R package 'randomForest' not installing

Question

I have been trying to install the R package 'randomForest', to do this I ran the usual installation command

install.packages("randomForest", dependencies = T)

This gives me the following error, which I've been having trouble interpreting. It seems to me that something is missing from the folder for another R package, 'RccpEigen', and that is causing an error, but I'm not sure and I haven't been able to find how to fix that.

The full error message is this:

Installing package into ‘/home/scott/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/randomForest_4.6-14.tar.gz'
Content type 'application/x-gzip' length 80074 bytes (78 KB)
==================================================
downloaded 78 KB

* installing *source* package ‘randomForest’ ...
** package ‘randomForest’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG   -I"/home/scott/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include/"  -I"/home/scott/R/x86_64-pc-linux-gnu-library/3.6/RcppEigen/include/"  -I"/home/scott/R/x86_64-pc-linux-gnu-library/3.6/RcppEigen/include/unsupported"  -I"/home/scott/R/x86_64-pc-linux-gnu-library/3.6/BH/include" -I"/home/scott/R/x86_64-pc-linux-gnu-library/3.6/StanHeaders/include/src/"  -I"/home/scott/R/x86_64-pc-linux-gnu-library/3.6/StanHeaders/include/"  -I"/home/scott/R/x86_64-pc-linux-gnu-library/3.6/rstan/include" -DEIGEN_NO_DEBUG  -D_REENTRANT  -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -include stan/math/prim/mat/fun/Eigen.hpp     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c classTree.c -o classTree.o
In file included from /home/scott/R/x86_64-pc-linux-gnu-library/3.6/RcppEigen/include/Eigen/Core:88:0,
                 from /home/scott/R/x86_64-pc-linux-gnu-library/3.6/RcppEigen/include/Eigen/Dense:1,
                 from /home/scott/R/x86_64-pc-linux-gnu-library/3.6/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4,
                 from <command-line>:0:
/home/scott/R/x86_64-pc-linux-gnu-library/3.6/RcppEigen/include/Eigen/src/Core/util/Macros.h:613:1: error: unknown type name ‘namespace’
 namespace Eigen {
 ^~~~~~~~~
/home/scott/R/x86_64-pc-linux-gnu-library/3.6/RcppEigen/include/Eigen/src/Core/util/Macros.h:613:17: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘{’ token
 namespace Eigen {
                 ^
In file included from /home/scott/R/x86_64-pc-linux-gnu-library/3.6/RcppEigen/include/Eigen/Dense:1:0,
                 from /home/scott/R/x86_64-pc-linux-gnu-library/3.6/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4,
                 from <command-line>:0:
/home/scott/R/x86_64-pc-linux-gnu-library/3.6/RcppEigen/include/Eigen/Core:96:10: fatal error: complex: No such file or directory
 #include <complex>
          ^~~~~~~~~
compilation terminated.
/usr/lib/R/etc/Makeconf:168: recipe for target 'classTree.o' failed
make: *** [classTree.o] Error 1
ERROR: compilation failed for package ‘randomForest’
* removing ‘/home/scott/R/x86_64-pc-linux-gnu-library/3.6/randomForest’
Warning in install.packages :
  installation of package ‘randomForest’ had non-zero exit status

The downloaded source packages are in
    ‘/tmp/RtmpbKxumd/downloaded_packages’ 

Here is my session info:

R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
 [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C               LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8    
 [5] LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.UTF-8    LC_PAPER=en_CA.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] RcppEigen_0.3.3.7.0 lme4_1.1-21         Matrix_1.2-18       ggplot2_3.3.0       Rmisc_1.5           plyr_1.8.6         
[7] lattice_0.20-38     brms_2.12.0         Rcpp_1.0.4         

loaded via a namespace (and not attached):
  [1] nlme_3.1-144         matrixStats_0.56.0   xts_0.12-0           threejs_0.3.3        rstan_2.19.3         tools_3.6.3         
  [7] backports_1.1.6      R6_2.4.1             DT_0.13              colorspace_1.4-1     withr_2.1.2          tidyselect_1.0.0    
 [13] gridExtra_2.3        prettyunits_1.1.1    processx_3.4.2       Brobdingnag_1.2-6    curl_4.3             compiler_3.6.3      
 [19] cli_2.0.2            shinyjs_1.1          labeling_0.3         colourpicker_1.0     checkmate_2.0.0      scales_1.1.0        
 [25] dygraphs_1.1.1.6     mvtnorm_1.1-0        readr_1.3.1          ggridges_0.5.2       callr_3.4.3          stringr_1.4.0       
 [31] digest_0.6.25        StanHeaders_2.19.2   foreign_0.8-75       minqa_1.2.4          rio_0.5.16           base64enc_0.1-3     
 [37] pkgconfig_2.0.3      htmltools_0.4.0      fastmap_1.0.1        readxl_1.3.1         htmlwidgets_1.5.1    rlang_0.4.5         
 [43] rstudioapi_0.11      shiny_1.4.0.2        farver_2.0.3         zoo_1.8-7            crosstalk_1.1.0.1    gtools_3.8.2        
 [49] zip_2.0.4            dplyr_0.8.5          car_3.0-7            inline_0.3.15        magrittr_1.5         loo_2.2.0           
 [55] bayesplot_1.7.1      munsell_0.5.0        fansi_0.4.1          abind_1.4-5          lifecycle_0.2.0      stringi_1.4.6       
 [61] carData_3.0-3        MASS_7.3-51.5        pkgbuild_1.0.6       grid_3.6.3           parallel_3.6.3       promises_1.1.0      
 [67] forcats_0.4.0        crayon_1.3.4         miniUI_0.1.1.1       haven_2.2.0          splines_3.6.3        hms_0.5.3           
 [73] ps_1.3.2             pillar_1.4.3         igraph_1.2.5         boot_1.3-24          markdown_1.1         shinystan_2.5.0     
 [79] codetools_0.2-16     reshape2_1.4.3       stats4_3.6.3         rstantools_2.0.0     glue_1.4.0           data.table_1.12.8   
 [85] vctrs_0.2.4          nloptr_1.2.1         httpuv_1.5.2         cellranger_1.1.0     gtable_0.3.0         purrr_0.3.3         
 [91] assertthat_0.2.1     openxlsx_4.1.4       mime_0.9             xtable_1.8-4         coda_0.19-3          later_1.0.0         
 [97] rsconnect_0.8.16     tibble_3.0.0         shinythemes_1.1.2    ellipsis_0.3.0       bridgesampling_1.0-0
> 

Any help would be greatly appreciated, as I'm in over my head here programming-wise.

Answer 1

I suspect this is an RStudio issue.

Install randomForest in base R, then you should be able to load in RStudio using library.