Re: [R-SIG-Mac] update.packages() cannot install from source
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" 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 jpeg0.1-8 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 spam2.3-0 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 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] update.packages() cannot install from source
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 , 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" > > 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 > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] update.packages() cannot install from source
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" 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 jpeg0.1-8 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 spam2.3-0 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 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] update.packages() cannot install from source
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 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
