Re: [R-SIG-Mac] Which command line tools for XCode 4.2.1
Dear Prof. Ripley, Thank you for this extensive information. You mention that you have been working hard on making R and CRAN packages installable using clang, which is quite an effort. Currently, the Bioconductor maintainers are doing the same, i.e. checking which BioC packages are installable using clang, and I was informed that my package 'xps' cannot be installed using clang. In my case the main problem seems to be that the version of clang used has a bug which prevents compilation of xps (and the necessary ROOT C++ framework). Concretely, both the Bioconductor server running Snow Leopard and my Snow Leopard Mac have versions of Xcode, which include clang Version 3.0. In order to compile ROOT successfully, at least clang Version 3.1 is necessary, see: http://root.cern.ch/phpBB3/viewtopic.php?f=3t=14614#p62969 On my Mac running Lion (10.7.5) I have currently also installed Xcode 4.2.1 which contains clang Version 3.0, so I could reproduce this error also on Lion. After downloading the the 'Command Line Tools (OS X Lion) for Xcode - March 2013' from the Apple developer site the version of clang is now: $ clang -v Apple LLVM version 4.2 (clang-425.0.27) (based on LLVM 3.2svn) Target: x86_64-apple-darwin11.4.2 Using this version I could successfully compile both ROOT and xps. The problem is that I do not know how to obtain a more recent version of clang for Snow Leopard, the system currently running on the BioC server. I would very much appreciate if you could propose a solution for this problem. Thank you in advance. Best regards, Christian On 4/18/13 11:03 AM, Prof Brian Ripley wrote: Since I have heard that R and Bioconductor packages should in the future be built with clang since Apple will be discontinuing support of gcc, my question is: I've not heard that, and you give no reference. It's a pretty safe prediction except for timing: it could be a year away. So your questions are not relevant until it is announced. The documentation in the current R manuals is currently the correct advice. Apple have announced the imminent discontinuation of llvm-gcc, and we take that to mean it will not be in Xcode 4.7 (or 5.0 if that is released first). That would mean that once that is released, for most users of Lion and later llvm-gcc will disappear (as most users will get an automatic upgrade from the AppStore, or as in my case, the sysadmins will push out an update). So we have been working hard on making R and CRAN packages installable using clang (there were too many problems at decision time for 3.0.0). How to switch a CRAN binary installation to use clang[++] is in the R = 3.0.0 manuals. That may not work for packages with configure scripts: for that you may need R-patched. There are now only seven CRAN packages which have bugs which stop installation under clang, and all the maintainers have been sent patches. (Two of those do not install under gcc 4.8.0 either.) Very likely at some point Simon will switch the CRAN binary distribution to use clang, but the real point is that many end-users will need to do so soon. Given that R 3.0.0 supports OS 10.6 (Snow Leopard), it is likely that we will do so for all of the 3.0.x series, even though 10.6 will almost certainly reach end-of-life well before 3.1.0 is due. In that case the CRAN builder could stick with llvm-gcc for that series, but it may prove more convenient for end-users to switch to the distribution to clang before then. Only time will tell. On 17/04/2013 18:45, cstrato wrote: Dear Prof. Ripley, dear Simon, Thank you for this information about Xcode and CLTs. Since I have heard that R and Bioconductor packages should in the future be built with clang since Apple will be discontinuing support of gcc, my question is: - Which version of Xcode and/or CLTs should Snow Leopard users install in the future? (the last official version for Snow Leopard is xcode_3.2.6) - Which version of Xcode and/or CLTs should Lion/Mountain Lion users install so that they can still compile their packages with gcc, too? (the current version is xcode_4.6.2) From the discussion I understand that it is no longer necessary to install Xcode at all, installing CLTs is sufficient. Is this correct? Best regards, Christian ___ 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] Which command line tools for XCode 4.2.1
