Re: [Fink-users] xcode issue with fink?
On Jun 10, 2015, at 04:14, Alan alanwil...@gmail.com wrote: Trying to update my fink and I found this: Can't resolve dependency xcode.app (= 5.1.1) for package qt5-mac-enginio-5.4.2-2 (no matching packages/versions found) — xcode-select version 2339. fink -V Package manager version: 0.38.5 Distribution version: selfupdate-rsync Wed Jun 10 12:11:30 2015, 10.10, x86_64 Trees: local/main stable/main stable/crypto Mac OS X 10.10.3 Thanks, Alan -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494588 ——— “xcode-select —version” isn’t very informative. What do “xcode-select --print-path” and “fink list xcode.app” give? -- Alexander Hansen, Ph.D. Fink User Liaison -- ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] xcode issue with fink?
Trying to update my fink and I found this: Can't resolve dependency xcode.app (= 5.1.1) for package qt5-mac-enginio-5.4.2-2 (no matching packages/versions found) — xcode-select version 2339. fink -V Package manager version: 0.38.5 Distribution version: selfupdate-rsync Wed Jun 10 12:11:30 2015, 10.10, x86_64 Trees: local/main stable/main stable/crypto Mac OS X 10.10.3 Thanks, Alan -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494588 -- ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] x11 issue with fink?
On Jun 10, 2015, at 04:30, Alan alanwil...@gmail.com wrote: Trying to update my fink in another Mac that has full xcode.app installed and I found this: Information about 1 packages read in 2 seconds. Can't resolve dependency x11-shlibs for package matplotlib-py27-1.4.3-1 (no matching packages/versions found) Exiting with failure. — x11 XQuartz 2.7.7 (xorg-server 1.15.2) xcode-select version 2339. fink -V Package manager version: 0.38.5 Distribution version: selfupdate-rsync Wed Jun 10 12:11:30 2015, 10.10, x86_64 Trees: local/main stable/main stable/crypto Mac OS X 10.10.3 Thanks, Alan -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494588 ——— I can’t read your machine’s history from here, but I expect that you lost the /usr/X11R6 and /usr/X11 convenience symlinks when you updated the OS on that machine. The Xquartz developers recommend that you reinstall Xquartz after updating the OS, so do that. -- Alexander Hansen, Ph.D. Fink User Liaison -- ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] xcode issue with fink?
Thanks Alexander and Haspeter! Now, I could live without qt5, but apparently matplotlib depends on it now. Oh well, so I have to install the whole xcode just for MPL… Alan On 10 June 2015 at 12:36, Hanspeter Niederstrasser f...@snaggledworks.com wrote: On 6/10/2015 6:14 AM, Alan wrote: Trying to update my fink and I found this: Can't resolve dependency xcode.app (= 5.1.1) for package qt5-mac-enginio-5.4.2-2 (no matching packages/versions found) — xcode-select version 2339. fink -V Package manager version: 0.38.5 Distribution version: selfupdate-rsync Wed Jun 10 12:11:30 2015, 10.10, x86_64 Trees: local/main stable/main stable/crypto Qt5 needs Xcode.app, not just the command line tools, to build. You need to get the full Xcode package from either the App Store or developer.apple.com. For 10.10, you want Xcode 6.3.2, and make sure that your command line tools are updated to match this version with 'xcode-select --install'. Hanspeter -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494588 -- ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] x11 issue with fink?
Trying to update my fink in another Mac that has full xcode.app installed and I found this: Information about 1 packages read in 2 seconds. Can't resolve dependency x11-shlibs for package matplotlib-py27-1.4.3-1 (no matching packages/versions found) Exiting with failure. — x11 XQuartz 2.7.7 (xorg-server 1.15.2) xcode-select version 2339. fink -V Package manager version: 0.38.5 Distribution version: selfupdate-rsync Wed Jun 10 12:11:30 2015, 10.10, x86_64 Trees: local/main stable/main stable/crypto Mac OS X 10.10.3 Thanks, Alan -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494588 -- ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] xcode issue with fink?
