<p><em>Answer from @atpoint, converted from comment:</em></p>
<p>There are dozens of threads in GitHub, SE and other support platforms that clearly explain what to do. (e.g. <a href="https://github.com/velocyto-team/velocyto.R/issues/2" rel="nofollow noreferrer">https://github.com/velocyto-team/velocyto.R/issues/2</a>) The issue is that the compiler does not support openMP, so you have to install one that does.</p>
<p><em>Answer from @devon-ryan, converted from comment:</em></p>
<p>In conda on OSX we solve this by installing llvm-openmp, which provides the -fopenmp flag. Maybe the same is possible outside of conda (no clue). Don't compile it, find an easier way to install it.</p>

CC BY-SA 4.0
2021-05-23T13:21:41.230Z
2021-05-23T13:21:41.230Z
gringer
<p>try <code>devtools::install_github('linxihui/NNLM')</code>, if it doesn't work you need to install the gfortran binary on Mac. </p>

<p>If it still doesn't work, try to upgrade to 4.0.0. </p>

<p>When you have this kind of trouble, look at the issue page of the github page. You will almost always see that others have had the same issue. </p>

CC BY-SA 4.0
2020-05-11T10:15:34.260Z
Thank you installing gfortran did not help
Zizogolu
CC BY-SA 4.0
2020-05-11T11:32:54.813Z
Did you try to update R to 4.0.0 ?
dantarno
CC BY-SA 4.0
2020-05-11T06:13:04.437Z
2020-05-11T06:13:04.437Z
dantarno
<p>I want to install <code>NNLM</code></p>
<pre><code>install_github('linxihui/NNLM')

lang: error: unsupported option '-fopenmp'
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘NNLM’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/NNLM’
Error: Failed to install 'NNLM' from GitHub:
  (converted from warning) installation of package ‘/var/folders/wk/qwgr9yqs6ts0czx__y_w8gch0000gq/T//RtmpA8PudK/filec5bce1f1309/NNLM_0.4.4.tar.gz’ had non-zero exit status
&gt; 
&gt; install.packages('NNLM')
Warning in install.packages :
  package ‘NNLM’ is not available (for R version 3.6.3)
&gt; 
</code></pre>
<p>What should I do?</p>
<pre><code>&gt; session_info()
─ Session info ─────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.6.3 (2020-02-29)
 os       macOS Mojave 10.14.6        
 system   x86_64, darwin15.6.0        
 ui       RStudio                     
 language (EN)                        
 collate  en_GB.UTF-8                 
 ctype    en_GB.UTF-8                 
 tz       Europe/London               
 date     2020-05-11                  