Sorry, it seems that I have used another thread by mistake, Christian On 4/16/13 9:13 PM, cstrato wrote: Dear Simon, On your developer site you mention: We use Xcode 4.2 but Xcode 3.2 and higher should work as well. Note that you will need Command Line Tools component of Xcode on Mac OS X 10.7 or higher. I am running OS X 10.7.5 and XCode 4.2.1 on my Mac, but have not downloaded the command line tools. My questions are: - why do I need the command line tools? - which version do I need to download from: https://developer.apple.com/downloads/index.action There are e.g. - Command Line Tools (OS X Lion) for Xcode - October 2012 (it is not mentioned which version of Xcode) - Command Line Tools (OS X Lion) for Xcode - November 2012 (Xcode 4.3 is mentioned but it is nor clear if it works with 4.2.1) - Command Line Tools (OS X Lion) for Xcode - April 2013 (Xcode 4.6.2 is mentioned but it is nor clear if it works with 4.2.1) (BTW, the Preferences for Xcode 4.2.1 do not list Command Line Tools in the Install window.) - do the Command Line Tools update clang/clang++? The reason for my question is that in order to compile the C++ code in my package with clang I need at least version 3.1 since 3.0 results in an error. Best regards, Christian ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Which command line tools for XCode 4.2.1
Thank you, but as I have mentioned already: the Preferences for Xcode 4.2.1 do not list Command Line Tools in the Install window. Best regards, Christian On 4/16/13 9:20 PM, Roy Mendelssohn - NOAA Federal wrote: Hi: The command line tools can be installed once you have Xcode by stating Xcode, going to Preference in the File menu and then there is a Download option. That is where you can install the CLI. You may have to give a terminal command the first time to point to it once installed - I would shave to look that up - I know this had to be done for Fink. HTH, -Roy M. On Apr 16, 2013, at 12:13 PM, cstrato cstr...@aon.at wrote: Dear Simon, On your developer site you mention: We use Xcode 4.2 but Xcode 3.2 and higher should work as well. Note that you will need Command Line Tools component of Xcode on Mac OS X 10.7 or higher. I am running OS X 10.7.5 and XCode 4.2.1 on my Mac, but have not downloaded the command line tools. My questions are: - why do I need the command line tools? - which version do I need to download from: https://developer.apple.com/downloads/index.action There are e.g. - Command Line Tools (OS X Lion) for Xcode - October 2012 (it is not mentioned which version of Xcode) - Command Line Tools (OS X Lion) for Xcode - November 2012 (Xcode 4.3 is mentioned but it is nor clear if it works with 4.2.1) - Command Line Tools (OS X Lion) for Xcode - April 2013 (Xcode 4.6.2 is mentioned but it is nor clear if it works with 4.2.1) (BTW, the Preferences for Xcode 4.2.1 do not list Command Line Tools in the Install window.) - do the Command Line Tools update clang/clang++? The reason for my question is that in order to compile the C++ code in my package with clang I need at least version 3.1 since 3.0 results in an error. Best regards, Christian ___ 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 1352 Lighthouse Avenue Pacific Grove, CA 93950-2097 e-mail: roy.mendelss...@noaa.gov (Note new e-mail address) voice: (831)-648-9029 fax: (831)-648-8440 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. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Which command line tools for XCode 4.2.1
Dear Simon, Thank you for your explanation, and see below. Best regards, Christian On 4/16/13 9:30 PM, Simon Urbanek wrote: On Apr 16, 2013, at 3:13 PM, cstrato wrote: Dear Simon, On your developer site you mention: We use Xcode 4.2 but Xcode 3.2 and higher should work as well. Note that you will need Command Line Tools component of Xcode on Mac OS X 10.7 or higher. I am running OS X 10.7.5 and XCode 4.2.1 on my Mac, but have not downloaded the command line tools. My questions are: - why do I need the command line tools? Because Xcode no longer installs compilers, linkers etc. in the system, so you won't be able to run them. It seems that my version of Xcode 4.2.1 does have all compilers installed, including clang, but version 3.0: $ clang -v Apple clang version 3.0 (tags/Apple/clang-211.12) (based on LLVM 3.0svn) Target: x86_64-apple-darwin11.4.2 - which version do I need to download from: https://developer.apple.com/downloads/index.action There are e.g. - Command Line Tools (OS X Lion) for Xcode - October 2012 (it is not mentioned which version of Xcode) - Command Line Tools (OS X Lion) for Xcode - November 2012 (Xcode 4.3 is mentioned but it is nor clear if it works with 4.2.1) - Command Line Tools (OS X Lion) for Xcode - April 2013 (Xcode 4.6.2 is mentioned but it is nor clear if it works with 4.2.1) It doesn't really matter (it may matter in the future, because Apple has announced that they'll be removing llvm-gcc from Xcode) - latest should be fine for now. The version is independent of your Xcode -- in fact if you download it by hand, you don't even need Xcode at all. (BTW, the Preferences for Xcode 4.2.1 do not list Command Line Tools in the Install window.) I'm not sure what you mean by Install window, but as Roy said, you'll find it in the download section