Installation Error

[xkluan]

Summary

Hi, all, I met a problems when I install ggrepel packages on my mac, can anyone help me?

My instructions and output:

> install.packages("ggrepel")

  There is a binary version available but the source version is later:
        binary source needs_compilation
ggrepel  0.9.0  0.9.1              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes
installing the source package ‘ggrepel’

trying URL 'https://cran.rstudio.com/src/contrib/ggrepel_0.9.1.tar.gz'
Content type 'application/x-gzip' length 271371 bytes (265 KB)
==================================================
downloaded 265 KB

* installing *source* package ‘ggrepel’ ...
** package ‘ggrepel’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c repel_boxes.cpp -o repel_boxes.o
In file included from repel_boxes.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
repel_boxes.cpp:718:39: error: expected expression
  std::vector<Point> Points(n_points, {0, 0});
                                      ^
repel_boxes.cpp:719:45: error: expected expression
  std::vector<Circle> DataCircles(n_points, {0, 0, 0});
                                            ^
repel_boxes.cpp:730:39: error: expected expression
  std::vector<Box> TextBoxes(n_texts, {0, 0, 0, 0});
                                      ^
repel_boxes.cpp:731:50: error: expected expression
  std::vector<Point> original_centroids(n_texts, {0, 0});
                                                 ^
repel_boxes.cpp:759:42: error: expected expression
  std::vector<Point> velocities(n_texts, {0, 0});
                                         ^
1 warning and 5 errors generated.
make: *** [repel_boxes.o] Error 1
ERROR: compilation failed for package ‘ggrepel’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/ggrepel’
Warning in install.packages :
  installation of package ‘ggrepel’ had non-zero exit status

The downloaded source packages are in
	‘/private/var/folders/y5/1f6_5lyx5cjdjmng1mxb4z280000gn/T/RtmpfwirSp/downloaded_packages’

Version information

Here is the output from sessionInfo() in my R session:

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_4.0.3 tools_4.0.3   

[slowkow]

Thanks for opening the issue. That's very curious. I think that if you just wait and do nothing, the package will eventually be compiled on the CRAN server without errors. Then, you can install the binary instead of attempting to compile the source on your machine.

However, it is puzzling that this C++ code compiles without errors on my macOS machine, and it also compiles without error on Github Actions (Windows, Linux, macOS).

I thought that adding the initialization statements might prevent other errors:

std::vector<Point> Points(n_points, {0, 0});

But, since you are getting an error at compile time, I deleted them from the latest version of ggrepel:

std::vector<Point> Points(n_points);

If you'd like to use ggrepel 0.9.1, you can try to install the latest GitHub version:

remotes::install_github("slowkow/ggrepel")

Please let me know if you run into any other issues.

[vrognas]

Hi, I have a similar issue:

> remotes::install_github("slowkow/ggrepel")
Downloading GitHub repo slowkow/ggrepel@HEAD
✓  checking for file ‘/private/var/folders/6w/8v84sxpj4rdbxfr4_qz4mt84vj3d0l/T/RtmpRsa5NL/remotesfe0c6ca3aa4d/slowkow-ggrepel-54838c6/DESCRIPTION’ ...
─  preparing ‘ggrepel’:
✓  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
─  building ‘ggrepel_0.9.1.9999.tar.gz’
   Warning: invalid uid value replaced by that for user 'nobody'
   Warning: invalid gid value replaced by that for user 'nobody'
   
Installing package into ‘/Users/vikro885/.config/r_packages’
(as ‘lib’ is unspecified)
n*** Successfully loaded .Rprofile ***n
* installing *source* package ‘ggrepel’ ...
** using staged installation
** libs
clang++ -I"/usr/local/Cellar/r/4.0.3_2/lib/R/include" -DNDEBUG  -I'/Users/vikro885/.config/r_packages/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -I"/usr/local/Cellar/r/4.0.3_2/lib/R/include" -DNDEBUG  -I'/Users/vikro885/.config/r_packages/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -g -O2  -c repel_boxes.cpp -o repel_boxes.o
repel_boxes.cpp:761:21: error: expected expression
    velocities[i] = {0, 0};
                    ^
1 error generated.
make: *** [repel_boxes.o] Error 1
ERROR: compilation failed for package ‘ggrepel’
* removing ‘/Users/vikro885/.config/r_packages/ggrepel’
Error: Failed to install 'ggrepel' from GitHub:
  (converted from warning) installation of package ‘/var/folders/6w/8v84sxpj4rdbxfr4_qz4mt84vj3d0l/T//RtmpRsa5NL/filefe0c7c48bbb0/ggrepel_0.9.1.9999.tar.gz’ had non-zero exit status

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin20.2.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
LAPACK: /usr/local/Cellar/r/4.0.3_2/lib/R/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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] colorout_1.2-2

loaded via a namespace (and not attached):
 [1] ps_1.5.0          fansi_0.4.2       prettyunits_1.1.1 withr_2.4.0       rprojroot_2.0.2   crayon_1.3.4      assertthat_0.2.1  R6_2.5.0         
 [9] cli_2.2.0         curl_4.3          remotes_2.2.0     rstudioapi_0.13   callr_3.5.1       tools_4.0.3       glue_1.4.2        compiler_4.0.3   
[17] processx_3.4.5    pkgbuild_1.2.0

[slowkow]

@vrognas @KRascal

Sorry for the issue, and thank you for reporting it.

