[R-sig-ME] testing OpenMP-enabled glmmTMB on various configurations

Edgar J Gonzalez edg@rjgonz@|ez @end|ng |rom c|enc|@@@un@m@mx
Tue Jan 14 02:33:13 CET 2020

Hi. This is what I got:

> library(remotes)
> remotes::install_github("glmmTMB/glmmTMB/glmmTMB using conditional_openmp")
Downloading GitHub repo glmmTMB/glmmTMB using conditional_openmp
These packages have more recent versions available.
Which would you like to update?

1: All                                      
2: CRAN packages only                       
3: None                                     
4: RcppEigen ( -> [CRAN]
5: Rcpp      (1.0.1     -> 1.0.3    ) [CRAN]

Enter one or more numbers, or an empty line to skip updates:
RcppEigen ( -> [CRAN]
Rcpp      (1.0.1     -> 1.0.3    ) [CRAN]
Installing 2 packages: RcppEigen, Rcpp
probando la URL 'https://cran.itam.mx/bin/macosx/el-capitan/contrib/3.6/RcppEigen_0. <https://cran.itam.mx/bin/macosx/el-capitan/contrib/3.6/RcppEigen_0.>'
Content type 'application/x-gzip' length 4842361 bytes (4.6 MB)
downloaded 4.6 MB

probando la URL 'https://cran.itam.mx/bin/macosx/el-capitan/contrib/3.6/Rcpp_1.0.3.tgz <https://cran.itam.mx/bin/macosx/el-capitan/contrib/3.6/Rcpp_1.0.3.tgz>'
Content type 'application/x-gzip' length 3099696 bytes (3.0 MB)
downloaded 3.0 MB

The downloaded binary packages are in
   checking for file ‘/private/var/folders/bt/kwm2wvnn0m37kj9j7b4dxdch0000gn/T/R✔  checking for file ‘/private/var/folders/bt/kwm2wvnn0m37kj9j7b4dxdch0000gn/T/RtmpYU7u2V/remotes486647c4e2db/glmmTMB-glmmTMB-42b0d9c/glmmTMB/DESCRIPTION’ (404ms)
─  preparing ‘glmmTMB’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
   Removed empty directory ‘glmmTMB/inst/misc’
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘glmmTMB_1.0.0.tar.gz’
* installing *source* package ‘glmmTMB’ ...
** using staged installation
** libs
clang++ -arch x86_64 -ftemplate-depth-256 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function  -Wno-macro-redefined -Wno-unknown-pragmas -c glmmTMB.cpp -o glmmTMB.o
clang: error: unsupported option '-fopenmp'
make: *** [glmmTMB.o] Error 1
ERROR: compilation failed for package ‘glmmTMB’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/glmmTMB’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/glmmTMB’
Error: Failed to install 'glmmTMB' from GitHub:
  (convertido del aviso) installation of package ‘/var/folders/bt/kwm2wvnn0m37kj9j7b4dxdch0000gn/T//RtmpYU7u2V/file48666cf3703/glmmTMB_1.0.0.tar.gz’ had non-zero exit status

Hope it helps...

> On Jan 13, 2020, at 4:04 PM, Ben Bolker <bbolker using gmail.com <mailto:bbolker using gmail.com>> wrote:
>  Hi folks,
>  We're trying to troubleshoot a version of glmmTMB that enables OpenMP
> support, but we have a fairly limited set of test platforms and it would
> be nice to know if many users are going to have installation difficulties.
>  If you have development tools (and the 'remotes' package) installed
> and a few free minutes, it would be great if you could try
> remotes::install_github("glmmTMB/glmmTMB/glmmTMB using conditional_openmp")
> and let us know if you have any trouble installing (it should install
> whether or not you have OpenMP enabled ...)
> If you're feeling energetic or distractible, you could try the tests here:
> https://github.com/glmmTMB/glmmTMB/issues/481#issuecomment-572767245 <https://github.com/glmmTMB/glmmTMB/issues/481#issuecomment-572767245>
> the expected result is you should see *either* warnings that OpenMP is
> not enabled *or* at least some speed-up for the parallel version over
> the serial version.
> Results (especially problematic ones!) welcome at
> https://github.com/glmmTMB/glmmTMB/issues/481
> _______________________________________________
> R-sig-mixed-models using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models

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