Please test R 4.0.0 pre-releases!
Thanks Simon, This simplifies things a lot and clears up the process. While the instructions on?https://mac.r-project.org/?are more clear now I think there is still simplification needed for the install process and custom modifications that are needed. This not only applies to the dev page but finally also to production end users if the SDK 10.15 issues (see below) persists. I?ve scripted all installation steps (R-devel, gfortran, SDK 10.13) and will probably write a blog post about it to make the R community more aware about it. Let me know if anything is wrong about it - otherwise I?ll use the code below in the blog post. # install R-devel wget https://mac.r-project.org/el-capitan/R-devel/R-devel-el-capitan-sa-x86_64.tar.gz sudo tar fvxz R*.tar.gz -C / rm R-devel-el-capitan-sa-x86_64.tar.gz # install gfortran wget https://github.com/fxcoudert/gfortran-for-macOS/releases/download/8.2/gfortran-8.2-Mojave.dmg sudo hdiutil attach gfortran*.dmg sudo installer -package /Volumes/gfortran*/gfortran*/gfortran*.pkg -target / sudo hdiutil detach /Volumes/gfortran-8.2-Mojave # install SDK10.13 wget https://github.com/phracker/MacOSX-SDKs/releases/download/10.15/MacOSX10.13.sdk.tar.xz tar fvxz MacOSX10.13.sdk.tar.xz sudo mv MacOSX10.13.sdk /Library/Developer/CommandLineTools/SDKs/ rm -rf MacOSX10.13* In addition people need to set custom CFLAGS in ~/.R/Makevars to actually use it: CFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk CCFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk CXXFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk CPPFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.13.sdk In addition there really seem to be major problems regarding the 10.15 SDK. For example, {igraph} which is a package on which lots of other packages depend, cannot be installed from source with SDK 10.15 but works with SDK 10.13. Patrick
On 1. Apr 2020, 09:38 +0200, Simon Urbanek <simon.urbanek at r-project.org>, wrote:
Herv?,
On 1/04/2020, at 6:19 PM, Herv? Pag?s <hpages at fredhutch.org> wrote: Thanks Simon. A couple of days ago we've started to use the R 4.0.0 alpha build from https://mac.r-project.org/ for the Bioconductor build system. Bioconductor packages depend on thousands of CRAN packages and one thing that makes it hard for us and for our users to build/check Bioconductor packages at the moment is the absence of Mac binary packages for R 4.0.0 on CRAN. Do you have an estimate of when they will become available?
Both the packages and R are now available. I always recommend using the Mac-master https://mac.R-project.org as "mirror" since that one is most up-to-date.
Another question is where they are going to be hosted on CRAN. We need to follow CRAN's layout for Bioconductor package repositories.
We have removed the extra layer, the package type is back to "mac.binary", so bin/macosx/contrib is the location. Cheers, Simon
Thanks! H. On 3/31/20 21:27, Simon Urbanek wrote:
Dear Mac users, R 4.0.0 will be using an entirely new toolchain, entirely new build system on entirely new macOS version and hardware. Therefore I would like to ask you kindly to test the binaries from https://urldefense.proofpoint.com/v2/url?u=https-3A__mac.R-2Dproject.org&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=-PNBcsZhHb1MLy6fZakmLP6WDLMwL-VigJVzeFtPxOI&s=FJYxweW9WiMXbNMPpMM0bHXy020Gx9P-dHMrWmt7YzE&e= before the release as much as you can. Raising any issues after the release is too late! So please, please, test the pre-releases. Report any issues either directly to me or this mailing list. The nightly builds are signed, but not necessarily notarized. However, the build fulfils Apple's conditions and is known to pass notarization (in fact the the package available for download today is actually notarized) so it should be a good test for the release which will be notarized and should work on Catalina. For those that want to replicate our setup - technical details: we are now building with macOS 10.13 (High Sierra) as target (i.e. the oldest supported system), regular Apple Xcode/command line tools and GNU Fortran 8.2. R builds are running on macOS 10.15 (Catalina) with Xcode 11.4 using macOS 10.13 target. Packages are built on macOS 10.13 VMs with just Apple command line tools (this should make it easy to replicate the setup using Travis, for example). All 3rd party libraries that CRAN uses are available in https://urldefense.proofpoint.com/v2/url?u=http-3A__mac.r-2Dproject.org_libs-2D4_&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=-PNBcsZhHb1MLy6fZakmLP6WDLMwL-VigJVzeFtPxOI&s=3ZbcXBticg_8MfXltGKdQ9SFNqqeLqqwK_pUhEet7QY&e= The new R build system is in https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.r-2Dproject.org_R-2Ddev-2Dweb_trunk_QA_Simon_R4&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=-PNBcsZhHb1MLy6fZakmLP6WDLMwL-VigJVzeFtPxOI&s=Mmt7_pVM5aUDR3hz93-e-PtadG7wSYpaZe8Ayi5Pv4I&e= Packages build system has not changed and is in https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.r-2Dproject.org_R-2Ddev-2Dweb_trunk_QA_Simon_packages&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=-PNBcsZhHb1MLy6fZakmLP6WDLMwL-VigJVzeFtPxOI&s=eId6n08LVeIAMhMXe3jvLFKn9QGi4_by8owFreDDc84&e= We also plan to have a mac-builder available with similar function as the win-builder where pre-submission tests can be performed and potentially a Travis template. Please test R pre-releases and provide feedback! Thanks, Simon
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-- Herv? Pag?s Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319
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