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

Tue Oct 29 22:12:47 CET 2019

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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