100:72:

100 | DO 10 I=1,M | 1 Warning: Fortran 2018 deleted feature: Shared DO termination label 10 at (1) fish1.f:132:72:

132 | 40 IWORK(I,1)=1 | 1 Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 40 at (1)

The classInt package installs successfully on a regular (non-mkl) R installation.

This happens when running r-mkl on an archlinux docker container, so there is no contamination from an earlier installation of mkl etc.

I appreciate it if anyone can help shed light on what may be happening here. Thanks!

The full stdout with error message can be found at https://gist.github.com/lmwang9527/48386437de1574aac45cb27725f129c7

alexanderp commented on 2019-07-26 07:45

Great @petronny. Thanks for your effort.

petronny commented on 2019-07-26 07:40

Hi, I provide a pre-built binary of this package at arch4edu.
Also please vote at this issue if you want more pre-built R packages.

petronny commented on 2019-07-24 07:06

Every time Intel MKL gets updated, compilation of R with icc needs to be adapted.

Actually I can deal with that, I can provide a well-built binary with every icc or r-mkl update. But I'll use gcc then since there is no gain when using icc.

alexanderp commented on 2019-07-24 06:40

Hi @petronny.

Every time Intel MKL gets updated, compilation of R with icc needs to be adapted.

I measured no gain when using icc, therefore this package defaults to gcc.

See some of my benchmarks here: https://github.com/alexisph/high_performance_r

Arch Linux User Repository