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cytomining / cytominer

Methods for Image-Based Cell Profiling
https://cytomining.github.io/cytominer/
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install_github fails #130

Closed cells2numbers closed 4 years ago

cells2numbers commented 5 years ago

install_github fails with 

> install_github("cytomining/cytominer")
Downloading GitHub repo cytomining/cytominer@master
Installing 2 packages: caret, ModelMetrics
Installing packages into ‘/usr/local/lib/R/3.5/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/caret_6.0-81.tar.gz'
Content type 'application/x-gzip' length 5235487 bytes (5.0 MB)
==================================================
downloaded 5.0 MB

trying URL 'https://cran.rstudio.com/src/contrib/ModelMetrics_1.2.2.tar.gz'
Content type 'application/x-gzip' length 16974 bytes (16 KB)
==================================================
downloaded 16 KB

* installing *source* package ‘ModelMetrics’ ...
** package ‘ModelMetrics’ successfully unpacked and MD5 sums checked
** libs
clang++  -I"/usr/local/Cellar/r/3.5.2_2/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include   -fPIC  -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I"/usr/local/Cellar/r/3.5.2_2/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/3.5/site-library/Rcpp/include" -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include   -fPIC  -g -O2  -c auc_.cpp -o auc_.o
auc_.cpp:2:10: fatal error: 'omp.h' file not found
#include <omp.h>
         ^~~~~~~
1 error generated.
make: *** [auc_.o] Error 1
ERROR: compilation failed for package ‘ModelMetrics’
* removing ‘/usr/local/lib/R/3.5/site-library/ModelMetrics’
Error in i.p(...) : 
  (converted from warning) installation of package ‘ModelMetrics’ had non-zero exit status
cells2numbers commented 5 years ago

The error generated when the package caret is installed and is due to a missing library (and after upgrading to R 3.5.2). On a Mac, the error can be fixed by installing the libomp library using

brew install libomp

Sessioninfo: 

> session_info()
─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.5.2 (2018-12-20)
 os       macOS High Sierra 10.13.6   
 system   x86_64, darwin17.7.0        
 ui       RStudio                     
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       America/New_York            
 date     2019-01-18                  

─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package     * version date       lib source        
 assertthat    0.2.0   2017-04-11 [1] CRAN (R 3.5.2)
 backports     1.1.3   2018-12-14 [1] CRAN (R 3.5.2)
 callr         3.1.1   2018-12-21 [1] CRAN (R 3.5.2)
 cli           1.0.1   2018-09-25 [1] CRAN (R 3.5.2)
 crayon        1.3.4   2017-09-16 [1] CRAN (R 3.5.2)
 curl          3.3     2019-01-10 [1] CRAN (R 3.5.2)
 desc          1.2.0   2018-05-01 [1] CRAN (R 3.5.2)
 devtools    * 2.0.1   2018-10-26 [1] CRAN (R 3.5.2)
 digest        0.6.18  2018-10-10 [1] CRAN (R 3.5.2)
 fs            1.2.6   2018-08-23 [1] CRAN (R 3.5.2)
 glue          1.3.0   2018-07-17 [1] CRAN (R 3.5.2)
 magrittr      1.5     2014-11-22 [1] CRAN (R 3.5.2)
 memoise       1.1.0   2017-04-21 [1] CRAN (R 3.5.2)
 pkgbuild      1.0.2   2018-10-16 [1] CRAN (R 3.5.2)
 pkgload       1.0.2   2018-10-29 [1] CRAN (R 3.5.2)
 prettyunits   1.0.2   2015-07-13 [1] CRAN (R 3.5.2)
 processx      3.2.1   2018-12-05 [1] CRAN (R 3.5.2)
 ps            1.3.0   2018-12-21 [1] CRAN (R 3.5.2)
 R6            2.3.0   2018-10-04 [1] CRAN (R 3.5.2)
 Rcpp          1.0.0   2018-11-07 [1] CRAN (R 3.5.2)
 remotes       2.0.2   2018-10-30 [1] CRAN (R 3.5.2)
 rlang         0.3.1   2019-01-08 [1] CRAN (R 3.5.2)
 rprojroot     1.3-2   2018-01-03 [1] CRAN (R 3.5.2)
 rstudioapi    0.9.0   2019-01-09 [1] CRAN (R 3.5.2)
 sessioninfo   1.1.1   2018-11-05 [1] CRAN (R 3.5.2)
 testthat      2.0.1   2018-10-13 [1] CRAN (R 3.5.2)
 usethis     * 1.4.0   2018-08-14 [1] CRAN (R 3.5.2)
 withr         2.1.2   2018-03-15 [1] CRAN (R 3.5.2)
 yaml          2.2.0   2018-07-25 [1] CRAN (R 3.5.2)

[1] /usr/local/lib/R/3.5/site-library
[2] /usr/local/Cellar/r/3.5.2_2/lib/R/library
shntnu commented 4 years ago

This appears to be fixed so I will close 

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin17.7.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /usr/local/Cellar/openblas/0.3.6_1/lib/libopenblasp-r0.3.6.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] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4          rstudioapi_0.11     magrittr_1.5        usethis_1.5.1       devtools_2.2.2.9000
 [6] pkgload_1.0.2       R6_2.4.1            rlang_0.4.5         fansi_0.4.1         tools_3.6.1        
[11] pkgbuild_1.0.6      packrat_0.5.0       sessioninfo_1.1.1   cli_2.0.2           withr_2.1.2        
[16] ellipsis_0.3.0      remotes_2.1.1       assertthat_0.2.1    digest_0.6.25       rprojroot_1.3-2    
[21] crayon_1.3.4        processx_3.4.2      callr_3.4.2         fs_1.3.1            ps_1.3.2           
[26] curl_4.2            testthat_2.3.2      memoise_1.1.0       glue_1.3.2          compiler_3.6.1     
[31] desc_1.2.0          backports_1.1.5     prettyunits_1.1.1