Installation Error: clang: error: unsupported option '-fopenmp'

[ShanSabri]

Installation Error:

> options(tz="America/Los_Angeles")
> library(devtools)
> install_github("velocyto-team/velocyto.R")
Downloading GitHub repo velocyto-team/velocyto.R@master
from URL https://api.github.com/repos/velocyto-team/velocyto.R/zipball/master
Installing velocyto.R
Running command /Library/Frameworks/R.framework/Resources/bin/R 
Arguments:
CMD
INSTALL
/private/var/folders/5m/jlrrrsfd719d0ks0qg48_pg80000gn/T/Rtmpv4UBqe/devtools1d0851a3bc6b/velocyto-team-velocyto.R-9741595
--library=/Library/Frameworks/R.framework/Versions/3.4/Resources/library
--install-tests

* installing *source* package ‘velocyto.R’ ...
Warning in as.POSIXlt.POSIXct(x, tz) :
  unknown timezone 'default/America/Los_Angeles'
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include  -std=c++11 -fopenmp -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang: error: unsupported option '-fopenmp'
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘velocyto.R’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/velocyto.R’
 
Installation failed: run(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdout),      stderr_line_callback = real_callback(stderr), stdout_callback = real_block_callback,      stderr_callback = real_block_callback, echo_cmd = echo, echo = show,      spinner = spinner, error_on_status = fail_on_status, timeout = timeout) : System command error
> 

Session info:

─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.4.1 (2017-06-30)
 os       macOS High Sierra 10.13     
 system   x86_64, darwin15.6.0        
 ui       RStudio                     
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       <NA>                        
 date     2017-10-24                  

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package     * version     date       source                            
 assertthat    0.2.0       2017-04-11 CRAN (R 3.4.0)                    
 backports     1.1.1       2017-09-25 CRAN (R 3.4.2)                    
 callr         1.0.0.9000  2017-08-23 Github (mangothecat/callr@2dffbbe)
 clisymbols    1.2.0       2017-05-21 CRAN (R 3.4.0)                    
 crayon        1.3.4       2017-09-16 CRAN (R 3.4.1)                    
 curl          3.0         2017-10-06 CRAN (R 3.4.2)                    
 debugme       1.1.0       2017-10-22 CRAN (R 3.4.2)                    
 devtools    * 1.13.3.9000 2017-08-23 Github (hadley/devtools@5517fdb)  
 digest        0.6.12      2017-01-27 CRAN (R 3.4.0)                    
 git2r         0.19.0      2017-07-19 CRAN (R 3.4.1)                    
 httr          1.3.1       2017-08-20 CRAN (R 3.4.1)                    
 memoise       1.1.0       2017-04-21 CRAN (R 3.4.0)                    
 pkgbuild      0.0.0.9000  2017-08-23 Github (r-lib/pkgbuild@6574561)   
 pkgload       0.0.0.9000  2017-08-23 Github (r-pkgs/pkgload@558aaac)   
 processx      2.0.0.1     2017-07-30 CRAN (R 3.4.1)                    
 R6            2.2.2       2017-06-17 CRAN (R 3.4.0)                    
 rlang         0.1.2.9000  2017-09-06 Github (tidyverse/rlang@6a589ec)  
 rprojroot     1.2         2017-01-16 CRAN (R 3.4.0)                    
 rstudioapi    0.7         2017-09-07 CRAN (R 3.4.1)                    
 sessioninfo   1.0.1       2017-08-23 Github (r-lib/sessioninfo@e813de4)
 usethis     * 1.0.0       2017-10-22 CRAN (R 3.4.2)                    
 withr         2.0.0       2017-07-28 CRAN (R 3.4.1)      

Any advice would be appreciated.

[pkharchenko]

I've made an updated to Makevars to remove explicit -fopenmp which only works on some platforms. Please try installing now.

[ShanSabri]

Unfortunately using the same installation protocol as above, I was returned the exact same error.

[tractatus]

@ShanSabri for macOS the default compiler Apple clang LLVM does not support openmp yet.
R uses the Apple clang compiler by default on macOS. The solution is simply to download another clang compiler that supports openmp using homebrew.

