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Package Details: r-mkl 4.4.1-1

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
Submitter:	giniu
Maintainer:	alexanderp
Last Packager:	alexanderp
Votes:	25
Popularity:	0.000106
First Submitted:	2010-05-06 00:10 (UTC)
Last Updated:	2024-07-04 19:34 (UTC)

Dependencies (28)

bzip2 (bzip2-git^AUR)
curl (curl-quiche-git^AUR, curl-http3-ngtcp2^AUR, curl-git^AUR, curl-c-ares^AUR)
icu (icu-git^AUR)
intel-oneapi-mkl (intel-oneapi-hpckit^AUR, intel-oneapi-basekit)
libjpeg (mozjpeg-git^AUR, libjpeg-turbo-git^AUR, mozjpeg^AUR, libjpeg-turbo)
libpng (libpng-git^AUR, libpng-apng^AUR)
libtiff (libtiff-git^AUR, libtiff-lerc^AUR)
libxmu
libxt
ncurses (ncurses-git^AUR)
openmp
pango (pango-git^AUR)
pcre2 (pcre2-git^AUR)
perl (perl-git^AUR)
readline (readline-git^AUR)
unzip (unzip-natspec^AUR, unzip-zstd^AUR)
which (busybox-coreutils^AUR)
xz (xz-git^AUR)
zip (zip-natspec^AUR)
zlib (zlib-ng-compat-git^AUR, zlib-git^AUR, zlib-ng-compat^AUR)
gcc-fortran (gcc-fortran-git^AUR, gcc11-fortran^AUR, gcc-fortran-snapshot^AUR) (make)
jdk-openjdk (jdk16-adoptopenjdk^AUR, zing-21-bin^AUR, jdk21-temurin^AUR, jdk11-temurin^AUR, jdk17-temurin^AUR, jdk-temurin^AUR) (make)
texlive-fontsrecommended (texlive-installer^AUR, texlive-full^AUR, texlive-dummy^AUR) (make)
texlive-latexrecommended (texlive-installer^AUR, texlive-full^AUR, texlive-dummy^AUR) (make)
tk (tk-fossil^AUR) (make)
gcc-fortran (gcc-fortran-git^AUR, gcc11-fortran^AUR, gcc-fortran-snapshot^AUR) (optional) – needed to compile some CRAN packages
texlive-latex (texlive-installer^AUR, texlive-full^AUR, texlive-dummy^AUR) (optional) – LaTeX sty files
tk (tk-fossil^AUR) (optional) – tcl-tk interface

Required by (3401)

