[Fink-users] Got a suspicious phishing email
Hi, I am just checking if the list is ok because I got a suspicious email: -- Hi fink-users@lists.sourceforge.net, Please note your account would be temporarily locked due to some certain updates with your server. Kindly *Click here* to unlock and continue your free usage by verifying you are the owner of this account. Ignorance will lead to temporary suspension of your service provision NOTE: This is a one time user verification carried out in purpose to provide a more secured platform and shut down robot or malicious users created in purpose of spamming and other fraudulent activities. Best, (C) 2017 Mail. All rights reserved. NMLSR ID 399801 -- The '*Click here*' link raised a warning in my Gmail account and Antivirus detector. Thanks, Alan -- Alan Wilter SOUSA da SILVA, DSc Senior 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 -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ Fink-users mailing list Fink-users@lists.sourceforge.net List archive: https://sourceforge.net/p/fink/mailman/fink-users/ Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] About libmagic
Many thanks! I thought apt-cache search would work too. But great to know about the site. Alan On 5 October 2016 at 00:53, Alexander Hansen <alexanderk.han...@gmail.com> wrote: > > > On Oct 4, 2016, at 15:55, Alan <alanwil...@gmail.com> wrote: > > > > I am wondering if it ever existed in Fink. I need libmagic.so and > magic.h. > > > > Using Mac Sierra and latest Fink. > > > > Thanks, > > > > Alan > > > > -- > > Alan Wilter SOUSA da SILVA, DSc > > Senior 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 > > ——— > > Well, libmagic.so probably shouldn’t exist on OS X, unless it’s a plugin > rather than a proper library. There’s a file search function on the Fink > webpage: > > http://pdb.finkproject.org/pdb/filefind.php > > But, in this case, I’m assuming that what you want is from the “file” > package family: > > $ dpkg -L file-dev > /. > /sw > /sw/include > /sw/include/magic.h > /sw/lib > /sw/lib/libmagic.a > /sw/lib/libmagic.la > /sw/share > /sw/share/man > /sw/share/man/man3 > /sw/share/man/man3/libmagic.3 > /sw/lib/libmagic.dylib > > Fionna-4:~ hansen$ dpkg -L file-shlibs > /. > /sw > /sw/lib > /sw/lib/libmagic.1.dylib > > (those really needs to have COPYING documents, if the maintainer happens > to read this) > > —Alex > > -- Alan Wilter SOUSA da SILVA, DSc Senior 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 -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ 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] About libmagic
I am wondering if it ever existed in Fink. I need libmagic.so and magic.h. Using Mac Sierra and latest Fink. Thanks, Alan -- Alan Wilter SOUSA da SILVA, DSc Senior 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 -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ 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] openssl failed on a Mac with Sierra and case-sensitive filesystem
I did pretty the modification as seen in the patch, but manually and it
worked.
Many thanks,
Alan
On 3 October 2016 at 18:17, Derek Homeier <
de...@astro.physik.uni-goettingen.de> wrote:
> On 3 Oct 2016, at 12:14 pm, Alan <alanwil...@gmail.com> wrote:
> >
> > However, can you be more specific please? I see only uppercase and even
> if I create the lowercase symlinks, if I run "fink install openssl" the
> folder is cleared again and I get the usual error.
> >
> I had just reported this on the developers’ list; does this patch fix the
> error for you?
>
> diff -Nurd /sw/fink/10.9-libcxx/{stable,local}/main/finkinfo/crypto/op
> enssl110-dev.info
> --- /sw/fink/10.9-libcxx/stable/main/finkinfo/crypto/openssl110-dev.info
> 2016-09-27 00:54:14.0 +0200
> +++ /sw/fink/10.9-libcxx/local/main/finkinfo/crypto/openssl110-dev.info
> 2016-09-27 16:45:56.0 +0200
> @@ -80,7 +80,7 @@
>
> ### for comptibility with libmd (don't know how to set up
> ## update-alternatives with original capitalisation).
> - mv %i/share/man/man3/md5.3 %i/share/man/man3/md5.3.openssl100
> + mv %i/share/man/man3/MD5.3 %i/share/man/man3/md5.3.openssl100
> for i in 2 4; do
> rm %i/share/man/man3/MD$i.3
> cp %i/share/man/man3/md5.3.openssl100 %i/share/man/man3/md$i.3.
