rstudio - Fatal Error (invalid active developer path ) After Upgrading R / R Studio

Question

I just upgraded R and R Studio to the most recent versions.

I am trying to load the package RHRV and R Studio aborts the session due to a fatal error. It is associated with the following error:

loading package: tcltk

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
Loading required package: tkrplot

The command:

library("tcltk")

gives the following error message:

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
Warning message:
running command ''/usr/bin/otool' -L '/Library/Frameworks/R.framework/Resources/library/tcltk/libs//tcltk.so'' had status 1

Running the following command crashes R Studio:

library("tkrplot")

Here is some additional information of interest:

sessionInfo("tcltk")

R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11 (El Capitan)

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

attached base packages:
[1] tcltk

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.2         Formula_1.2-1       cluster_2.0.3       magrittr_1.5            splines_3.2.2       MASS_7.3-43         grDevices_3.2.2    
 [8] munsell_0.4.2       colorspace_1.2-6    lattice_0.20-33     minqa_1.2.4            stringr_1.0.0       plyr_1.8.3          tools_3.2.2        
[15] utils_3.2.2         nnet_7.3-10         grid_3.2.2          gtable_0.1.2            nlme_3.1-121        latticeExtra_0.6-26 stats_3.2.2        
[22] datasets_3.2.2      survival_2.38-3     lme4_1.1-10         digest_0.6.8        base_3.2.2          Matrix_1.2-2        gridExtra_2.0.0    
[29] RColorBrewer_1.1-2  nloptr_1.0.4        reshape2_1.4.1      ggplot2_1.0.1       acepack_1.3-3.3     graphics_3.2.2      effects_3.0-4      
[36] rpart_4.1-10        stringi_1.0-1       methods_3.2.2       scales_0.3.0            Hmisc_3.17-0        lmerTest_2.0-29     foreign_0.8-65     
[43] proto_0.3-10

sessionInfo("tkrplot")
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11 (El Capitan)

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

attached base packages:
character(0)

other attached packages:
[1] tkrplot_0.0-23

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.2         Formula_1.2-1       cluster_2.0.3       magrittr_1.5        splines_3.2.2       MASS_7.3-43         grDevices_3.2.2    
 [8] munsell_0.4.2       colorspace_1.2-6    lattice_0.20-33     minqa_1.2.4         stringr_1.0.0       plyr_1.8.3          tcltk_3.2.2        
[15] tools_3.2.2         utils_3.2.2         nnet_7.3-10         grid_3.2.2           gtable_0.1.2        nlme_3.1-121        latticeExtra_0.6-26
[22] stats_3.2.2         datasets_3.2.2      survival_2.38-3     lme4_1.1-10         digest_0.6.8        base_3.2.2          Matrix_1.2-2       
[29] gridExtra_2.0.0     RColorBrewer_1.1-2  nloptr_1.0.4        reshape2_1.4.1      ggplot2_1.0.1       acepack_1.3-3.3     graphics_3.2.2     
[36] effects_3.0-4       rpart_4.1-10        stringi_1.0-1       methods_3.2.2       scales_0.3.0        Hmisc_3.17-0        lmerTest_2.0-29    
[43] foreign_0.8-65      proto_0.3-10             

Matt

Answer 1

With many thanks to Ben, I can provide a solution to the problem. The issue is that El Capitan has a somewhat unknown xcode issue.

Open the Terminal App and enter:

xcode-select --install

It takes a few minutes to load the patch needed to run xcode. The error described above is highlighted in several instances, and this was the workaround.

I then restarted my computer and loaded the package "tkrplot" directly from the source with the code:

install.packages("tkrplot", type="source")

Once I completed these three steps, I was able to load the package "RHRV" and the associated packages "tkrplot" and "tcltk" without issue.