On 6/10/2015 6:14 AM, Alan wrote: Trying to update my fink and I found this: Can't resolve dependency xcode.app (= 5.1.1) for package qt5-mac-enginio-5.4.2-2 (no matching packages/versions found) — xcode-select version 2339. fink -V Package manager version: 0.38.5 Distribution version: selfupdate-rsync Wed Jun 10 12:11:30 2015, 10.10, x86_64 Trees: local/main stable/main stable/crypto Qt5 needs Xcode.app, not just the command line tools, to build. You need to get the full Xcode package from either the App Store or developer.apple.com. For 10.10, you want Xcode 6.3.2, and make sure that your command line tools are updated to match this version with 'xcode-select --install'. Hanspeter -- ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] GUI - start?
On Jun 9, 2015, at 11:11 PM, Sunil Shah ssha...@gmail.com wrote: On Tue, Jun 9, 2015 at 7:00 PM, Alexander Hansen alexanderk.han...@gmail.com mailto:alexanderk.han...@gmail.com wrote: On Jun 9, 2015, at 18:48, Sunil Shah ssha...@gmail.com mailto:ssha...@gmail.com wrote: I should have been careful in my statement about what worked for me. I am trying to understand the problem you referred to about octave 4.0.0 not building on clang++. I have been quite impressed with the performance of Octave code on Mac OSX using fink. My tests used octave382-atlas-qtmac 3.8.2-6. It has also been quite reliable. The fact that the code works much faster on four year old hardware with a lot fewer cpu cores and even after using the latest Ubuntu tools / libraries on the high end Intel machines on EC2 is remarkable. Apple does claim that its Accelerate framework is much faster than standard BLAS / ATLAS. A lot of the improvements were part of 10.9 / 10.10 update (see WWDC 2013-2014 videos). I will check if the default octave performs faster than the octave-atlas version. Now, as you imply in your last email, if the default octave variant uses clang already, what is the issue with octave 4.0.0 and clang++? Or is it a new issue in octave 4.0.0 in moving from 3.8.2? Almost everything in Fink uses clang/clang++ to build on 10.7 and later. I don’t happen to have a transcript handy, but it’s a new issue in moving from 3.8.2, and the issue is that Apple’s clang doesn’t like some of the source code and thus Octave can’t be built. — I suppose it does not help that Apple is moving over to Metal from OpenGL. Do the offending modules have to do with OpenGL? No. The problem is with clang syntax. It is possible to overcome by patching Octave (beyond my skill set) or by fixing the clang compiler bug(s) on Apple’s end. OpenGL is the basis for Octave’s native graphics. My understanding is that both Metal and OpenGL support will coexist. So Metal shouldn’t be a problem for Octave. Ben -- ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] x11 issue with fink?
Thanks Alexander, it worked as you said. Alan On 10 June 2015 at 12:36, Alexander Hansen alexanderk.han...@gmail.com wrote: On Jun 10, 2015, at 04:30, Alan alanwil...@gmail.com wrote: Trying to update my fink in another Mac that has full xcode.app installed and I found this: Information about 1 packages read in 2 seconds. Can't resolve dependency x11-shlibs for package matplotlib-py27-1.4.3-1 (no matching packages/versions found) Exiting with failure. — x11 XQuartz 2.7.7 (xorg-server 1.15.2) xcode-select version 2339. fink -V Package manager version: 0.38.5 Distribution version: selfupdate-rsync Wed Jun 10 12:11:30 2015, 10.10, x86_64 Trees: local/main stable/main stable/crypto Mac OS X 10.10.3 Thanks, Alan -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494588 ——— I can’t read your machine’s history from here, but I expect that you lost the /usr/X11R6 and /usr/X11 convenience symlinks when you updated the OS on that machine. The Xquartz developers recommend that you reinstall Xquartz after updating the OS, so do that. -- Alexander Hansen, Ph.D. Fink User Liaison -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494588 -- ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] GUI - start?