> openssl100
>
>
> Cheers,
> Derek
>
>
--
Alan Wilter SOUSA da SILVA, DSc
Senior 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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot___
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Re: [Fink-users] Error in installing guile20
Thanks for the explanation! Alan On 3 October 2016 at 18:23, Derek Homeier < de...@astro.physik.uni-goettingen.de> wrote: > Hi Alan, > > On 2 Oct 2016, at 9:03 pm, Alan <alanwil...@gmail.com> wrote: > > > > Weird, I used Jack's files and it worked on Sierra. Fighting now to get > openssl (another email submitted). > > the patch failure seemed to be related to a broken installation of the > Command Line Tools, > fixed after I redid the OS update to Sierra (discussed offline with Jack). > With the clean 10.12 CLT the patch works, but Jack’s alternative > suggestion to configure with > ac_cv_func_clock_gettime=no solves the build failure as well. > > Cheers, > Derek > > > -- Alan Wilter SOUSA da SILVA, DSc Senior 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 -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ 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] openssl failed on a Mac with Sierra and case-sensitive filesystem
Hi Schindler, thanks for your help. However, can you be more specific please? I see only uppercase and even if I create the lowercase symlinks, if I run "fink install openssl" the folder is cleared again and I get the usual error. So, which steps did you do exactly to get openssl to install? Many thanks in advance, Alan On 3 October 2016 at 10:03, Schindler Karl-Michael < karl-michael.schind...@web.de> wrote: > > > Am 02.10.2016 um 21:03 schrieb fink-users-requ...@lists.sourceforge.net: > > > > Date: Sun, 2 Oct 2016 00:07:27 +0100 > > From: Alan <alanwil...@gmail.com> > > Subject: [Fink-users] openssl failed on a Mac with Sierra and > case-sensitive filesystem > > To: <fink-users@lists.sourceforge.net> > > Cc: Daniel Johnson <dan...@daniel-johnson.org> > > Message-ID:
Re: [Fink-users] Error in installing guile20
Weird, I used Jack's files and it worked on Sierra. Fighting now to get openssl (another email submitted). Many thanks, Alan On 1 October 2016 at 02:41, Derek Homeier < de...@astro.physik.uni-goettingen.de> wrote: > Jack, > > > On 30 Sep 2016, at 8:23 pm, Jack Howarth <howarth.at.f...@gmail.com> > wrote: > > > > Does the attached guile20 packaging for the 2.0.12 release work? > Both MacPorts and Homebrew are building on Sierra with the same patch using > the 2.0.12 release. > > Jack > > ps This packaging works fine here on El Capitan with Xcode 8.1 beta > (don't have hardware for Sierra). > > > got my MacBook upgraded to Sierra now, and now the build in fact defaults > to ac_cv_func_clock_gettime=yes, > which fails again with > > CC libguile_2.0_la-stime.lo > ../../libguile/stime.c:119:3: warning: implicit declaration of function > 'clock_gettime' is invalid in C99 [-Wimplicit-function-declaration] > clock_gettime (CLOCK_REALTIME, ); > ^ > ../../libguile/stime.c:119:18: error: use of undeclared identifier > 'CLOCK_REALTIME' > clock_gettime (CLOCK_REALTIME, ); > ^ > ../../libguile/stime.c:828:22: error: use of undeclared identifier > 'CLOCK_REALTIME' > if (clock_gettime (CLOCK_REALTIME, _real_time_base) == 0) > > Adding ac_cv_func_clock_gettime=no to ConfigParams instead lets the build > succeed. > I am a bit confused about my Xcode installation now, though, because after > the failure > with the first variant fink tells me: > > Also include the following system information: > Package manager version: 0.41.0 > Distribution version: selfupdate-rsync Fri Sep 30 23:54:16 2016, 10.12, > x86_64 > Trees: stable/main local/main local/injected unstable/main > Xcode.app: 8.0 > Xcode command-line tools: 7.3.1.0.1.1461711523 > Max. Fink build jobs: 1 > > However according to AppStore I have installed both the update to > “Command Line Tools (OS X 10.11) for Xcode Version 7.3” and > “Command Line Tools (macOS Sierra version 10.12) for Xcode Version 8.0” > > and gcc -v > Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr > --with-gxx-include-dir=/usr/include/c++/4.2.1 > Apple LLVM version 8.0.0 (clang-800.0.38) > > xcode-select does not offer any useful options here. > > I should perhaps also note that updating llvm-gcc42 failed with this > rather nondescriptive error: > > Adding multilib support to Makefile in /scratch.noindex/fink.build/ > llvm-gcc42-2336.11-37/objroot/src/libiberty > with_multisubdir=i386 > make[2]: *** [all] Error 2 > + exit 1 > make[1]: *** [llvmgcc42] Error 1 > make: *** [install] Error 2 > > > Anyway, with just the modified ConfigParams guile20 seems to work both on > El Capitan and Sierra, > and I was also able to rebuild ffmpeg with the new guile20 installed… > > Cheers, > Derek > > > > On Fri, Sep 30, 2016 at 10:30 AM, Derek Homeier <de...