From terminal if you do not have boost install that as well since boost is not included in macOS. This will also install hdf5 if you want to tryout with loom.
Note that this will overwrite your Makevars to use clang installed by homebrew rather than apple's. In terminal:

brew install llvm
brew install boost
brew install homebrew/science/hdf5 --enable-cxx
mkdir -p ~/.R
cat <<- EOF > ~/.R/Makevars
	 # The following statements are required to use the clang4 binary
	 CC=/usr/local/clang4/bin/clang
	 CXX=/usr/local/clang4/bin/clang++
	 CXX11=/usr/local/clang4/bin/clang++
	 CXX14=/usr/local/clang4/bin/clang++
	 CXX17=/usr/local/clang4/bin/clang++
	 CXX1X=/usr/local/clang4/bin/clang++
	 LDFLAGS=-L/usr/local/clang4/lib
	 # End clang4 inclusion statements
	 EOF

Or you can simply just try my fork of this package that does this for you in the package configure file. From R:
devtools::install_github('tractatus/velocyto.R')

I have the same issue with the python version. Is there any fix planned?

[gioelelm]

I solved compiler problem on Mac relying on compilers installed using conda (try both conda install gcc and llvm). I realize this solution is a bit vague, but I don't remember exactly what command solved it for me but pretty sure that the conda provided one do the job with openmp.

[pkharchenko]

@tractatus Thanks for providing a solution for the OS X installation! Do you think it's general enough that I should merge it into the main repo?

[tractatus]

@pkharchenko my solution is a hack because of Apple's LLVM. However, openmp has been compatible for clang for a long time and there is no indication Apple are going to include it anytime soon (recent Xcode 9 didn't include it). Most kosher thing to do would maybe split the C++ code into openmp dependent and non-openmp dependent but that is a bunch of work.

Personally, I think for users who do not know about build environments and "just want to get going" being able to install and get going using devtools::github_install() with a single line is the way to go. For that, the configure file will do its job. Another alternative is OS specific prerequirements installation instructions in the README.md. For windows support, you'll have to do this at some point regardless.

If the configure file is used I would maybe just ad to the shell script that it asks the user y/n if you want to proceed since the ~/.R/Makevars will be changed.

Then there will be the issue of users that have already installed the package and wants to update. It is highly annoying to wait for a bunch of shell script before having reinstalled. For those occasions maybe include a R function named update.velocyto.R() in NAMESPACE that ignores the configure file:

update.velocyto.R<-function(){
 detach('package:velocyto.R', unload=TRUE)
 remove.packages('velocyto.R')
 devtools::install_github('velocyto-team/velocyto.R', args='--no-configure')
}

This function also has the benefit of not requiring users to remove the package quit R and reinstall the package but rather they can continue with the updated package in the current session. They'll just run:

update.velocyto.R()
library(velocyto.R)

And they'll know they running the latest version from GitHub.

[Puriney]

Quote from R (https://cloud.r-project.org/):

Important note: R 3.4.0 El Capitan binaries are using Clang 4.0.0 and GNU Fortran 6.1 to provide OpenMP parallelization support and C++17 standard features. If you want to compile R packages from sources, please download GNU Fortran binary from the official GNU Fortran Binaries page - in particular OS X 10.11 gfortran 6.1. We are also providing Clang 4.0.0 binaries for OS X 10.11 and higher in our libs directory (note that the offical Clang 4.0.0 binaries only support macOS 10.12) and will provide an Apple Installer package here soon. For the time being you may want to either create ~/.R/Makevars such as

CC=/usr/local/clang4/bin/clang
CXX=/usr/local/clang4/bin/clang++
LDFLAGS=-L/usr/local/clang4/lib

I followed the R's suggestion and no more errors:

• Install gfortran as suggested: https://gcc.gnu.org/wiki/GFortranBinaries
• Download clang-4.0.0-darwin15.6-Release.tar.gz and uncompress. Move to /usr/local/. Modify the ~/.R/Makevars file.

---

Update Oct 16, 2018.

export PATH=/usr/local/clang4/bin:$PATH

[marzamKI]

Hello,
I also had the same problem for OpenMP and followed instruction at this website: http://thecoatlessprofessor.com/programming/openmp-in-r-on-os-x/#bash-clang4

Now I'm faced with another error though.