─ Packages ─────────────────────────────────────────────────────────────────────
 package      * version date       lib source                               
 abind          1.4-5   2016-07-21 [1] CRAN (R 3.6.0)                       
 assertthat     0.2.1   2019-03-21 [1] CRAN (R 3.6.0)                       
 backports      1.1.6   2020-04-05 [1] CRAN (R 3.6.3)                       
 broom          0.5.6   2020-04-20 [1] CRAN (R 3.6.3)                       
 callr          3.4.3   2020-03-28 [1] CRAN (R 3.6.2)                       
 car            3.0-7   2020-03-11 [1] CRAN (R 3.6.0)                       
 carData        3.0-3   2019-11-16 [1] CRAN (R 3.6.0)                       
 cellranger     1.1.0   2016-07-27 [1] CRAN (R 3.6.0)                       
 cli            2.0.2   2020-02-28 [1] CRAN (R 3.6.0)                       
 colorspace     1.4-1   2019-03-18 [1] CRAN (R 3.6.0)                       
 crayon         1.3.4   2017-09-16 [1] CRAN (R 3.6.0)                       
 curl           4.3     2019-12-02 [1] CRAN (R 3.6.0)                       
 data.table   * 1.12.8  2019-12-09 [1] CRAN (R 3.6.0)                       
 desc           1.2.0   2018-05-01 [1] CRAN (R 3.6.0)                       
 devtools     * 2.3.0   2020-04-10 [1] CRAN (R 3.6.3)                       
 digest         0.6.25  2020-02-23 [1] CRAN (R 3.6.0)                       
 dplyr          0.8.5   2020-03-07 [1] CRAN (R 3.6.0)                       
 ellipsis       0.3.0   2019-09-20 [1] CRAN (R 3.6.0)                       
 fansi          0.4.1   2020-01-08 [1] CRAN (R 3.6.0)                       
 farver         2.0.3   2020-01-16 [1] CRAN (R 3.6.0)                       
 forcats        0.5.0   2020-03-01 [1] CRAN (R 3.6.0)                       
 foreign        0.8-76  2020-03-03 [1] CRAN (R 3.6.0)                       
 fs             1.4.1   2020-04-04 [1] CRAN (R 3.6.3)                       
 generics       0.0.2   2018-11-29 [1] CRAN (R 3.6.0)                       
 ggplot2      * 3.3.0   2020-03-05 [1] CRAN (R 3.6.0)                       
 ggpubr       * 0.3.0   2020-05-04 [1] CRAN (R 3.6.3)                       
 ggsignif     * 0.6.0   2019-08-08 [1] CRAN (R 3.6.0)                       
 glue           1.4.0   2020-04-03 [1] CRAN (R 3.6.3)                       
 gtable         0.3.0   2019-03-25 [1] CRAN (R 3.6.0)                       
 haven          2.2.0   2019-11-08 [1] CRAN (R 3.6.0)                       
 hms            0.5.3   2020-01-08 [1] CRAN (R 3.6.0)                       
 labeling       0.3     2014-08-23 [1] CRAN (R 3.6.0)                       
 lattice        0.20-41 2020-04-02 [1] CRAN (R 3.6.3)                       
 lifecycle      0.2.0   2020-03-06 [1] CRAN (R 3.6.0)                       
 maftools     * 2.4.05  2020-05-10 [1] Github (PoisonAlien/maftools@6ddf526)
 magrittr       1.5     2014-11-22 [1] CRAN (R 3.6.0)                       
 Matrix         1.2-18  2019-11-27 [1] CRAN (R 3.6.3)                       
 memoise        1.1.0   2017-04-21 [1] CRAN (R 3.6.0)                       
 munsell        0.5.0   2018-06-12 [1] CRAN (R 3.6.0)                       
 nlme           3.1-147 2020-04-13 [1] CRAN (R 3.6.2)                       
 openxlsx       4.1.5   2020-05-06 [1] CRAN (R 3.6.2)                       
 pillar         1.4.4   2020-05-05 [1] CRAN (R 3.6.3)                       
 pkgbuild       1.0.8   2020-05-07 [1] CRAN (R 3.6.2)                       
 pkgconfig      2.0.3   2019-09-22 [1] CRAN (R 3.6.0)                       
 pkgload        1.0.2   2018-10-29 [1] CRAN (R 3.6.0)                       
 plyr           1.8.6   2020-03-03 [1] CRAN (R 3.6.0)                       
 prettyunits    1.1.1   2020-01-24 [1] CRAN (R 3.6.0)                       
 processx       3.4.2   2020-02-09 [1] CRAN (R 3.6.0)                       
 ps             1.3.3   2020-05-08 [1] CRAN (R 3.6.2)                       
 purrr          0.3.4   2020-04-17 [1] CRAN (R 3.6.2)                       
 R6             2.4.1   2019-11-12 [1] CRAN (R 3.6.0)                       
 RColorBrewer   1.1-2   2014-12-07 [1] CRAN (R 3.6.0)                       
 Rcpp           1.0.4.6 2020-04-09 [1] CRAN (R 3.6.3)                       
 readxl         1.3.1   2019-03-13 [1] CRAN (R 3.6.0)                       
 remotes      * 2.1.1   2020-02-15 [1] CRAN (R 3.6.0)                       
 reshape      * 0.8.8   2018-10-23 [1] CRAN (R 3.6.0)                       
 rio            0.5.16  2018-11-26 [1] CRAN (R 3.6.0)                       
 rlang          0.4.6   2020-05-02 [1] CRAN (R 3.6.2)                       
 rprojroot      1.3-2   2018-01-03 [1] CRAN (R 3.6.0)                       
 rstatix        0.5.0   2020-04-28 [1] CRAN (R 3.6.2)                       
 rstudioapi     0.11    2020-02-07 [1] CRAN (R 3.6.0)                       
 scales         1.1.0   2019-11-18 [1] CRAN (R 3.6.0)                       
 sessioninfo    1.1.1   2018-11-05 [1] CRAN (R 3.6.0)                       
 stringi        1.4.6   2020-02-17 [1] CRAN (R 3.6.0)                       
 survival       3.1-12  2020-04-10 [1] CRAN (R 3.6.3)                       
 testthat       2.3.2   2020-03-02 [1] CRAN (R 3.6.0)                       
 tibble         3.0.1   2020-04-20 [1] CRAN (R 3.6.3)                       
 tidyr          1.0.3   2020-05-07 [1] CRAN (R 3.6.2)                       
 tidyselect     1.0.0   2020-01-27 [1] CRAN (R 3.6.0)                       
 usethis      * 1.6.1   2020-04-29 [1] CRAN (R 3.6.2)                       
 vctrs          0.2.4   2020-03-10 [1] CRAN (R 3.6.0)                       
 withr          2.2.0   2020-04-20 [1] CRAN (R 3.6.2)                       
 zip            2.0.4   2019-09-01 [1] CRAN (R 3.6.0)                       

