Re: [R-SIG-Mac] PCRE JIT compilation error
Hello together, i´ve got this message too, but my systems show me first the list of all installed libraries on my MAC. Best regards and take care…. Matthias Krawutschke, Dipl. Inf. Universität Potsdam ZIM - Zentrum für Informationstechnologie und Medienmanagement Team Infrastruktur Server und Storage Spezialized: High-Performance-Computing and Kubernetes Campus Am Neuen Palais: Am Neuen Palais 10 | 14469 Potsdam Tel: +49 331 977-153065, Fax: +49 331 977-1750 Internet: https://www.uni-potsdam.de/de/zim/angebote-loesungen/hpc.html -Ursprüngliche Nachricht- Von: R-SIG-Mac Im Auftrag von Bryan Hanson Gesendet: Mittwoch, 1. April 2020 13:30 An: r-sig-mac R Betreff: [R-SIG-Mac] PCRE JIT compilation error On a fresh install of the binary from mac.r-project.org, if I simply do: library() I see: R > library() There were 30 warnings (use warnings() to see them) R > warnings() Warning messages: 1: In strsplit(x, "\n[ \t\n]*\n", perl = TRUE) : PCRE JIT compilation error 'no more memory' 2: In FUN(X[[i]], ...) : PCRE JIT compilation error 'no more memory' etc. The usual window with installed packages does open. Starting the conversation here on the Mac list, though it may be a bigger problem. Thanks, Bryan Prof. Bryan Hanson (emeritus) Dept of Chemistry & Biochemistry DePauw University Greencastle IN 46135 USA Web: academic.depauw.edu/~hanson/index.html Repo: github.com/bryanhanson Nerdy Blog: ChemoSpec.org The Twit: @ProfBryanHanson I’m usually @ -4 GMT/UTC R > sessionInfo() R version 4.0.0 alpha (2020-03-29 r78109) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Mojave 10.14.6 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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 methods [7] base loaded via a namespace (and not attached): [1] compiler_4.0.0 [[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] Robust compiler toolchain for R-devel
Hey Patrick, i had the same issue /problem on my MAC. First of all you need from Apple XCODE the Command-Line. I find here a good instruction to do that: https://wiki.helsinki.fi/display/HUGG/GNU+compiler+install+on+Mac+OS+X But, I´m not sure if you can compile the GNU-C 9.x - Version. Try it and if you have found out, how - please let me know. Best regards…. Matthias Krawutschke, Dipl. Inf. Universität Potsdam ZIM - Zentrum für Informationstechnologie und Medienmanagement Arbeitsbereich: High-Performance-Computing on Cluster - Environment Campus Am Neuen Palais: Am Neuen Palais 10 | 14469 Potsdam Tel: +49 331 977-, Fax: +49 331 977-1750 Internet: https://www.uni-potsdam.de/de/zim/angebote-loesungen/hpc.html -Ursprüngliche Nachricht- Von: R-SIG-Mac Im Auftrag von Patrick Schratz Gesendet: Dienstag, 18. Februar 2020 09:15 An: Martin Jean via R-SIG-Mac Betreff: [R-SIG-Mac] Robust compiler toolchain for R-devel Hi, I am experimenting since some days to find the “best” compiler toolchain for R-devel to get R-devel package source installs on the new macOS Github Actions runners work in a somewhat stable way. I am also on macOS locally which I use for testing as well. I am aware of https://github.com/rmacoslib/r-macos-rtools. However, using clang7 for all (CC, CXX, etc) leads to some packages failing to build (sometimes due to missing OpenMP capabilities, sometimes undefined). Therefore I decided to try out gcc (v8 and v9). While this solves most of the OpenMP issues, I am running into problems for other packages regarding CC compilation. Turns out that using any clang version for CC solves most problems but not all. However then I have a mix of gcc and clang which is most likely cause other issues. Currently Jeroen is developing a new gcc8 based toolchain for Windows. I was reading the macOS CRAN dev pages but could not find any reasoning why • clang7 is suggested • gcc is not used • What future plans are there for the toolchain on macOS Could someone shine some light on this? Thanks :) Cheers, Patrick [[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] R-latest.pkg link returning a 403 Forbidden error
Dear Simon, thank you so much. If I want to download the latest R-package with this link - i´ve got the cryptic signs in the window, but not the file ☹ Best regars…. Matthias Krawutschke, Dipl. Inf. Universität Potsdam ZIM - Zentrum für Informationstechnologie und Medienmanagement Team High-Performance-Computing on Cluster - Environment Campus Am Neuen Palais: Am Neuen Palais 10 | 14469 Potsdam Tel: +49 331 977-, Fax: +49 331 977-1750 Internet: https://www.uni-potsdam.de/de/zim/angebote-loesungen/hpc.html -Ursprüngliche Nachricht- Von: R-SIG-Mac Im Auftrag von Simon Urbanek Gesendet: Freitag, 14. Februar 2020 19:15 An: Jim Hester Cc: r-sig-mac@r-project.org Betreff: Re: [R-SIG-Mac] R-latest.pkg link returning a 403 Forbidden error Thanks, should be fixed now (adding index removed symlink following permission). Simon > On Feb 15, 2020, at 4:50 AM, Jim Hester wrote: > > The link https://mac.r-project.org/bin/macosx/R-latest.pkg which > previously served the latest version of R is now returning a 403. Is > this an intentional change, or is it an unintentional? This link is > used by the Travis-CI build scripts for macOS, so if the link is no > longer valid we will need to update the script. > > Thanks, > > Jim > ___ 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] Using R on MacOS Catalina.....