Downloading GitHub repo velocyto-team/velocyto.R@master
from URL https://api.github.com/repos/velocyto-team/velocyto.R/zipball/master
Installing velocyto.R
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet  \
  CMD INSTALL  \
  '/private/var/folders/xk/7tdpfsld6g9143qcprkkh9sw0000gp/T/RtmpgkbvRB/devtools833bdb1c4f6/velocyto-team-velocyto.R-cf4c571'  \
  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library' --install-tests 

* installing *source* package ‘velocyto.R’ ...
Warning in as.POSIXlt.POSIXct(x, tz) :
  unknown timezone 'zone/tz/2017c.1.0/zoneinfo/Europe/Stockholm'
** libs
/usr/local/clang4/bin/clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include  -std=c++11 -fopenmp -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
/usr/local/clang4/bin/clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include  -std=c++11 -fopenmp -fPIC  -Wall -g -O2  -c points_within.cpp -o points_within.o
/usr/local/clang4/bin/clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include  -std=c++11 -fopenmp -fPIC  -Wall -g -O2  -c routines.cpp -o routines.o
/usr/local/clang4/bin/clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/clang4/lib -o velocyto.R.so RcppExports.o points_within.o routines.o -lboost_filesystem -lboost_system -lstdc++ -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.4/Resources/library/velocyto.R/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error: package or namespace load failed for ‘velocyto.R’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/velocyto.R/libs/velocyto.R.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/velocyto.R/libs/velocyto.R.so, 6): Library not loaded: libboost_filesystem.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/velocyto.R/libs/velocyto.R.so
  Reason: image not found
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/velocyto.R’
Installation failed: Command failed (1)

I have installed boost. Actually, I've tried both brew install boost as well as

git clone --recursive https://github.com/boostorg/boost.git
cd boost
sudo ./bootstrap.sh
sudo ./b2 install

Any idea what I should be doing?

Session info:

R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.2

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Seurat_2.1.0        Biobase_2.38.0      BiocGenerics_0.24.0 Matrix_1.2-12       cowplot_0.9.1      
[6] ggplot2_2.2.1      

loaded via a namespace (and not attached):
  [1] backports_1.1.1        Hmisc_4.0-3            VGAM_1.0-4             NMF_0.20.6            
  [5] sn_1.5-1               plyr_1.8.4             igraph_1.1.2           lazyeval_0.2.1        
  [9] splines_3.4.2          densityClust_0.3       fastICA_1.2-1          gridBase_0.4-7        
 [13] digest_0.6.12          foreach_1.4.3          htmltools_0.3.6        viridis_0.4.0         
 [17] lars_1.2               gdata_2.18.0           memoise_1.1.0          magrittr_1.5          
 [21] checkmate_1.8.5        cluster_2.0.6          doParallel_1.0.11      mixtools_1.1.0        
 [25] ROCR_1.0-7             sfsmisc_1.1-1          limma_3.34.3           recipes_0.1.1         
 [29] gower_0.1.2            dimRed_0.1.0           matrixStats_0.52.2     R.utils_2.6.0         
 [33] colorspace_1.3-2       ggrepel_0.7.0          dplyr_0.7.4            bindr_0.1             
 [37] survival_2.41-3        iterators_1.0.8        ape_5.0                glue_1.2.0            
 [41] DRR_0.0.2              registry_0.5           gtable_0.2.0           ipred_0.9-6           
 [45] kernlab_0.9-25         ddalpha_1.3.1          prabclus_2.2-6         DEoptimR_1.0-8        
 [49] scales_0.5.0           pheatmap_1.0.8         mvtnorm_1.0-6          rngtools_1.2.4        
 [53] Rcpp_0.12.14           dtw_1.18-1             viridisLite_0.2.0      xtable_1.8-2          
 [57] htmlTable_1.11.0       tclust_1.3-1           foreign_0.8-69         proxy_0.4-19          
 [61] mclust_5.4             SDMTools_1.1-221       Formula_1.2-2          tsne_0.1-3            
 [65] stats4_3.4.2           lava_1.5.1             prodlim_1.6.1          httr_1.3.1            
 [69] htmlwidgets_0.9        FNN_1.1                gplots_3.0.1           RColorBrewer_1.1-2    
 [73] fpc_2.1-10             acepack_1.4.1          modeltools_0.2-21      ica_1.0-1             
 [77] pkgconfig_2.0.1        R.methodsS3_1.7.1      flexmix_2.3-14         nnet_7.3-12           
 [81] caret_6.0-77           tidyselect_0.2.3       rlang_0.1.4            reshape2_1.4.2        
 [85] munsell_0.4.3          tools_3.4.2            ranger_0.8.0           devtools_1.13.4       
 [89] ggridges_0.4.1         broom_0.4.3            stringr_1.2.0          yaml_2.1.15           
 [93] ModelMetrics_1.1.0     knitr_1.17             robustbase_0.92-8      caTools_1.17.1        
 [97] DDRTree_0.1.5          purrr_0.2.4            RANN_2.5.1             bindrcpp_0.2          
[101] pbapply_1.3-3          nlme_3.1-131           monocle_2.6.1          slam_0.1-40           
[105] R.oo_1.21.0            RcppRoll_0.2.2         compiler_3.4.2         rstudioapi_0.7        
[109] curl_3.0               ggjoy_0.4.0            tibble_1.3.4           stringi_1.1.6         
[113] lattice_0.20-35        trimcluster_0.1-2      psych_1.7.8            HSMMSingleCell_0.112.0
[117] diffusionMap_1.1-0     combinat_0.0-8         data.table_1.10.4-3    bitops_1.0-6          
[121] irlba_2.3.2            R6_2.2.2               latticeExtra_0.6-28    KernSmooth_2.23-15    
[125] gridExtra_2.3          codetools_0.2-15       MASS_7.3-47            gtools_3.5.0          
[129] assertthat_0.2.0       CVST_0.2-1             pkgmaker_0.22          withr_2.1.0           
[133] qlcMatrix_0.9.5        mnormt_1.5-5           diptest_0.75-7         grid_3.4.2            
[137] rpart_4.1-11           timeDate_3042.101      tidyr_0.7.2            class_7.3-14          
[141] segmented_0.5-3.0      Rtsne_0.13             git2r_0.19.0           numDeriv_2016.8-1     
[145] scatterplot3d_0.3-40   lubridate_1.7.1        base64enc_0.1-3