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r-singler (requires r)
r-singscore (requires r)
r-sitepath (requires r)
r-sitmo (requires r)
r-sizepower (requires r)
r-sjlabelled (requires r)
r-sjmisc (requires r)
r-skewhyperbolic (requires r)
r-skewr (requires r)
r-slalom (requires r)
r-slam (requires r)
r-slgi (requires r)
r-slider (requires r)
r-slingshot (requires r)
r-slinky (requires r)
r-slqpcr (requires r)
r-sm (requires r)
r-smacof (requires r)
r-smad (requires r)
r-smap (requires r)
r-smartsva (requires r)
r-smatr (requires r)
r-smite (requires r)
r-smoother (requires r)
r-smoothie (requires r)
r-smoothwin (requires r)
r-smurf (requires r)
r-smvar (requires r)
r-sn (requires r)
r-sna (requires r)
r-snageedata (requires r)
r-snakecase (requires r)
r-snapcgh (requires r)
r-snapcount (requires r)
r-snifter (requires r)
r-snm (requires r)
r-snow (requires r)
r-snowballc (requires r)
r-snpediar (requires r)
r-snphood (requires r)
r-snplocs.hsapiens.dbsnp144.grch37 (requires r)
r-snplocs.hsapiens.dbsnp150.grch38 (requires r)
r-snprelate (requires r)
r-sodium (requires r)
r-softimpute (requires r)
r-soggi (requires r)
r-sojourner (requires r)
r-som (requires r)
r-somaticsignatures (requires r)
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r-soniclength (requires r)
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r-sparseinv (requires r)
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r-sparsematrixstats (requires r)
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r-spatstat.model (requires r)
r-spatstat.random (requires r)
r-spatstat.utils (requires r)
r-spatzie (requires r)
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r-spidermir (requires r)
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r-splicingfactory (requires r)
r-splicinggraphs (requires r)
r-splines2 (requires r)
r-splinetimer (requires r)
r-splus2r (requires r)
r-spp (requires r)
r-spqn (requires r)
r-spscomps (requires r)
r-spsimseq (requires r)
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r-stargazer (requires r)
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r-stmomo (requires r)
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r-styler (requires r)
r-subcellbarcode (requires r)
r-subseq (requires r)
r-subspace (requires r)
r-summarizedbenchmark (requires r)
r-summarizedexperiment (requires r)
r-summarytools (requires r)
r-superheat (requires r)
r-superlearner (requires r)
r-supersigs (requires r)
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r-suprahex (requires r)
r-surfaltr (requires r)
r-survcomp (requires r)
r-survivalanalysis (requires r)
r-survivalroc (requires r)
r-survivalsvm (requires r)
r-survminer (requires r)
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r-survpresmooth (requires r)
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r-tbsignatureprofiler (requires r)
r-tbx20bamsubset (requires r)
r-tcc (requires r)
r-tcgabiolinks (requires r)
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r-tcgabiolinksgui.data (requires r)
r-tcgautils (requires r)
r-tcltk2 (requires r)
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r-tdaracne (requires r)
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r-ternarynet (requires r)
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r-testit (requires r)
r-testthat (requires r)
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r-text2vec (requires r)
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r-tfmpvalue (requires r)
r-tfruns (requires r)
r-tfutils (requires r)
r-th.data (requires r)
r-this.path (requires r)
r-threejs (requires r)
r-tictoc (requires r)
r-tidybayes (requires r)
r-tidybulk (requires r)
r-tidygraph (requires r)
r-tidysinglecellexperiment (requires r)
r-tidysummarizedexperiment (requires r)
r-tidytext (requires r)
r-tidytidbits (requires r)
r-tiff (requires r)
r-tigre (requires r)
r-tikzdevice (requires r)
r-tiledbarray (requires r)
r-tilingarray (requires r)
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r-timedate (requires r)
r-timescape (requires r)
r-timeseriesexperiment (requires r)
r-timirgen (requires r)
r-timsac (requires r)
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r-tkrplot (requires r)
r-tloh (requires r)
r-tm (requires r)
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r-tmixclust (requires r)
r-tmvnsim (requires r)
r-tmvtnorm (requires r)
r-tnbc.cms (requires r)
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r-tofsims (requires r)
r-tokenizers (requires r)
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r-topconfects (requires r)
r-topdownr (requires r)
r-topgo (requires r)
r-topicmodels (requires r)
r-toster (requires r)
r-toxicogx (requires r)
r-tpp (requires r)
r-tpp2d (requires r)
r-tracktables (requires r)
r-tractor.base (requires r)
r-tradeseq (requires r)
r-trajectorygeometry (requires r)
r-trajectoryutils (requires r)
r-traminer (requires r)
r-traminerextras (requires r)
r-transcriptogramer (requires r)
r-transcriptr (requires r)
r-transformgampoi (requires r)
r-transite (requires r)
r-translatome (requires r)
r-transomics2cytoscape (requires r)
r-transport (requires r)
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r-traviz (requires r)
r-tree (requires r)
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r-treekor (requires r)
r-treemap (requires r)
r-treesummarizedexperiment (requires r)
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r-triebeard (requires r)
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r-tsrchitect (requires r)
r-ttgsea (requires r)
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r-ttr (requires r)
r-tuner (requires r)
r-turbonorm (requires r)
r-tweedeseq (requires r)
r-tweedie (requires r)
r-twoddpcr (requires r)
r-txdb.celegans.ucsc.ce6.ensgene (requires r)
r-txdb.dmelanogaster.ucsc.dm3.ensgene (requires r)
r-txdb.dmelanogaster.ucsc.dm6.ensgene (requires r)
r-txdb.hsapiens.ucsc.hg18.knowngene (requires r)
r-txdb.hsapiens.ucsc.hg19.knowngene (requires r)
r-txdb.hsapiens.ucsc.hg38.knowngene (requires r)
r-txdb.mmusculus.ucsc.mm10.knowngene (requires r)
r-txdb.mmusculus.ucsc.mm9.knowngene (requires r)
r-txdb.rnorvegicus.ucsc.rn4.ensgene (requires r)
r-tximport (requires r)
r-tximportdata (requires r)
r-typeinfo (requires r)
r-tzdb (requires r)
r-ucell (requires r)
r-ucminf (requires r)
r-udapi (requires r)
r-ularcirc (requires r)
r-umap (requires r)
r-umi4cats (requires r)
r-uncoverapplib (requires r)
r-unifiedwmwqpcr (requires r)
r-uniprot.ws (requires r)
r-uniqtag (requires r)
r-uniquorn (requires r)
r-units (requires r)
r-universalmotif (requires r)
r-unix (requires r)
r-unmarked (requires r)
r-upsetr (requires r)
r-urca (requires r)
r-urlchecker (requires r)
r-urltools (requires r)
r-usethis (requires r)
r-usort (requires r)
r-utf8 (requires r)
r-uuid (requires r)
r-vader (requires r)
r-vaexprs (requires r)
r-valr (requires r)
r-vam (requires r)
r-vanillaice (requires r)
r-varcon (requires r)
r-varhandle (requires r)
r-variantexperiment (requires r)
r-variantfiltering (requires r)
r-varianttools (requires r)
r-vars (requires r)
r-vasp (requires r)
r-vbmp (requires r)
r-vbsr (requires r)
r-vcd (requires r)
r-vcdextra (requires r)
r-vcfarray (requires r)
r-vcfr (requires r)
r-vctrs (requires r)
r-vegamc (requires r)
r-veloviz (requires r)
r-venndetail (requires r)
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r-verification (requires r)
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r-vplotr (requires r)
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r-waiter (requires r)
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r-watermelon (requires r)
r-wavcluster (requires r)
r-wavethresh (requires r)
r-wdi (requires r)
r-weaver (requires r)
r-webbioc (requires r)
r-webchem (requires r)
r-webfakes (requires r)
r-webshot (requires r)
r-weibullness (requires r)
r-weightr (requires r)
r-weights (requires r)
r-weitrix (requires r)
r-wesanderson (requires r)
r-wgcna (requires r)
r-whisker (requires r)
r-whoami (requires r)
r-widgettools (requires r)
r-wiggleplotr (requires r)
r-withr (requires r)
r-wk (requires r)
r-wordcloud (requires r)
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r-wpm (requires r)
r-wppi (requires r)
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r-writexl (requires r)
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r-wrswor (requires r)
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r-xcir (requires r)
r-xcms (requires r)
r-xde (requires r)
r-xeva (requires r)
r-xfun (requires r)
r-xina (requires r)
r-xlsx (requires r)
r-xmapbridge (requires r)
r-xml (requires r)
r-xmlparsedata (requires r)
r-xopen (requires r)
r-xtable (requires r)
r-xtrasnplocs.hsapiens.dbsnp144.grch37 (requires r)
r-xvector (requires r)
r-yaimpute (requires r)
r-yaml (requires r)
r-yamss (requires r)
r-yapsa (requires r)
r-yarn (requires r)
r-yeastexpdata (requires r)
r-yesno (requires r)
r-zeallot (requires r)
r-zellkonverter (requires r)
r-zfpkm (requires r)
r-zinbwave (requires r)
r-zip (requires r)
r-zlibbioc (requires r)
r-zoo (requires r)
radian (requires r)
rkward-git (requires r)
rnalysis (requires r)
rsem (requires r)
rstudio-desktop (requires r)
rstudio-desktop-bin (requires r)
rstudio-desktop-daily-bin (requires r)
rstudio-server-bin (requires r)
rstudio-server-git (requires r)
ruby-simpleitk (requires r) (make)
shiny-server (requires r)
shiny-server-git (requires r)
simpleitk (requires r) (make)
tcl-simpleitk (requires r) (make)
vcflib (requires r) (optional)
vcflib-git (requires r) (optional)
vinecopulib (requires r) (make)
wolframengine (requires r) (optional)
yap (requires r) (optional)
zim-git (requires r) (optional)

