Re: [R-SIG-Mac] M1+ R package test failures (local and Mac Builder)
Dear Simon, Thanks for your reply, much appreciated. My question is precisely how I can reproduce the CRAN test results (which all pass) for the Mac build of mmrm 0.2.2. I can't with Macbuilder, and I can't locally. My understanding from reading the Writing R extensions section is that there might well be problems when using different compilers for R itself and the R packages for compilation on Mac. This is the situation I have on Macbuilder and locally, but also on CRAN. I am not sure though it would be worthwhile to try debug the test failures on Macbuilder and locally, when all tests pass on CRAN, and on Windows and Linux platforms. Any additional tips would be appreciated, best regards Daniel On Wed, Jul 26, 2023 at 11:56 PM Simon Urbanek wrote: > Daniel, > > I'm not sure I understand your question. The package mmrm 0.2.2 fails its > tests for me as well. If you can reproduce the problem locally (as you > indicated), then that's good as you should be in the position to fix it. > > Cheers, > Simon > > > > On 26/07/2023, at 1:50 AM, Sabanes Bove, Daniel via R-SIG-Mac < > r-sig-mac@r-project.org> wrote: > > > > Hi R@Mac developers, > > > > I switched yesterday to a new M2 MacBook, coming from a 3+ year old Intel > > MacBook. > > The concrete problem is that my R package mmrm (including C++ and in > > particular Eigen/TMB code) successfully compiles, but the tests fail, > i.e. > > the compiled and installed R package does not behave correctly. > > > > First I thought that this is just my local toolchain which is not yet > > appropriately configured, but I tried to read more on that and got OpenMP > > and gfortran and it should be ok. > > So I thought ok, maybe I will try the Mac Builder website and find out in > > which commit the R package broke. > > > > Unfortunately, the problem is that the Mac Builder does not help us > > sufficiently here, because even the current CRAN release (0.2.2, where > > tests based on CRAN binary pass fine locally and on CRAN) leads to test > > failures on Mac Builder. > > > > I do see a few differences between the CRAN reported setup and the mac > > Builder: > > - CRAN is running under macOS Big Sur 11.6.7, while Mac Builder is > running > > under macOS Ventura 13.3.1 (same as my local machine) > > - CRAN uses C++ compiler ‘Apple clang version 13.0.0 > (clang-1300.0.29.30)’ > > (and not 14.0.0 as used for the R compilation!) for the package build, > > while Mac Builder uses ‘Apple clang version 14.0.3 > (clang-1403.0.22.14.1)’ > > (this is the same as on my local machine) > > > > At least Mac Builder and my local machine thus use a similar setup it > > seems (even though M1 vs M2 difference exists) > > > > My question is: what are your tips on how to move forward here? How can > we > > set up the Apple clang version and maybe other build flags locally - as > > well as on Mac Builder for the whole community - to really match the CRAN > > configuration sufficiently well and thus allow for successful package > > builds? > > > > Thanks all, > > best regards > > Daniel > > > > [[alternative HTML version deleted]] > > > > ___ > > R-SIG-Mac mailing list > > R-SIG-Mac@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > > > -- *Dr. Daniel Sabanés Bové* Senior Principal Data Scientist F. Hoffmann-La Roche Ltd PD Data Sciences - Data Science Acceleration (DSX) B. 663 CH-4070 Basel Switzerland Discover our products at go.roche.com/statistical-engineering (internal page) and go.roche.com/statistical-engineering-presentation (public) www.roche.com *Confidentiality Note: *This message is intended only for the use of the named recipient(s) and may contain confidential and/or proprietary information. If you are not the intended recipient, please contact the sender and delete this message. Any unauthorized use of the information contained in this message is prohibited. [[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] M1+ R package test failures (local and Mac Builder)
Daniel, I'm not sure I understand your question. The package mmrm 0.2.2 fails its tests for me as well. If you can reproduce the problem locally (as you indicated), then that's good as you should be in the position to fix it. Cheers, Simon > On 26/07/2023, at 1:50 AM, Sabanes Bove, Daniel via R-SIG-Mac > wrote: > > Hi R@Mac developers, > > I switched yesterday to a new M2 MacBook, coming from a 3+ year old Intel > MacBook. > The concrete problem is that my R package mmrm (including C++ and in > particular Eigen/TMB code) successfully compiles, but the tests fail, i.e. > the compiled and installed R package does not behave correctly. > > First I thought that this is just my local toolchain which is not yet > appropriately configured, but I tried to read more on that and got OpenMP > and gfortran and it should be ok. > So I thought ok, maybe I will try the Mac Builder website and find out in > which commit the R package broke. > > Unfortunately, the problem is that the Mac Builder does not help us > sufficiently here, because even the current CRAN release (0.2.2, where > tests based on CRAN binary pass fine locally and on CRAN) leads to test > failures on Mac Builder. > > I do see a few differences between the CRAN reported setup and the mac > Builder: > - CRAN is running under macOS Big Sur 11.6.7, while Mac Builder is running > under macOS Ventura 13.3.1 (same as my local machine) > - CRAN uses C++ compiler ‘Apple clang version 13.0.0 (clang-1300.0.29.30)’ > (and not 14.0.0 as used for the R compilation!) for the package build, > while Mac Builder uses ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’ > (this is the same as on my local machine) > > At least Mac Builder and my local machine thus use a similar setup it > seems (even though M1 vs M2 difference exists) > > My question is: what are your tips on how to move forward here? How can we > set up the Apple clang version and maybe other build flags locally - as > well as on Mac Builder for the whole community - to really match the CRAN > configuration sufficiently well and thus allow for successful package > builds? > > Thanks all, > best regards > Daniel > > [[alternative HTML version deleted]] > > ___ > 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] M1+ R package test failures (local and Mac Builder)
