Re: [R-SIG-Mac] [External] Re: Xcode 10.2.1
Indeed. Thanks. el Sent from Dr Lisse's iPad mini 4 On 29 Apr 2019, 01:48 +0200, Bert Gunter , wrote: > ?installed.packages > > (Sometimes trying the obvious works) > > Bert Gunter > > "The trouble with having an open mind is that people keep coming along and > sticking things into it." > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) > > > > On Sun, Apr 28, 2019 at 4:11 PM wrote: > > > Is there a command to list installed packages? > > > > > > I currently keep track manually and just run a script. > > > > > > el > > > > > > — > > > Sent from Dr Lisse’s iPhone Xs > > > > > > [[alternative HTML version deleted]] > > > > > > ___ > > > 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] [External] Re: Xcode 10.2.1
?installed.packages (Sometimes trying the obvious works) Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Sun, Apr 28, 2019 at 4:11 PM wrote: > Is there a command to list installed packages? > > I currently keep track manually and just run a script. > > el > > — > Sent from Dr Lisse’s iPhone Xs > > [[alternative HTML version deleted]] > > ___ > 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] [External] Re: Xcode 10.2.1
Is there a command to list installed packages? I currently keep track manually and just run a script. el — Sent from Dr Lisse’s iPhone Xs [[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] [External] Re: Xcode 10.2.1
I'm not saying you should upgrade, just that I hope this is now fixed in the latest R release. > On Apr 28, 2019, at 18:22, Roy Mendelssohn - NOAA Federal > wrote: > > I just saw that the Mac version was now available. given the numbering this > would mean reinstalling packages correct? Yes, correct. > If i use in mechanism in the R GUI to do so, does it preserve location - > that is the packages in the Framework directory are update to that system > location, and the packages in my own library stay in my own library? > The GUI allows you to replicate the package install, but the each library is separate (so it doesn't break). It works for the system location, I don't think it knows or handles any custom user libraries - that you' dhave to do with a script. Cheers, Simon > If not, I should be able to write a script to do so, but if the GUI will > already do it, i would prefer to use that. May wait a few days for packages > to keep up. > > thanks for all your work, > > -roy > > >> On Apr 28, 2019, at 3:13 PM, Simon Urbanek >> wrote: >> >> Yes, I did, if you used R 3.6.0 there would be no issue (as long as you have >> command line tools installed). >> >> Cheers, >> Simon >> >> >>> On Apr 24, 2019, at 12:06, Roy Mendelssohn - NOAA Federal via R-SIG-Mac >>> wrote: >>> >>> Yes that is where I found the command. I would add though that I had done >>> that for Xcode 10.2.0, and appears that when you install the new versions >>> that the installer actually deletes the headers at that location. At least >>> that is what happened to me when I updated to Xcode 10.2.1. So people >>> should be aware of this. Each update may delete the headers. >>> >>> In the previous thread, Simon was looking into possibly changing where the >>> R tools look for the headers, but that sort of thing is beyond my pay >>> grade. >>> >>> -Roy >>> On Apr 24, 2019, at 9:01 AM, Tierney, Luke wrote: Also documented in the 'R Installation and Administration' manual -- always a good place to look. Best, luke On Wed, 24 Apr 2019, Kasper Daniel Hansen wrote: > Doh! Sorry to have missed that email thread. > > This advice solved the issue for me. > > On Wed, Apr 24, 2019 at 11:41 AM Roy Mendelssohn - NOAA Federal < > roy.mendelss...@noaa.gov> wrote: > >> Hi Kaspar: >> >> There is an issue of where Xcode puts headers. I have posted on this >> previously. I did the same update as you, and not only doesn't Xcode >> put >> the headers where R expects, it appears to delete the existing headers. >> >> Anyhow, try running the following and see if your problems go away: >> >>> sudo installer -pkg \ >>> >> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg >> \ >>> -target / >> >> -Roy >> >>> On Apr 24, 2019, at 8:36 AM, Kasper Daniel Hansen < >> kasperdanielhan...@gmail.com> wrote: >>> >>> I am on Mojave. I recently updated to Xcode 10.2.1 and I did the >> associated >>> update of the command line tools. Following this, I reinstalled clang6 >> and >>> gfortran 6 from CRAN. >>> >>> When I use the clang6 compiler from CRAN, it is unable to find stdio.h. >>> >>> When I compare the include path from clang6 to the Apple suppled clang >> with >>> `$CC -E - -v` I get >>> >>> with Apple clang >>> #include <...