Thanks

[SamAllon]

@tractatus I really appreciate your suggestion:
devtools::install_github('tractatus/velocyto.R')
However, at least for me, this command results in the error:

installing source package ‘velocyto.R’ ...
++ set -e
./configure: line 46: syntax error: unexpected end of file
ERROR: configuration failed for package ‘velocyto.R’
removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/velocyto.R’
Installation failed: Command failed (1)

[tractatus]

@SamAllon running homebrew as root in configure file is no longer supported for obvious safety reasons.

Just open terminal and run the part yourself (assuming you have homebrew).

brew install llvm
brew install boost
brew install homebrew/science/hdf5 --enable-cxx
mkdir -p ~/.R
cat <<- EOF > ~/.R/Makevars
	 # The following statements are required to use the clang4 binary
	 CC=/usr/local/clang4/bin/clang
	 CXX=/usr/local/clang4/bin/clang++
	 CXX11=/usr/local/clang4/bin/clang++
	 CXX14=/usr/local/clang4/bin/clang++
	 CXX17=/usr/local/clang4/bin/clang++
	 CXX1X=/usr/local/clang4/bin/clang++
	 LDFLAGS=-L/usr/local/clang4/lib
	 # End clang4 inclusion statements
	 EOF

Then install this repo as ordinary:

devtools::install_github('velocyto-team/velocyto.R')

[SamAllon]

@tractatus Thank you so much! For whatever reason, /usr/local/clang4/ did not exist on my system after your first 4 steps. But your advice totally set me on the right direction. In addition to your steps, I did the following:

1. Download clang-4.0.0 from http://r.research.att.com/libs/
2. tar xvzf clang-4.0.0-darwin15.6-Release.tar in my Downloads directory
3. cd usr/local/
4. sudo mv clang4 /usr/local/

[Caleb-Huo]

@tractatus
In encounter the following error message by running the Makevars code.
Any suggestion how could I fix that?
/Users/zhuo/.R/Makevars:10: *** missing separator. Stop.

Thanks

[tractatus]

@Caleb-Huo this sounds like a tab as separator issue. Since no other info is provided I can only guess your problem. But copy-paste the text you want to run into your preferred text editor and make sure tabs are tabs and not spaces.

[sejiro]

Hi all,
I tried the above solutions but I think there is some other error with my compiler configuration as I am getting the following dyld_stub_binding_helper not found error. Any help or advice would be appreciated.

Also I got the same error trying to fork from tractatus