Dear Simon, To test the error, please do the following on a Mac with Big Sur:
1. Install GDAL The available binaries I could find out are Mac OS Frameworks from https://www.kyngchaos.com/software/frameworks/ and “homebrew”. 2. Install rgdal binary from CRAN I am using R version 4.0.3 Patched (2020-11-25 r79505) and the rgdal version is 1.5-18 (SVN revision 1082), the latest ones available on CRAN. 3. Do the following R commands: > drvs <- rgdal::gdalDrivers()$name; drvs[grep("JP2", drvs)] character(0) The response indicates that the JPEG2000 driver is not installed. After installing both GDAL and rgdal from source with Apple clang 12.0, we get > drvs <- rgdal::gdalDrivers()$name; drvs[grep("JP2", drvs)] “JP2OpenJPEG" More details on the rgdal version compiled from source with the new GDAL: > library(rgdal) Loading required package: sp rgdal: version: 1.5-18, (SVN revision 1082) Geospatial Data Abstraction Library extensions to R successfully loaded Loaded GDAL runtime: GDAL 3.2.0, released 2020/10/26 Path to GDAL shared files: /Users/gilbertocamara/Library/R/4.0/library/sf/gdal GDAL binary built with GEOS: TRUE Loaded PROJ runtime: Rel. 7.1.1, September 1st, 2020, [PJ_VERSION: 711] Path to PROJ shared files: /Users/gilbertocamara/Library/Application Support/proj:/usr/local/share/proj:/usr/local/share/proj PROJ CDN enabled: FALSE Linking to sp version:1.4-4 Hope this helps Gilberto > On 3 Dec 2020, at 01:07, Simon Urbanek <simon.urba...@r-project.org> wrote: > > Gilberto, > > can you provide details, please? (code, file to test etc.) The claim was that > this is specific to BigSur which I doubt from your description. Please start > a new thread about that at it seem entirely unrelated to the discussion at > hand. There was an incompatibility with BigSur, but that was addressed. > > Thanks, > Simon > > > > >> On 3/12/2020, at 11:11 AM, GilbertoCamara <gilberto.camara.i...@gmail.com> >> wrote: >> >> Dear Simon >> >> Unfortunately, the problems reported are real. The rgdal version from CRAN >> fails to recognise images in JPEG2000 format used by Copernicus Sentinel-2 >> satellite. I have investigated the matter carefully with Roger Bivand. >> >> I tried many combinations on Mac OS Big Sur: >> (a) rgdal from CRAN (binary) + GDAL from homebrew. >> (b) rgdal from CRAN (source) + GDAL from homebrew. >> (c) rgdal from CRAN (binary) + GDAL Mac OS Frameworks from >> https://www.kyngchaos.com/software/frameworks/ >> (d) rgdal from CRAN (source) + GDAL from kyngchaos. >> (e) rgdal from CRAN (source) + GDAL/GEOS/etc (source) with Apple clang 11.0 >> (f) rgdal from CRAN (source) + GDAL/GEOS/etc (source) with Apple clang 12.0 >> >> Only option (f) works correctly. >> >> Best regards >> Gilberto >> >>> On 2 Dec 2020, at 22:44, Simon Urbanek <simon.urba...@r-project.org> wrote: >>> >>> Are you chasing a red herring here? Switching tools won help you - in fact >>> they cause more issues since you'd need R-devel version of R to avoid >>> breakage with the most recent tools or extra flags. I'm not sure which >>> issue you are trying to solve. For gdal et al - make sure you install the >>> latest version for CRAN - it is compatible with BigSur, older versions >>> (before BigSur) were not. >>> >>> Please start a new thread about questions unrelated to the original post as >>> it's unclear if there are any open questions in the thread. Also please >>> only answer if your have anything useful to say - if someone asks a >>> question about the GUI it's rather pointless to post when you say you don't >>> use it ... And if you ask a question, please be specific so we can help. >>> >>> There is a lot of misinformation around, so be careful with random >>> suggestions, they are very often plain wrong. >>> >>> Cheers, >>> Simon >>> >>> >>> >>> >>>> On 3/12/2020, at 6:52 AM, Spencer Graves <spencer.gra...@prodsyse.com> >>>> wrote: >>>> >>>> Sorry: Typo: I tried "sudo xcode-select --install" and got the same >>>> error. This was in Terminal where "The default interactive shell is now >>>> zsh." It's not critical, because "I was able to update Xcode from App >>>> Store." >>>> >>>> >>>> Thanks for the reply. sg >>>> >>>> >>>> On 2020-12-02 11:48, Dr Eberhard W Lisse wrote: >>>>> sudo xcode-select --install >>>>> el >>>>> On 2020-12-02 18:52 , Spencer Graves wrote: >>>>>> $ clang --version >>>>>> Apple clang version 11.0.3 (clang-1103.0.32.59) >>>>>> Target: x86_64-apple-darwin20.1.0 >>>>>> Thread model: posix >>>>>> InstalledDir: >>>>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin >>>>>> >>>>>> >>>>>> >>>>>> ** "sudo rm -rf /Library/Developer/CommandLineTools" deleted >>>>>> "CommandLineTools". Then "sudo xcode-select —install" gave me "invalid >>>>>> argument '—install'". "sudo xcode-select —install" gave me the same. >>>>>> >>>>>> >>>>>> ** Fortunately, I was able to update Xcode from App Store. Now I >>>>>> get: >>>>>> >>>>>> >>>>>> $ clang --version >>>>>> Apple clang version 12.0.0 (clang-1200.0.32.27) >>>>>> Target: x86_64-apple-darwin20.1.0 >>>>>> Thread model: posix >>>>>> InstalledDir: >>>>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin >>>>>> >>>>>> >>>>>> >>>>>> If you also have a problem with "sudo xcode-select —install", you >>>>>> might try the App Store. >>>>>> >>>>>> >>>>>> Thanks, Spencer >>>>>> >>>>>> >>>>>> On 2020-12-02 08:18, Gilberto Camara wrote: >>>>>>> For me, it worked as follows >>>>>>> >>>>>>> sudo rm -rf /Library/Developer/CommandLineTools >>>>>>> sudo xcode-select —install >>>>>>> >>>>>>> Best >>>>>>> Gilberto >>>>>>> >>>>>>> >>>>>>>> On 2 Dec 2020, at 15:15, Spencer Graves <spencer.gra...