I suppose it does not help that Apple is moving over to Metal from OpenGL. Do the offending modules have to do with OpenGL? On Tue, Jun 9, 2015 at 7:00 PM, Alexander Hansen alexanderk.han...@gmail.com wrote: On Jun 9, 2015, at 18:48, Sunil Shah ssha...@gmail.com wrote: I should have been careful in my statement about what worked for me. I am trying to understand the problem you referred to about octave 4.0.0 not building on clang++. I have been quite impressed with the performance of Octave code on Mac OSX using fink. My tests used octave382-atlas-qtmac 3.8.2-6. It has also been quite reliable. The fact that the code works much faster on four year old hardware with a lot fewer cpu cores and even after using the latest Ubuntu tools / libraries on the high end Intel machines on EC2 is remarkable. Apple does claim that its Accelerate framework is much faster than standard BLAS / ATLAS. A lot of the improvements were part of 10.9 / 10.10 update (see WWDC 2013-2014 videos). I will check if the default octave performs faster than the octave-atlas version. Now, as you imply in your last email, if the default octave variant uses clang already, what is the issue with octave 4.0.0 and clang++? Or is it a new issue in octave 4.0.0 in moving from 3.8.2? Almost everything in Fink uses clang/clang++ to build on 10.7 and later. I don’t happen to have a transcript handy, but it’s a new issue in moving from 3.8.2, and the issue is that Apple’s clang doesn’t like some of the source code and thus Octave can’t be built. -- Alexander Hansen, Ph.D. Fink User Liaison -- ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] GUI - start?
On Jun 10, 2015, at 16:05, Sunil Shah ssha...@gmail.com wrote: Is there a link to the clang syntax bug(s) in the Octave / fink forums? Ben sent me this, and I’ll cc our mailing list http://savannah.gnu.org/bugs/?41178 http://savannah.gnu.org/bugs/?41178 If Apple needs to address the bug, has any one filed a bug report to Apple? Apple's Xcode 7 (pre-release) did fix some bugs. I haven’t. My Mac development time has recently been more devoted to updating the fink code than on the packages that I’m the listed maintainer for. -- Alexander Hansen, Ph.D. Fink User Liaison -- ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] GUI - start?
On Jun 10, 2015, at 9:35 PM, Sunil Shah ssha...@gmail.com wrote: On Wed, Jun 10, 2015 at 4:10 PM, Alexander Hansen alexanderk.han...@gmail.com mailto:alexanderk.han...@gmail.com wrote: On Jun 10, 2015, at 16:05, Sunil Shah ssha...@gmail.com mailto:ssha...@gmail.com wrote: Is there a link to the clang syntax bug(s) in the Octave / fink forums? Ben sent me this, and I’ll cc our mailing list http://savannah.gnu.org/bugs/?41178 http://savannah.gnu.org/bugs/?41178 If Apple needs to address the bug, has any one filed a bug report to Apple? Apple's Xcode 7 (pre-release) did fix some bugs. I haven’t. My Mac development time has recently been more devoted to updating the fink code than on the packages that I’m the listed maintainer for. Per Michael Grant's comments in the octave bug report, this is a non-compliant (illegal) C11++ construct in octave code (but happens to work in gcc and MSVC). We can not ask Apple to fix it. Octave community needs fix the illegal construct. As the majority of Octave’s development community works with gcc clang on Linux, and are able to build Octave without. So, there is little motive for Octave’s developers to fix the problem. I am not proficient in clang/c++ but am willing to contribute to fixing Octave’s source code. I have no problem arranging for testing of patches and converting patches to the necessary mercurial changesets and ultimately pushing the changes. I may also be able to assist in fixing the syntax issues, but will need clear instructions with some illustrative examples. If anyone is interested in fixing the incompatibilities between Octave and Apple’s clang let me know. I can provide instructions on how to set up your own personal archive and instructions on how to build Octave 3.8.2. That should be sufficient to allow individuals to attempt to compile Octave 4.0 and start fixing the clang non-compliant code. Ben-- ___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