[1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library
</code></pre>
<p>Update: I tried installing llvm, but don't know what put here to finish installing llvm-openmp pc-133-235:build fi1d18</p>
<pre><code>$ cmake ../llvm -DLLVM_ENABLE_PROJECTS=openmp -DCMAKE_C_COMPILER=&lt;C compiler&gt; -DCMAKE_CXX_COMPILER=&lt;C++ compiler&gt;
-bash: syntax error near unexpected token `newline' 
</code></pre>

<r><software-installation><software-usage>
Permanent error in installing R package
# Permanent error in installing R package

(Asked by: username_0 on 2020-05-11)

I want to install NNLM
install_github('linxihui/NNLM')

lang: error: unsupported option '-fopenmp'
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘NNLM’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/NNLM’
Error: Failed to install 'NNLM' from GitHub:
  (converted from warning) installation of package ‘/var/folders/wk/qwgr9yqs6ts0czx__y_w8gch0000gq/T//RtmpA8PudK/filec5bce1f1309/NNLM_0.4.4.tar.gz’ had non-zero exit status
> 
> install.packages('NNLM')
Warning in install.packages :
  package ‘NNLM’ is not available (for R version 3.6.3)
> 

What should I do?
> session_info()
─ Session info ─────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.6.3 (2020-02-29)
 os       macOS Mojave 10.14.6        
 system   x86_64, darwin15.6.0        
 ui       RStudio                     
 language (EN)                        
 collate  en_GB.UTF-8                 
 ctype    en_GB.UTF-8                 
 tz       Europe/London               
 date     2020-05-11                  

