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

[Eberhard W Lisse]

The

xcode-select —install

is required after upgrading to Catalina.

I have several machines so I usually only need to figure out once what Apple has done this time :-)-O.

Once I know that, the other machines usually go without a hitch. And after a while one settles in and doesn’t even notice Apple being Nanny any longer. But I still write it into my handbook so next version I can remember :-)-O

I usually do homebrew first and when that works the other stuff usually compiles as well.

Or you can run

	make

if that works, xcode-cli is installed properly.


el

—
Sent from Dr Lisse’s iPhone Xs
On 29 Oct 2019, 23:13 +0200, Balamuta, James Joseph <balamut2 using illinois.edu>, 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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>
>
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