Here are your options for overcoming this error:

1. In R, run remotes::install_github("slowkow/ggrepel") to get the latest version of the code that should compile without errors.
2. Install a new compiler and use it instead of /usr/bin/clang++.

---

Details

When we use this version of clang:

Apple clang version 11.0.3 (clang-1103.0.32.62)

Then, this C++ expression gives an error:

repel_boxes.cpp:761:21: error: expected expression
    velocities[i] = {0, 0};
                    ^
1 error generated.

The error can be avoided if we install llvm:

brew install llvm

and add this to our ~/.R/Makevars

CXX=/usr/local/opt/llvm/bin/clang++

Alternatively, we can install gcc like this:

brew install gcc

and then add this to our ~/.R/Makevars

CXX=/usr/local/opt/gcc/bin/g++-10

[conorotompkins]

I think I am hitting the same issue with the version on CRAN. I was able to successfully install the package from GitHub.

* installing *source* package ‘ggrepel’ ...
** package ‘ggrepel’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang++ -I"/usr/local/Cellar/r/4.0.3_2/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.0/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -I"/usr/local/Cellar/r/4.0.3_2/lib/R/include" -DNDEBUG  -I'/usr/local/lib/R/4.0/site-library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include   -fPIC  -g -O2  -c repel_boxes.cpp -o repel_boxes.o
repel_boxes.cpp:718:39: error: expected expression
  std::vector<Point> Points(n_points, {0, 0});
                                      ^
repel_boxes.cpp:719:45: error: expected expression
  std::vector<Circle> DataCircles(n_points, {0, 0, 0});
                                            ^
repel_boxes.cpp:730:39: error: expected expression
  std::vector<Box> TextBoxes(n_texts, {0, 0, 0, 0});
                                      ^
repel_boxes.cpp:731:50: error: expected expression
  std::vector<Point> original_centroids(n_texts, {0, 0});
                                                 ^
repel_boxes.cpp:759:42: error: expected expression
  std::vector<Point> velocities(n_texts, {0, 0});
                                         ^
5 errors generated.
make: *** [repel_boxes.o] Error 1
ERROR: compilation failed for package ‘ggrepel’
* removing ‘/usr/local/lib/R/4.0/site-library/ggrepel’
Warning in install.packages :
  installation of package ‘ggrepel’ had non-zero exit status

Session info:

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin20.2.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
LAPACK: /usr/local/Cellar/r/4.0.3_2/lib/R/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] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] rstudioapi_0.13   magrittr_2.0.1    usethis_2.0.0     devtools_2.3.2   
 [5] pkgload_1.1.0     R6_2.5.0          rlang_0.4.10      fansi_0.4.2      
 [9] tools_4.0.3       pkgbuild_1.2.0    sessioninfo_1.1.1 cli_2.3.0        
[13] withr_2.4.1       ellipsis_0.3.1    remotes_2.2.0     assertthat_0.2.1 
[17] digest_0.6.27     rprojroot_2.0.2   lifecycle_0.2.0   crayon_1.4.0     
[21] processx_3.4.5    purrr_0.3.4       callr_3.5.1       fs_1.5.0         
[25] ps_1.5.0          curl_4.3          testthat_3.0.1    memoise_1.1.0    
[29] glue_1.4.2        compiler_4.0.3    desc_1.2.0        prettyunits_1.1.1

[slowkow]

@conorotompkins Thanks, Conor. When time permits, I will send a new release to CRAN.

For anyone else running into this issue, your options are:

1. Install ggrepel from GitHub.
2. Install a new C++ compiler and use it instead of the default one.

See my comment above for more details.

[conorotompkins]

I think my specific issue was caused by RStudio. The issue is described here: rstudio/rstudio#8800

I installed RStudio daily version 1.4.1554 and it resolved the compilation issue.

[sjmgarnier]

I second @conorotompkins' comment. On Mac, Rstudio silently creates a Makevars file that causes all sorts of compilation issues with ggrepel and other packages. Removing that Makevars file (it's in the .r/ folder in the user's home) and installing the preview version of Rstudio solves the issue with installing ggrepel.