─ Packages ─────────────────────────────────────────────────────────────────────
 package      * version date       lib source                               
 abind          1.4-5   2016-07-21 [1] CRAN (R 3.6.0)                       
 assertthat     0.2.1   2019-03-21 [1] CRAN (R 3.6.0)                       
 backports      1.1.6   2020-04-05 [1] CRAN (R 3.6.3)                       
 broom          0.5.6   2020-04-20 [1] CRAN (R 3.6.3)                       
 callr          3.4.3   2020-03-28 [1] CRAN (R 3.6.2)                       
 car            3.0-7   2020-03-11 [1] CRAN (R 3.6.0)                       
 carData        3.0-3   2019-11-16 [1] CRAN (R 3.6.0)                       
 cellranger     1.1.0   2016-07-27 [1] CRAN (R 3.6.0)                       
 cli            2.0.2   2020-02-28 [1] CRAN (R 3.6.0)                       
 colorspace     1.4-1   2019-03-18 [1] CRAN (R 3.6.0)                       
 crayon         1.3.4   2017-09-16 [1] CRAN (R 3.6.0)                       
 curl           4.3     2019-12-02 [1] CRAN (R 3.6.0)                       
 data.table   * 1.12.8  2019-12-09 [1] CRAN (R 3.6.0)                       
 desc           1.2.0   2018-05-01 [1] CRAN (R 3.6.0)                       
 devtools     * 2.3.0   2020-04-10 [1] CRAN (R 3.6.3)                       
 digest         0.6.25  2020-02-23 [1] CRAN (R 3.6.0)                       
 dplyr          0.8.5   2020-03-07 [1] CRAN (R 3.6.0)                       
 ellipsis       0.3.0   2019-09-20 [1] CRAN (R 3.6.0)                       
 fansi          0.4.1   2020-01-08 [1] CRAN (R 3.6.0)                       
 farver         2.0.3   2020-01-16 [1] CRAN (R 3.6.0)                       
 forcats        0.5.0   2020-03-01 [1] CRAN (R 3.6.0)                       
 foreign        0.8-76  2020-03-03 [1] CRAN (R 3.6.0)                       
 fs             1.4.1   2020-04-04 [1] CRAN (R 3.6.3)                       
 generics       0.0.2   2018-11-29 [1] CRAN (R 3.6.0)                       
 ggplot2      * 3.3.0   2020-03-05 [1] CRAN (R 3.6.0)                       
 ggpubr       * 0.3.0   2020-05-04 [1] CRAN (R 3.6.3)                       
 ggsignif     * 0.6.0   2019-08-08 [1] CRAN (R 3.6.0)                       
 glue           1.4.0   2020-04-03 [1] CRAN (R 3.6.3)                       
 gtable         0.3.0   2019-03-25 [1] CRAN (R 3.6.0)                       
 haven          2.2.0   2019-11-08 [1] CRAN (R 3.6.0)                       
 hms            0.5.3   2020-01-08 [1] CRAN (R 3.6.0)                       
 labeling       0.3     2014-08-23 [1] CRAN (R 3.6.0)                       
 lattice        0.20-41 2020-04-02 [1] CRAN (R 3.6.3)                       
 lifecycle      0.2.0   2020-03-06 [1] CRAN (R 3.6.0)                       
 maftools     * 2.4.05  2020-05-10 [1] Github (PoisonAlien/maftools@6ddf526)
 magrittr       1.5     2014-11-22 [1] CRAN (R 3.6.0)                       
 Matrix         1.2-18  2019-11-27 [1] CRAN (R 3.6.3)                       
 memoise        1.1.0   2017-04-21 [1] CRAN (R 3.6.0)                       
 munsell        0.5.0   2018-06-12 [1] CRAN (R 3.6.0)                       
 nlme           3.1-147 2020-04-13 [1] CRAN (R 3.6.2)                       
 openxlsx       4.1.5   2020-05-06 [1] CRAN (R 3.6.2)                       
 pillar         1.4.4   2020-05-05 [1] CRAN (R 3.6.3)                       
 pkgbuild       1.0.8   2020-05-07 [1] CRAN (R 3.6.2)                       
 pkgconfig      2.0.3   2019-09-22 [1] CRAN (R 3.6.0)                       
 pkgload        1.0.2   2018-10-29 [1] CRAN (R 3.6.0)                       
 plyr           1.8.6   2020-03-03 [1] CRAN (R 3.6.0)                       
 prettyunits    1.1.1   2020-01-24 [1] CRAN (R 3.6.0)                       
 processx       3.4.2   2020-02-09 [1] CRAN (R 3.6.0)                       
 ps             1.3.3   2020-05-08 [1] CRAN (R 3.6.2)                       
 purrr          0.3.4   2020-04-17 [1] CRAN (R 3.6.2)                       
 R6             2.4.1   2019-11-12 [1] CRAN (R 3.6.0)                       
 RColorBrewer   1.1-2   2014-12-07 [1] CRAN (R 3.6.0)                       
 Rcpp           1.0.4.6 2020-04-09 [1] CRAN (R 3.6.3)                       
 readxl         1.3.1   2019-03-13 [1] CRAN (R 3.6.0)                       
 remotes      * 2.1.1   2020-02-15 [1] CRAN (R 3.6.0)                       
 reshape      * 0.8.8   2018-10-23 [1] CRAN (R 3.6.0)                       
 rio            0.5.16  2018-11-26 [1] CRAN (R 3.6.0)                       
 rlang          0.4.6   2020-05-02 [1] CRAN (R 3.6.2)                       
 rprojroot      1.3-2   2018-01-03 [1] CRAN (R 3.6.0)                       
 rstatix        0.5.0   2020-04-28 [1] CRAN (R 3.6.2)                       
 rstudioapi     0.11    2020-02-07 [1] CRAN (R 3.6.0)                       
 scales         1.1.0   2019-11-18 [1] CRAN (R 3.6.0)                       
 sessioninfo    1.1.1   2018-11-05 [1] CRAN (R 3.6.0)                       
 stringi        1.4.6   2020-02-17 [1] CRAN (R 3.6.0)                       
 survival       3.1-12  2020-04-10 [1] CRAN (R 3.6.3)                       
 testthat       2.3.2   2020-03-02 [1] CRAN (R 3.6.0)                       
 tibble         3.0.1   2020-04-20 [1] CRAN (R 3.6.3)                       
 tidyr          1.0.3   2020-05-07 [1] CRAN (R 3.6.2)                       
 tidyselect     1.0.0   2020-01-27 [1] CRAN (R 3.6.0)                       
 usethis      * 1.6.1   2020-04-29 [1] CRAN (R 3.6.2)                       
 vctrs          0.2.4   2020-03-10 [1] CRAN (R 3.6.0)                       
 withr          2.2.0   2020-04-20 [1] CRAN (R 3.6.2)                       
 zip            2.0.4   2019-09-01 [1] CRAN (R 3.6.0)                       