Sources (5)

Latest Comments

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herraiz commented on 2016-11-20 17:25 (UTC)

Could you add a patch for Makeconf.in? The patch is the following one: 14c14 < BLAS_LIBS = @BLAS_LIBS@ --- > BLAS_LIBS = @BLAS_LIBS@ -lifcore -lifport It prevents problems when compiling some R packages. With that change, I was able to install quantreg and igraph. See comment from AnRe005 2016-08-07 09:22

hike commented on 2016-11-08 04:26 (UTC)

For people struggling with this. If you are a student, you can download and install intel dependencies (intel-compiler-base, intel-fortran-compiler, intel-mkl) for free from here https://software.intel.com/en-us/qualify-for-free-software/student When you install the latest version, compilers are installed in a different folder, so you have to change the path in line 89 in PKGBUILD from /opt/intel/composerxe/linux/bin/compilervars.sh to /opt/intel/compilers_and_libraries/linux/bin/compilervars.sh You will have to source compilervars.sh in bash before running R, otherwise, it won't run (just put it in .bashrc, but know that other compilations will be affected by this). In addition, intel installer might complain that your gcc and other libs are outdated, but if you have everything installed from core and multilib, you should be fine (I didn't get the -git packages).

leonardof commented on 2016-10-03 21:17 (UTC)

Follow-up: it turns out the community license is not meant for compiling software, after all... Too bad I don't know any binary package of r-mkl for Arch Linux.

leonardof commented on 2016-09-17 20:42 (UTC)

Thank you, alexanderp!

alexanderp commented on 2016-09-17 10:16 (UTC)

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 (UTC) (edited on 2016-09-25 16:49 (UTC) by leonardof)

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 (UTC)

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 (UTC)

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 (UTC)

GeorgeChao commented on 2016-09-09 06:31 (UTC)

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...

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herraiz commented on 2016-11-20 17:25 (UTC)

hike commented on 2016-11-08 04:26 (UTC)

leonardof commented on 2016-10-03 21:17 (UTC)

leonardof commented on 2016-09-17 20:42 (UTC)

alexanderp commented on 2016-09-17 10:16 (UTC)

leonardof commented on 2016-09-17 03:51 (UTC) (edited on 2016-09-25 16:49 (UTC) by leonardof)

alexanderp commented on 2016-09-09 07:14 (UTC)

GeorgeChao commented on 2016-09-09 06:47 (UTC)

GeorgeChao commented on 2016-09-09 06:47 (UTC)

GeorgeChao commented on 2016-09-09 06:31 (UTC)