Patrick, thank you so much for your help /answer. But the “official” R on this WebSite doesn´t allow to install the software on an other Volume (I wrote that in my first eMail). YES, 256 GB is a lot for a MAC, but if you have less than 50% free of your harddisk, the system goes slow, because it is a SSD – HardDrive……… So it is better to install the software on an other HardDisk /Volume….. and it is faster HomeBrew is nice, that´s right, but I don´t want to install that. Herzlichst grüßt Sie das HPC - Team Matthias Krawutschke Universität Potsdam ZIM - Zentrum für Informationstechnologie und Medienmanagement Team High-Performance-Computing Campus Am Neuen Palais: Am Neuen Palais 10 | 14469 Potsdam Tel: +49 331 977-, Fax: +49 331 977-1750 Internet: <http://www.uni-potsdam.de/zim> http://www.uni-potsdam.de/zim Von: Patrick Schratz Gesendet: Mittwoch, 29. Januar 2020 06:59 An: Matthias Krawutschke Cc: e...@lisse.na; Byron Ellis ; R-SIG-Mac@r-project.org Betreff: Re: [R-SIG-Mac] Using R on MacOS Catalina. Why not use the official installer and adjust the installation path? https://cran.r-project.org/bin/macosx/ Also allows multiple versions being installed, all from the CLI (but I guess guess it's a normal desktop machine and you can just use the gui installer). 256GB is a normal size for a disk, don't see the problem. 90% of all macs probably don't have more. Homebrew R differs slightly from the official R installer and might cause problems in some cases. Matthias Krawutschke mailto:krawutsc...@uni-potsdam.de> > schrieb am Di., 28. Jan. 2020, 20:15: Thank you so much for you assistance. My problem is not solved, because I must install R, etc. on a different Volume like SYS-Volume & I can´t find this option under "homebrew". Best regards from Berlin, Germany Herzlichst grüßt Sie das HPC - Team Matthias Krawutschke Universität Potsdam ZIM - Zentrum für Informationstechnologie und Medienmanagement Team High-Performance-Computing Campus Am Neuen Palais: Am Neuen Palais 10 | 14469 Potsdam Tel: +49 331 977-, Fax: +49 331 977-1750 Internet: http://www.uni-potsdam.de/zim -Ursprüngliche Nachricht- Von: Dr Eberhard W Lisse mailto:e...@lisse.na> > Gesendet: Dienstag, 28. Januar 2020 11:09 An: Byron Ellis mailto:byron.el...@gmail.com> >; Matthias Krawutschke mailto:krawutsc...@uni-potsdam.de> > Cc: e...@lisse.na <mailto:e...@lisse.na> ; R-SIG-Mac@r-project.org <mailto:R-SIG-Mac@r-project.org> Betreff: Re: [R-SIG-Mac] Using R on MacOS Catalina. For me it usually had to resort to the latter when there were connectivity issues (more common in Namibia than in Potsdam :-)-O). And maybe once or twice when I wanted to try something special. It also has a 'cask' option with which it installs apps so I do brew install r brew cask install rstudio All in all rock solid. el On 28/01/2020 11:43, Byron Ellis wrote: > Homebrew is Linux-style packaging for OS X. Think of it as an > equivalent to apt-get—either it will retrieve a binary or it will > attempt to build one. > ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org <mailto: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] Using R on MacOS Catalina.....