[1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library

Update: I tried installing llvm, but don't know what put here to finish installing llvm-openmp pc-133-235:build fi1d18
$ cmake ../llvm -DLLVM_ENABLE_PROJECTS=openmp -DCMAKE_C_COMPILER= -DCMAKE_CXX_COMPILER=
-bash: syntax error near unexpected token `newline'

**Tags:** r, software-installation, software-usage

---

## 2 answers

### Answer by username_1 on 2021-05-23. Score: 0 | Accepted answer

*Answer from @atpoint, converted from comment:*

There are dozens of threads in GitHub, SE and other support platforms that clearly explain what to do. (e.g. <https://github.com/velocyto-team/velocyto.R/issues/2>) The issue is that the compiler does not support openMP, so you have to install one that does.

*Answer from @devon-ryan, converted from comment:*

In conda on OSX we solve this by installing llvm-openmp, which provides the -fopenmp flag. Maybe the same is possible outside of conda (no clue). Don't compile it, find an easier way to install it.


---

### Answer by username_2 on 2020-05-11. Score: 1

try `devtools::install_github('linxihui/NNLM')`, if it doesn't work you need to install the gfortran binary on Mac.

If it still doesn't work, try to upgrade to 4.0.0.

When you have this kind of trouble, look at the issue page of the github page. You will almost always see that others have had the same issue.

> **Comments:**
> **username_0**: Thank you installing gfortran did not help  
> **username_2**: Did you try to update R to 4.0.0 ?  

---