> search starts here: >>> /usr/local/include >>> >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/10.0.1/include >>> >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include >>> >> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include >>> >> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks >>> (framework directory) >>> End of search list. >>> >>> with clang6 from CRAN >>> #include <...> search starts here: >>> /usr/local/include >>> /usr/local/clang6/lib/clang/6.0.0/include >>> /System/Library/Frameworks (framework directory) >>> /Library/Frameworks (framework directory) >>> End of search list. >>> >>> Did Apple move the headers around? Or have I somehow hosed my system? >>> >>> Best, >>> Kasper >>> >>> [[alternative HTML version deleted]] >>> >>> ___ >>> R-SIG-Mac mailing list >>> R-SIG-Mac@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> >> ** >> "The contents of this message do not reflect any position of the U.S. >> Government or NOAA." >> ** >> Roy
Re: [R-SIG-Mac] [External] Re: Xcode 10.2.1
I just saw that the Mac version was now available. given the numbering this would mean reinstalling packages correct? If i use in mechanism in the R GUI to do so, does it preserve location - that is the packages in the Framework directory are update to that system location, and the packages in my own library stay in my own library? If not, I should be able to write a script to do so, but if the GUI will already do it, i would prefer to use that. May wait a few days for packages to keep up. thanks for all your work, -roy > On Apr 28, 2019, at 3:13 PM, Simon Urbanek > wrote: > > Yes, I did, if you used R 3.6.0 there would be no issue (as long as you have > command line tools installed). > > Cheers, > Simon > > >> On Apr 24, 2019, at 12:06, Roy Mendelssohn - NOAA Federal via R-SIG-Mac >> wrote: >> >> Yes that is where I found the command. I would add though that I had done >> that for Xcode 10.2.0, and appears that when you install the new versions >> that the installer actually deletes the headers at that location. At least >> that is what happened to me when I updated to Xcode 10.2.1. So people >> should be aware of this. Each update may delete the headers. >> >> In the previous thread, Simon was looking into possibly changing where the >> R tools look for the headers, but that sort of thing is beyond my pay grade. >> >> >> -Roy >> >>> On Apr 24, 2019, at 9:01 AM, Tierney, Luke wrote: >>> >>> Also documented in the 'R Installation and Administration' manual -- >>> always a good place to look. >>> >>> Best, >>> >>> luke >>> >>> On Wed, 24 Apr 2019, Kasper Daniel Hansen wrote: >>> Doh! Sorry to have missed that email thread. This advice solved the issue for me. On Wed, Apr 24, 2019 at 11:41 AM Roy Mendelssohn - NOAA Federal < roy.mendelss...@noaa.gov> wrote: > Hi Kaspar: > > There is an issue of where Xcode puts headers. I have posted on this > previously. I did the same update as you, and not only doesn't Xcode put > the headers where R expects, it appears to delete the existing headers. > > Anyhow, try running the following and see if your problems go away: > >> sudo installer -pkg \ >> > /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg > \ >> -target / > > -Roy > >> On Apr 24, 2019, at 8:36 AM, Kasper Daniel Hansen < > kasperdanielhan...@gmail.com> wrote: >> >> I am on Mojave. I recently updated to Xcode 10.2.1 and I did the > associated >> update of the command line tools. Following this, I reinstalled clang6 > and >> gfortran 6 from CRAN. >> >> When I use the clang6 compiler from CRAN, it is unable to find stdio.h. >> >> When I compare the include path from clang6 to the Apple suppled clang > with >> `$CC -E - -v` I get >> >> with Apple clang >> #include <...> search starts here: >> /usr/local/include >> > /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/10.0.1/include >> > /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include >> > /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include >> > /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks >> (framework directory) >> End of search list. >> >> with clang6 from CRAN >> #include <...> search starts here: >> /usr/local/include >> /usr/local/clang6/lib/clang/6.0.0/include >> /System/Library/Frameworks (framework directory) >> /Library/Frameworks (framework directory) >> End of search list. >> >> Did Apple move the headers around? Or have I somehow hosed my system? >> >> Best, >> Kasper >> >>[[alternative HTML version deleted]] >> >> ___ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > ** > "The contents of this message do not reflect any position of the U.S. > Government or NOAA." > ** > Roy Mendelssohn > Supervisory Operations Research Analyst > NOAA/NMFS > Environmental Research Division > Southwest Fisheries Science Center > ***Note new street address*** > 110 McAllister Way > Santa Cruz, CA 95060 > Phone: (831)-420-3666 > Fax: (831) 420-3980 > e-mail: roy.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/ > > "Old age and treachery will overcome youth and skill." > "From those who have been given much, much will be expected" > "the arc of the moral universe is long, but it bends toward justice" -MLK > Jr. > >