Thank you so much for you assistance. My problem is not solved, because I must install R, etc. on a different Volume like SYS-Volume & I can´t find this option under "homebrew". Best regards from Berlin, Germany Herzlichst grüßt Sie das HPC - Team Matthias Krawutschke Universität Potsdam ZIM - Zentrum für Informationstechnologie und Medienmanagement Team High-Performance-Computing Campus Am Neuen Palais: Am Neuen Palais 10 | 14469 Potsdam Tel: +49 331 977-, Fax: +49 331 977-1750 Internet: http://www.uni-potsdam.de/zim -Ursprüngliche Nachricht- Von: Dr Eberhard W Lisse Gesendet: Dienstag, 28. Januar 2020 11:09 An: Byron Ellis ; Matthias Krawutschke Cc: e...@lisse.na; R-SIG-Mac@r-project.org Betreff: Re: [R-SIG-Mac] Using R on MacOS Catalina. For me it usually had to resort to the latter when there were connectivity issues (more common in Namibia than in Potsdam :-)-O). And maybe once or twice when I wanted to try something special. It also has a 'cask' option with which it installs apps so I do brew install r brew cask install rstudio All in all rock solid. el On 28/01/2020 11:43, Byron Ellis wrote: > Homebrew is Linux-style packaging for OS X. Think of it as an > equivalent to apt-get—either it will retrieve a binary or it will > attempt to build one. > ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Using R on MacOS Catalina.....
Eberhard, thank you so much for your quick response. Yes, my MacBook has only 256 GB HDD (Standard) ☹ Oh, well, I know & I don´t use X-Code as well. I take the small version of that: xcode-select --install (It installed only the command-line tools, header, etc. for using their own c-compiler) Hm, I never used "Homebrew" - I come from the UNIX - World and I like the command-line . Well, I can create the files for R via "make" - after them it breaks the installation ☹ Best regards Herzlichst grüßt Sie das HPC - Team i.A. Matthias Krawutschke Universität Potsdam ZIM - Zentrum für Informationstechnologie und Medienmanagement Team High-Performance-Computing Campus Am Neuen Palais: Am Neuen Palais 10 | 14469 Potsdam Tel: +49 331 977-, Fax: +49 331 977-1750 Internet: http://www.uni-potsdam.de/zim -Ursprüngliche Nachricht- Von: Dr Eberhard W Lisse Gesendet: Dienstag, 28. Januar 2020 10:18 An: Matthias Krawutschke ; R-SIG-Mac@r-project.org Cc: e...@lisse.na Betreff: Re: [R-SIG-Mac] Using R on MacOS Catalina. Matthias, A Mac with Catalina and a small hard disk? I use the Homebrew package manager and while there is a short delay between R and Homebrew this works out very well. It has two options, one with out the app, which is what I use because I for GUI I use RStudio exclusively. There is really no need to compile from source :-)-O XCode is huge, though the XCode command line tools are required. Gruss aus dem Süden :-)-O el On 28/01/2020 11:05, Matthias Krawutschke wrote: > Hello everybody, > > > > I am new at this Mailinglist and I have a question about R on MacOS > Catalina. > > On your Website I had found a package for R. If I want to install it > on my MacBook – the program told me, that I can´t install the software > on an other volume like “system”….. That is bad, because I had a > small Volume on my MacBook ☹ > > > > If I want to compile the R-System new with GNU-C Compiler 9.2.0 – I > can “make” the files, but “make install” return it with an ERROR. > > So, did you have any ideas what kind of problems that here I had? > > > > I thank you very much for your assistance and have a nice day….. > > > > Herzlichst grüßt Sie das HPC - Team > > > > > > > > Matthias Krawutschke [...] -- Dr. Eberhard W. Lisse \ / Obstetrician & Gynaecologist e...@lisse.na / * | Telephone: +264 81 124 6733 (cell) PO Box 8421 \ / Bachbrecht 10007, Namibia ;/ ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Using R on MacOS Catalina.....
Hello everybody, I am new at this Mailinglist and I have a question about R on MacOS Catalina. On your Website I had found a package for R. If I want to install it on my MacBook – the program told me, that I can´t install the software on an other volume like “system”….. That is bad, because I had a small Volume on my MacBook ☹ If I want to compile the R-System new with GNU-C Compiler 9.2.0 – I can “make” the files, but “make install” return it with an ERROR. So, did you have any ideas what kind of problems that here I had? I thank you very much for your assistance and have a nice day….. Herzlichst grüßt Sie das HPC - Team Matthias Krawutschke Universität Potsdam ZIM - Zentrum für Informationstechnologie und Medienmanagement Team High-Performance-Computing Campus Am Neuen Palais: Am Neuen Palais 10 | 14469 Potsdam Tel: +49 331 977-, Fax: +49 331 977-1750 Internet: <http://www.uni-potsdam.de/zim> http://www.uni-potsdam.de/zim [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
