Package Details: r-mkl 3.6.2-1

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=3.6.2
Submitter: giniu
Maintainer: alexanderp
Last Packager: alexanderp
Votes: 19
Popularity: 0.197930
First Submitted: 2010-05-06 00:10
Last Updated: 2020-01-07 12:22

Dependencies (26)

Required by (265)

Sources (4)

Latest Comments

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alexanderp commented on 2016-06-03 11:21

No problem. Please keep us updated.

nacnudus commented on 2016-06-03 11:14

I think this is an R problem, since by running the test script mgcv-Ex.R with R version 3.2.4 (binary install), it encountered the same error in line 1940:
cl <- makeCluster(nc)
A workaround is to change the PKGBUILD to do `make check` instead of `make check-recommended`, to avoid this check altogether.
I'll follow this up with the R maintainers.

nacnudus commented on 2016-06-03 10:06

Intel(R) Core(TM) i7-4600U CPU @ 2.10GHz

Sorry for my slow replies. I don't seem to be getting notifications despite subscribing to the thread.

alexanderp commented on 2016-06-02 18:59

Yes, the default is GCC. On my i7-2640m the "checking examples" step doesn't take more than 1-2min. Which CPU do you have?

nacnudus commented on 2016-06-02 18:10

Yes, I interrupted it after about eight hours with no activity on the process. Am I compiling it with GCC? It seems to be the default since
#_CC="icc" # comment to build without the Intel compiler
has been commented out by default.

alexanderp commented on 2016-06-02 16:27

I compiled again with GCC and get no such error.

This line seems strange to me:

* checking examples ...^C ERROR

Did you press Ctrl+C while in the middle of checking the examples?

nacnudus commented on 2016-06-02 14:00

Installation stalls on package mgcv with the following:

checking package 'mgcv'
* using log directory ‘/tmp/yaourt-tmp-nacnudus/aur-r-mkl/src/R-3.3.0/tests/mgcv.Rcheck’
* using R version 3.3.0 (2016-05-03)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘mgcv/DESCRIPTION’ ... OK
* this is package ‘mgcv’ version ‘1.8-12’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 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
Package unavailable to check Rd xrefs: ‘gam’
* 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 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 examples ...^C ERROR
Running examples in ‘mgcv-Ex.R’ failed
The error most likely occurred in:

> ### Name: mgcv.parallel
> ### Title: Parallel computation in mgcv.
> ### Aliases: mgcv.parallel
> ### Keywords: package models smooth regression
>
> ### ** Examples
>
> ## illustration of multi-threading with gam...
>
> require(mgcv);set.seed(9)
> dat <- gamSim(1,n=2000,dist="poisson",scale=.1)
Gu & Wahba 4 term additive model
> k <- 12;bs <- "cr";ctrl <- list(nthreads=2)
>
> system.time(b1<-gam(y~s(x0,bs=bs)+s(x1,bs=bs)+s(x2,bs=bs,k=k)
+ ,family=poisson,data=dat,method="REML"))[3]
elapsed
0.088
>
> system.time(b2<-gam(y~s(x0,bs=bs)+s(x1,bs=bs)+s(x2,bs=bs,k=k),
+ family=poisson,data=dat,method="REML",control=ctrl))[3]


Then hundreds of lines of:

OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.

Finally:

elapsed
5.795
>
> ## Poisson example on a cluster with 'bam'.
> ## Note that there is some overhead in initializing the
> ## computation on the cluster, associated with loading
> ## the Matrix package on each node. For this reason the
> ## sample sizes here are very small to keep CRAN happy, but at
> ## this low sample size you see little advantage of parallel computation.
>
> k <- 13
> dat <- gamSim(1,n=6000,dist="poisson",scale=.1)
Gu & Wahba 4 term additive model
> require(parallel)
Loading required package: parallel
> nc <- 2 ## cluster size, set for example portability
> if (detectCores()>1) { ## no point otherwise
+ cl <- makeCluster(nc)
+ ## could also use makeForkCluster, but read warnings first!
+ } else cl <- NULL

Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
‘/tmp/yaourt-tmp-nacnudus/aur-r-mkl/src/R-3.3.0/tests/mgcv.Rcheck/00check.log’
for details.


Makefile.common:404: recipe for target 'test-Packages-Recommended' failed
make[1]: *** [test-Packages-Recommended] Interrupt
Makefile:239: recipe for target 'check-recommended' failed
make: *** [check-recommended] Interrupt

syne commented on 2016-05-17 13:39

if you're installing intel-mkl etc, edit the PKGBUILD line 299-300 from
ln -s ./${_composer_xe_dir} composerxe-${_year}
ln -s ./composerxe-${_year} composerxe
to
ln -s ./${_composer_xe_dir} composerxe


don't even know why that second symlink is necessary... that fixed the mklvars problem for me.

alexanderp commented on 2016-05-16 22:04

Hmm I cannot seem to be able to reproduce your error.
Is mklvars.sh present on your system?

Anonymous comment on 2016-05-16 21:17

I get an error when this tries to install. It complains that:

/opt/intel/mkl/bin/mklvars.sh: No such file or directory