[R-SIG-Mac] update.packages() cannot install from source

[Spencer Graves]

       Thanks to James Joseph Balamuta and Eberhard W. Lisse.  I 
followed the 2-step procedure outlined by Balamuta, and it fixed the 
problem for all but the jpeg package.  I will write the maintainer of 
that package.  (The one-step would probably have worked, but I didn't 
try it.)


       Thanks again,
       Spencer Graves


On 2019-10-29 16:12, Balamuta, James Joseph wrote:
> Greetings and Salutations,
>
> Note that Xcode Command Line Tools is not the same as Xcode IDE. In fact, only Xcode CLI Tools are required, which are light-weight compared to the IDE.
>
> Regarding your error, this is symptomatic of an Xcode update tied to an OS point-release. Note in the session information 10.15.1 (the .1 being the bump)
>
>      R version 3.6.1 (2019-07-05)
>      Platform: x86_64-apple-darwin15.6.0 (64-bit)
>      Running under: macOS Catalina 10.15.1
>
> Both of the commands highlighted are accurate. Though, the order should be changed to:
>
> sudo xcode-select --reset
> sudo xcode-select --install
>
> The reset changes back to using the default command line tools path. This was needed for Mojave.
>
> Sincerely,
>
> JJB
>
> On 10/29/19, 4:01 PM, "R-SIG-Mac on behalf of Spencer Graves" <r-sig-mac-bounces using r-project.org on behalf of spencer.graves using prodsyse.com> wrote:
>
>      Hello, All:
>      
>      
>             "update.packages()" fails for me on packages DescTools, digest,
>      jpeg, mgcv, openxlsx, rlang, and spam.  It first says:
>      
>      
>         There are binary versions available but the
>         source versions are later:
>                  binary  source needs_compilation
>      DescTools 0.99.29 0.99.30              TRUE
>      digest     0.6.21  0.6.22              TRUE
>      jpeg        0.1-8 0.1-8.1              TRUE
>      mgcv       1.8-29  1.8-30              TRUE
>      openxlsx  4.1.0.1   4.1.2              TRUE
>      rlang       0.4.0   0.4.1              TRUE
>      spam        2.3-0 2.3-0.2              TRUE
>      
>      
>             It then asks, "Do you want to install from sources the packages
>      which need compilation? (Yes/no/cancel)".  I reply "y" or "Yes".  For
>      each package, it says it was
>      
>      ... successfully unpacked and MD5 sums checked
>      ** using staged installation
>      ** libs
>      xcrun: error: invalid active developer path
>      (/Library/Developer/CommandLineTools), missing xcrun at:
>      /Library/Developer/CommandLineTools/usr/bin/xcrun
>      ERROR: compilation failed for package ‘DescTools’
>      * removing
>      ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/DescTools’
>      * restoring previous
>      ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/DescTools’
>      
>      
>             A web search for "xcrun: error: invalid active developer path"
>      identified a couple of discussions on StackExchange that say that I need
>      to have Xcode installed correctly.  I think I have everything up to
>      date:  macOS 10.15.1 Catalina with Xcode downloaded and installed via
>      the App store.  RStudio 1.2.5001 with:
>      
>      
>      sessionInfo()
>      R version 3.6.1 (2019-07-05)
>      Platform: x86_64-apple-darwin15.6.0 (64-bit)
>      Running under: macOS Catalina 10.15.1
>      
>      Matrix products: default
>      BLAS:
>      /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
>      LAPACK:
>      /Library/Frameworks/R.framework/Versions/3.6/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
>      [6] methods   base
>      
>      loaded via a namespace (and not attached):
>      [1] compiler_3.6.1 tools_3.6.1
>      
>      
>      "https://apple.stackexchange.com/questions/254380/why-am-i-getting-an-invalid-active-developer-path-when-attempting-to-use-git-a"
>      recommends, "xcode-select --install", which to me seems like it should
>      be equivalent to the install I just did via the App Store. This
>      StackExchange discussion also said, "If the above alone doesn't do it,
>      then also run:  xcode-select --reset".  However, before I do that, I
>      thought I'd ask here if anyone else is having a problem like this.  And
>      if yes, and if they've fixed it, what did they do to fix it?
>      
>      
>             Thanks,
>             Spencer Graves
>      
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