Apple Clang 14.0.3 and its associated SDK change to MacOSX13.3.sdk broke about 25 CRAN packages (3 with segfaults) and 17 remain broken (and also with Xcode/CLT 15 beta 4 which uses a newer build of 14.0.3). But in my checks mmrm 0.2.2 is not one of them. Packages should aim to be platform-independent. So rather than expect all check systems to run the same toolchain, make sure your package works on all that are available. I believe mac-builder uses different ones for 'release' and for 'development' but you write as if it uses just one -- and I know that there have been changes since R 4.3.0 was released. It is possible to download different CLTs from https://developer.apple.com/download/all/ and switch between them (for the compiler you will need to install them in turn but you can switch between installed SDKs). I have 14.2, 14.3.1 and 15 beta 4 downloaded and switch between them. Given the several recent security alerts, if you are running macOS 13.3.1 I would suggest you update to 13.5. On 25/07/2023 14:50, Sabanes Bove, Daniel via R-SIG-Mac wrote: Hi R@Mac developers, I switched yesterday to a new M2 MacBook, coming from a 3+ year old Intel MacBook. The concrete problem is that my R package mmrm (including C++ and in particular Eigen/TMB code) successfully compiles, but the tests fail, i.e. the compiled and installed R package does not behave correctly. You give us no idea of the problems. Please do re-read the posting guide. First I thought that this is just my local toolchain which is not yet appropriately configured, but I tried to read more on that and got OpenMP and gfortran and it should be ok. So I thought ok, maybe I will try the Mac Builder website and find out in which commit the R package broke. Unfortunately, the problem is that the Mac Builder does not help us sufficiently here, because even the current CRAN release (0.2.2, where tests based on CRAN binary pass fine locally and on CRAN) leads to test failures on Mac Builder. I do see a few differences between the CRAN reported setup and the mac Builder: - CRAN is running under macOS Big Sur 11.6.7, while Mac Builder is running under macOS Ventura 13.3.1 (same as my local machine) - CRAN uses C++ compiler ‘Apple clang version 13.0.0 (clang-1300.0.29.30)’ (and not 14.0.0 as used for the R compilation!) for the package build, while Mac Builder uses ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’ (this is the same as on my local machine) At least Mac Builder and my local machine thus use a similar setup it seems (even though M1 vs M2 difference exists) My question is: what are your tips on how to move forward here? How can we set up the Apple clang version and maybe other build flags locally - as well as on Mac Builder for the whole community - to really match the CRAN configuration sufficiently well and thus allow for successful package builds? Thanks all, best regards Daniel [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Brian D. Ripley, rip...@stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] M1+ R package test failures (local and Mac Builder)
Hi R@Mac developers, I switched yesterday to a new M2 MacBook, coming from a 3+ year old Intel MacBook. The concrete problem is that my R package mmrm (including C++ and in particular Eigen/TMB code) successfully compiles, but the tests fail, i.e. the compiled and installed R package does not behave correctly. First I thought that this is just my local toolchain which is not yet appropriately configured, but I tried to read more on that and got OpenMP and gfortran and it should be ok. So I thought ok, maybe I will try the Mac Builder website and find out in which commit the R package broke. Unfortunately, the problem is that the Mac Builder does not help us sufficiently here, because even the current CRAN release (0.2.2, where tests based on CRAN binary pass fine locally and on CRAN) leads to test failures on Mac Builder. I do see a few differences between the CRAN reported setup and the mac Builder: - CRAN is running under macOS Big Sur 11.6.7, while Mac Builder is running under macOS Ventura 13.3.1 (same as my local machine) - CRAN uses C++ compiler ‘Apple clang version 13.0.0 (clang-1300.0.29.30)’ (and not 14.0.0 as used for the R compilation!) for the package build, while Mac Builder uses ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’ (this is the same as on my local machine) At least Mac Builder and my local machine thus use a similar setup it seems (even though M1 vs M2 difference exists) My question is: what are your tips on how to move forward here? How can we set up the Apple clang version and maybe other build flags locally - as well as on Mac Builder for the whole community - to really match the CRAN configuration sufficiently well and thus allow for successful package builds? Thanks all, best regards Daniel [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
