Package Details: r-mkl 3.6.2-1

Git Clone URL: (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:
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: 0.192670
First Submitted: 2010-05-06 00:10
Last Updated: 2020-01-07 12:22

Dependencies (26)

Required by (265)

Sources (4)

Latest Comments

« First ‹ Previous 1 2 3 4 5 6 7 8 9 10 11 ... Next › Last »

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/ 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 :(.

nessuno commented on 2018-03-17 20:33

I hope to be helpful, even though I'm not a so expert user.

I have the same error of @pat-s. I think that the problem is at row 1031 of Simple.R. It uses checkMatrix that requires to convert the sparse matrix in a "simple" matrix, but for the matrix named "" it gives me

Error in as(, "martix") : 
  no method or default for coercing “dgCMatrix” to “martix”

Enter a frame number, or 0 to exit   

1: as(, "martix")

Selection: as(, "matrix")
Enter an item from the menu, or 0 to exit

But it gives me errors also in other three files

  • Comparisons.Rnw
  • sparseModels.Rnw
  • mgcv-parallel.R

but I didn't understand precisely where by the moment.

Said that, if I skip them, by killing the R process each time (I don't how to do it in a cleaner way), it compiles and everithing seems to work then. But I don't know if it's ok or not.

Hoping it can help, let me know if I can do something else.

pat-s commented on 2018-03-17 11:39

Here's a gist:

Idk which additional information you would need. Just tell me :)

As said, this happens with the standard PKGBUILD and gcc v7.3

alexanderp commented on 2018-03-16 20:11

Updated to 3.4.4

@jbmorgado and @pat-s: I cannot reproduce the Simple.R issue on my machine when compiling with gcc. Only when compiling with icc

Can you send a log file with more information?