of the preferences. When I open the Preferences and go to the download section I see a checkbox Check for and install updates automatically, and below the list of items, which are: - iOS 4.3 Simulator (499.2 MB) - iOS 4.0 - 4.1 Device Debugging Support (505.1 MB) - iOS 3.0 - 3.2.2 Device Debugging Support (686.3 MB) None of these three items do I want to install since the download would be 1.7 GB and my internet connection is not very fast. - do the Command Line Tools update clang/clang++? Yes This is good news. The reason for my question is that in order to compile the C++ code in my package with clang I need at least version 3.1 since 3.0 results in an error. You'll need to tweak your local ~/.R/Makevars for that to work since CRAN's R uses llvm-gcc. This seems not to be possible since then I cannot compile my C++ code at all. It seems to interfere with the ROOT framework compiled with clang and does not find an include file. My Makefile depends on the ROOT config file. Cheers, Simon ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Which command line tools for XCode 4.2.1
Dear Roy, Thank you for this info. It seems that only the versions of Xcode which you download from the AppStore need the Command Line Tools installed. Nevertheless, in order to install a new version of clang I need to install the CLTs. Best regards, Christian On 4/16/13 9:51 PM, Roy Mendelssohn - NOAA Federal wrote: My apologies, I didn't notice carefully that you were using Xcode 4.2.1. But Google is your friend, Apple has changed the name of what you need to download, see: http://comments.gmane.org/gmane.os.apple.macports.user/26340 HTH. -Roy On Apr 16, 2013, at 12:44 PM, cstrato cstr...@aon.at wrote: Dear Simon, Thank you for your explanation, and see below. Best regards, Christian On 4/16/13 9:30 PM, Simon Urbanek wrote: On Apr 16, 2013, at 3:13 PM, cstrato wrote: Dear Simon, On your developer site you mention: We use Xcode 4.2 but Xcode 3.2 and higher should work as well. Note that you will need Command Line Tools component of Xcode on Mac OS X 10.7 or higher. I am running OS X 10.7.5 and XCode 4.2.1 on my Mac, but have not downloaded the command line tools. My questions are: - why do I need the command line tools? Because Xcode no longer installs compilers, linkers etc. in the system, so you won't be able to run them. It seems that my version of Xcode 4.2.1 does have all compilers installed, including clang, but version 3.0: $ clang -v Apple clang version 3.0 (tags/Apple/clang-211.12) (based on LLVM 3.0svn) Target: x86_64-apple-darwin11.4.2 - which version do I need to download from: https://developer.apple.com/downloads/index.action There are e.g. - Command Line Tools (OS X Lion) for Xcode - October 2012 (it is not mentioned which version of Xcode) - Command Line Tools (OS X Lion) for Xcode - November 2012 (Xcode 4.3 is mentioned but it is nor clear if it works with 4.2.1) - Command Line Tools (OS X Lion) for Xcode - April 2013 (Xcode 4.6.2 is mentioned but it is nor clear if it works with 4.2.1) It doesn't really matter (it may matter in the future, because Apple has announced that they'll be removing llvm-gcc from Xcode) - latest should be fine for now. The version is independent of your Xcode -- in fact if you download it by hand, you don't even need Xcode at all. (BTW, the Preferences for Xcode 4.2.1 do not list Command Line Tools in the Install window.) I'm not sure what you mean by Install window, but as Roy said, you'll find it in the download section of the preferences. When I open the Preferences and go to the download section I see a checkbox Check for and install updates automatically, and below the list of items, which are: - iOS 4.3 Simulator (499.2 MB) - iOS 4.0 - 4.1 Device Debugging Support (505.1 MB) - iOS 3.0 - 3.2.2 Device Debugging Support (686.3 MB) None of these three items do I want to install since the download would be 1.7 GB and my internet connection is not very fast. - do the Command Line Tools update clang/clang++? Yes This is good news. The reason for my question is that in order to compile the C++ code in my package with clang I need at least version 3.1 since 3.0 results in an error. You'll need to tweak your local ~/.R/Makevars for that to work since CRAN's R uses llvm-gcc. This seems not to be possible since then I cannot compile my C++ code at all. It seems to interfere with the ROOT framework compiled with clang and does not find an include file. My Makefile depends on the ROOT config file. Cheers, Simon ___ 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 1352 Lighthouse Avenue Pacific Grove, CA 93950-2097 e-mail: roy.mendelss...@noaa.gov (Note new e-mail address) voice: (831)-648-9029 fax: (831)-648-8440 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. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