Re: [R-SIG-Mac] [External] Re: Xcode 10.2.1
Yes, I did, if you used R 3.6.0 there would be no issue (as long as you have command line tools installed). Cheers, Simon > On Apr 24, 2019, at 12:06, Roy Mendelssohn - NOAA Federal via R-SIG-Mac > wrote: > > Yes that is where I found the command. I would add though that I had done > that for Xcode 10.2.0, and appears that when you install the new versions > that the installer actually deletes the headers at that location. At least > that is what happened to me when I updated to Xcode 10.2.1. So people should > be aware of this. Each update may delete the headers. > > In the previous thread, Simon was looking into possibly changing where the R > tools look for the headers, but that sort of thing is beyond my pay grade. > > -Roy > >> On Apr 24, 2019, at 9:01 AM, Tierney, Luke wrote: >> >> Also documented in the 'R Installation and Administration' manual -- >> always a good place to look. >> >> Best, >> >> luke >> >> On Wed, 24 Apr 2019, Kasper Daniel Hansen wrote: >> >>> Doh! Sorry to have missed that email thread. >>> >>> This advice solved the issue for me. >>> >>> On Wed, Apr 24, 2019 at 11:41 AM Roy Mendelssohn - NOAA Federal < >>> roy.mendelss...@noaa.gov> wrote: >>> Hi Kaspar: There is an issue of where Xcode puts headers. I have posted on this previously. I did the same update as you, and not only doesn't Xcode put the headers where R expects, it appears to delete the existing headers. Anyhow, try running the following and see if your problems go away: > sudo installer -pkg \ > /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg \ > -target / -Roy > On Apr 24, 2019, at 8:36 AM, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > > I am on Mojave. I recently updated to Xcode 10.2.1 and I did the associated > update of the command line tools. Following this, I reinstalled clang6 and > gfortran 6 from CRAN. > > When I use the clang6 compiler from CRAN, it is unable to find stdio.h. > > When I compare the include path from clang6 to the Apple suppled clang with > `$CC -E - -v` I get > > with Apple clang > #include <...> search starts here: > /usr/local/include > /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/10.0.1/include > /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include > /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include > /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks > (framework directory) > End of search list. > > with clang6 from CRAN > #include <...> search starts here: > /usr/local/include > /usr/local/clang6/lib/clang/6.0.0/include > /System/Library/Frameworks (framework directory) > /Library/Frameworks (framework directory) > End of search list. > > Did Apple move the headers around? Or have I somehow hosed my system? > > Best, > Kasper > > [[alternative HTML version deleted]] > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac ** "The contents of this message do not reflect any position of the U.S. Government or NOAA." ** Roy Mendelssohn Supervisory Operations Research Analyst NOAA/NMFS Environmental Research Division Southwest Fisheries Science Center ***Note new street address*** 110 McAllister Way Santa Cruz, CA 95060 Phone: (831)-420-3666 Fax: (831) 420-3980 e-mail: roy.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/ "Old age and treachery will overcome youth and skill." "From those who have been given much, much will be expected" "the arc of the moral universe is long, but it bends toward justice" -MLK Jr. >>> >>> [[alternative HTML version deleted]] >>> >>> ___ >>> R-SIG-Mac mailing list >>> R-SIG-Mac@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>> >> >> -- >> Luke Tierney >> Ralph E. Wareham Professor of Mathematical Sciences >> University of Iowa Phone: 319-335-3386 >> Department of Statistics andFax: 319-335-3017 >> Actuarial Science >> 241 Schaeffer Hall email: luke-tier...@uiowa.edu >> Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu > > ** > "The contents of this message do not reflect any position of the U.S. > Government or NOAA." >