@prodsyse.com> >>>>>>>> wrote: >>>>>>>> >>>>>>>> What should I do to "make sure to have installed the latest >>>>>>>> version of Apple's development environment, including version 12.0 of >>>>>>>> the compiler"? >>>>>>>> >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Spencer Graves >>>>>>>> >>>>>>>> >>>>>>>> On 2020-12-02 07:36, GilbertoCamara wrote: >>>>>>>>> Dear all, >>>>>>>>> I am running R 4.0.3 on BigSur without major performance issues. I >>>>>>>>> am using RStudio instead of the R GUI. >>>>>>>>> I had to build all spatial packages (rgdal, sf, terra and raster) >>>>>>>>> from source using the Apple clang version 12.0.0 compiler. I also >>>>>>>>> had to build GDAL from scratch, since neither the “homebrew” version >>>>>>>>> nor the “kyngchaos” version work well with BigSur. >>>>>>>>> If anyone is building packages from source, please make sure to have >>>>>>>>> installed the latest version of Apple’s development environment, >>>>>>>>> including version 12.0 of the compiler as earlier versions do not >>>>>>>>> work well in BigSur. >>>>>>>>> Best >>>>>>>>> Gilberto >>>>>>>>> =========================== >>>>>>>>> Prof Dr Gilberto Camara >>>>>>>>> Secretariat Director >>>>>>>>> GEO - Group on Earth Observations >>>>>>>>>> On 2 Dec 2020, at 14:15, Bob Rudis <b...@rud.is> wrote: >>>>>>>>>> >>>>>>>>>> After a bit of git and google poking it seems this is happening to >>>>>>>>>> users >>>>>>>>>> of MacVim (https://github.com/macvim-dev/macvim/issues/1114) and a >>>>>>>>>> few >>>>>>>>>> other FOSS projects. >>>>>>>>>> >>>>>>>>>> In various GH issues (like that one) the issue claims to be >>>>>>>>>> resolved by >>>>>>>>>> using the latest Xcode & SDK but that’s not likely to be a solution >>>>>>>>>> for R >>>>>>>>>> GUI (which I’m assuming you're using and where this error is coming >>>>>>>>>> up). >>>>>>>>>> >>>>>>>>>> Some of the threads I saw made it seem like it was happening >>>>>>>>>> especially on >>>>>>>>>> Touch Bar-equipped MacBook Pros (but that’s not confirmed). >>>>>>>>>> >>>>>>>>>> When I try R GUI on Big Sur (on the new M1 Mini) — either just plain >>>>>>>>>> R >>>>>>>>>> scripts or plotting — I do not see this, nor do I see this on my >>>>>>>>>> Intel >>>>>>>>>> MacBook Pro (both are on the latest Big Sur beta and R 4.0.3). >>>>>>>>>> >>>>>>>>>> On Dec 2, 2020 at 7:53:26 AM, Spencer Graves >>>>>>>>>> <spencer.gra...@prodsyse.com> >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>>> I didn't get this with R 4.0.3 under macOS Big Sur 11.0.1 with "time >>>>>>>>>>> R CMD build" / check. I have not tried it under RStudio. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> sg >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On 2020-12-02 05:01, Dr Eberhard W Lisse wrote: >>>>>>>>>>> >>>>>>>>>>> I don't get this in 4.0.3 (using the command line version of R) and >>>>>>>>>>> I >>>>>>>>>>> >>>>>>>>>>> don't get this in RStudio 1.3.1093 either. I use the homebrew >>>>>>>>>>> versions >>>>>>>>>>> >>>>>>>>>>> without the R GUI even installed. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> I am sure more detail will be helpful to the developers. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> el >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On 02/12/2020 11:09, Maria-Angeles Casares-de-Cal via R-SIG-Mac >>>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>>> To those in charge of R for Mac OS X: >>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> I have installed the new Big Sur operating system and now I >>>>>>>>>>>> always get >>>>>>>>>>> >>>>>>>>>>>> a warning similar to: >>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> 2020-12-02 09:52:00.647 R[703:11786] Warning: Expected min height >>>>>>>>>>>> of >>>>>>>>>>> >>>>>>>>>>>> view: (<NSPopoverTouchBarItemButton: 0x7f9c6bb3df50>) to be less >>>>>>>>>>>> than >>>>>>>>>>> >>>>>>>>>>>> or equal to 30 but got a height of 32.000000. This error will be >>>>>>>>>>> >>>>>>>>>>>> logged once per view in violation. >>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> and the computer becomes very slow. >>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> Can I do something to fix it, or will we have to wait for an R >>>>>>>>>>>> update? >>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> Thank you very much for your attention. >>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> Sincerely, >>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> María-Ángeles Casares-de-Cal >>>>>>>>>>> >>>>>>>>>>> [...] >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> 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 >>>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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 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 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 mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
