Package Details: r-mkl 3.4.4-4

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: r
Provides: r=3.4.4,r-mkl=3.4.4
Submitter: giniu
Maintainer: alexanderp
Last Packager: alexanderp
Votes: 18
Popularity: 0.763483
First Submitted: 2010-05-06 00:10
Last Updated: 2018-04-14 17:33

Required by (173)

Sources (4)

Pinned Comments

alexanderp commented on 2018-03-27 22:51

Thanks for the reports. The Matrix hangup issue when using gcc is fixed as of 3.4.4-2.

Version 3.4.4-3 fixes compilation with icc as well.

Please note that there's a bug in intel-tbb_psxe. Specifically, /etc/ld.so.conf.d/intel-tbb.conf should contain /opt/intel/composerxe/linux/tbb/lib/intel64/gcc4.7

Latest Comments

alexanderp commented on 2018-03-30 13:20

@pat-s In my experience, no, I've never had freezes during normal usage. I've been using R with the Intel MKL on all my computers for several years.

The only drawback I found was that some packages are not compatible with icc/icpc, therefore I sometimes need to fallback to gcc/gfortran in ~/.R/Makevars (e.g. for the forecast package)

Glad to hear it's working properly on your side now.

pat-s commented on 2018-03-29 19:35

Usage related: I encountered several "freezes" during usage that only occurred with the "intel-mkl" library (not with openblas or default blas). No error is thrown, the process is just stuck at some point and there is no way to track down the problem. I'll try it again with the latest version, maybe something changed. Just wondering if anyone else faced similar problems in the past?

EDIT: Installation worked and the errors mentioned have vanished. Thanks!

mys_721tx commented on 2018-03-29 02:55

@alexanderp : r-mkl-3.4.4-3 compiled with icc without any problem!

mys_721tx commented on 2018-03-29 02:01

@alexanderp : I remembered it wrong. It was hung on the check stage.

checking package 'Matrix'
* using log directory ‘/home/mys_721tx/r-mkl/src/R-3.4.4/tests/Matrix.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘Matrix/DESCRIPTION’ ... OK
* this is package ‘Matrix’ version ‘1.2-12’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: ‘expm’

Packages which this enhances but not available for checking:
  ‘MatrixModels’ ‘graph’ ‘SparseM’ ‘sfsmisc’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* skipping installation test
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘SparseM’, ‘spdep’, ‘expm’, ‘graph’, ‘igraph’, ‘sfsmisc’, ‘MatrixModels’
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘Class+Meth.R’
  Running ‘Simple.R’

alexanderp commented on 2018-03-29 01:45

@mys_721tx compilation with icc should be fixed now.

@nessuno I'll look into it.

nessuno commented on 2018-03-28 13:26

There's still an error (I don't know if significant)

Running the tests in ‘tests/sigma-fixed-etc.R’ failed.
Last 13 lines of output:
  > ##------------------------------------------------------ REML ---
  > method <- "REML"
  > cat("\nFixed sigma= ",sigma,"  estimation method ", method,"\n")

  Fixed sigma=  1   estimation method  REML 
  > t7.fix.REML.lme <- lme( current ~voltage + I(voltage^2), data = Wafer,
  +                        random = list(Wafer = pdDiag(~voltage + I(voltage^2)),
  +                                      Site  = pdDiag(~voltage + I(voltage^2)) ),
  +                        control = lmeControl(sigma = 1),
  +                        method = method)
  Error in lme.formula(current ~ voltage + I(voltage^2), data = Wafer, random = list(Wafer = pdDiag(~voltage +  : 
    nlminb problem, convergence error code = 1
    message = false convergence (8)
  Calls: lme -> lme.formula
  Execution halted

but now it works for me, thanks!

alexanderp commented on 2018-03-28 13:01

@mys_721tx, it must be due to a missing dependency from Intel Parallel Studio. I'll have another look. Just to clarify, you're getting the hangup during checking, not building, right?

mys_721tx commented on 2018-03-28 00:33

So I enabled icc and was hang on "Running ‘Simple.R’" when building Matrix. I have openmp and ice installed. It seems to be the same problem as the one jbmorgado had. What kind of log should I provide?

alexanderp commented on 2018-03-27 22:51

Thanks for the reports. The Matrix hangup issue when using gcc is fixed as of 3.4.4-2.

Version 3.4.4-3 fixes compilation with icc as well.

Please note that there's a bug in intel-tbb_psxe. Specifically, /etc/ld.so.conf.d/intel-tbb.conf should contain /opt/intel/composerxe/linux/tbb/lib/intel64/gcc4.7

japhir commented on 2018-03-22 12:00

I have the same errors as nessuno. I htop to see what's causing the hang-up after waiting for a reasonable time, and then F9 sigterm the offending process. They are the same as he listed, plus a checking of vignette output thing that keeps hanging. It now succesfully builds, but somehow when I run a function from a package that falls back to fortran code, it causes a segfault :(.

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