@astro.physik.uni- > goettingen.de> wrote: > > On 30 Sep 2016, at 12:02 pm, Alan <alanwil...@gmail.com> wrote: > > > > > > Well, I gave a try, I copied from stable to local and appended > > > > > > /sw/fink/dists/local/main/finkinfo/languages/guile20.patch > > > > > > with lines from https://gist.github.com/rahulg/ > baa500e84136f0965e9ade2fb36b90ba > > > > > > but, alas, it didn't work. > > > > > That patch file is outdated and no longer used; you'd need to replace it > completely with the new > > patch and then modify the info file to use it again in the internal > patch script it is using now. > > But note that this issue has been discussed on the list before: > > > > > On 15 Aug 2016, at 8:35 pm, Jack Howarth <howarth.at.f...@gmail.com> > wrote: > > > > > > Alternatively, rather than applying that ugly unreviewed patch, we > could probably just pass ac_cv_func_clock_gettime=no to configure to avoid > the new system calls until upstream catches up with the deviations in the > Mac OS X implementation. > > >Jack > > -- Alan Wilter SOUSA da SILVA, DSc Senior 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 -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ 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] openssl failed on a Mac with Sierra and case-sensitive filesystem
Hi there, I always had case-sensitive filesystem, but since I am installing Fink from scratch on a Mac with Sierra, I am not sure if the error reported below is really due to a case-sensitive filesystem. ... ## skipped-links contains symlink commands that fail because they ## would involve filenames that differ only by case (rebuild on a ## case-insensitive filesystem to make sure the list is complete). ## as of 1.0.0k-3, the list is: ## ln -s "bn_internal.3" "bn_print.3" # created iff build on case-sens fs ## ln -s "hmac.3" "HMAC.3"# not created anywhere ## ln -s "md5.3" "MD5.3" # not created anywhere ## ln -s "mdc2.3" "MDC2.3"# not created anywhere ## ln -s "pem.3" "PEM.3" # not created anywhere ## ln -s "rc4.3" "RC4.3" # not created anywhere ## ln -s "ssl.3" "SSL.3" # not created anywhere ## i.e., those symlink names already exist as something else. ## Should patch build to avoid even trying to create these so get ## same .deb on all build FS even without hacks. ## There remain symlinks BN_print.3 -> BN_bn2bin.3 and bn_print.3 -> bn_internal.3, we rename the latter. rm -f /sw/src/fink.build/root-openssl110-dev-1.1.0a-1/sw/share/man/man3/BN_print.3 /sw/src/fink.build/root-openssl110-dev-1.1.0a-1/sw/share/man/man3/bn_print.3 || true ln -fs BN_bn2bin.3 /sw/src/fink.build/root-openssl110-dev-1.1.0a-1/sw/share/man/man3/BN_print.3 ln -fs bn_internal.3 /sw/src/fink.build/root-openssl110-dev-1.1.0a-1/sw/share/man/man3/_bn_print.3 ### for comptibility with libmd (don't know how to set up ## update-alternatives with original capitalisation). mv /sw/src/fink.build/root-openssl110-dev-1.1.0a-1/sw/share/man/man3/md5.3 /sw/src/fink.build/root-openssl110-dev-1.1.0a-1/sw/share/man/man3/md5.3.openssl100 mv: cannot stat '/sw/src/fink.build/root-openssl110-dev-1.1.0a-1/sw/share/man/man3/md5.3': No such file or directory ### execution of /tmp/fink.7p4Nh failed, exit code 1 ### execution of /tmp/fink.rCSzT failed, exit code 1 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-openssl110-dev-1.1.0a-1 (Reading database ... 232976 files and directories currently installed.) Removing fink-buildlock-openssl110-dev-1.1.0a-1 ... Failed: phase installing: openssl110-dev-1.1.0a-1 failed Package manager version: 0.41.0 Distribution version: selfupdate-rsync Sat Oct 1 17:25:26 2016, 10.12, x86_64 Trees: local/main stable/main Xcode.app: 8.0 Xcode command-line tools: 8.0.0.0.1.1472435881 openssl110-dev-1.1.0a-1 is set to build with only one job. Thanks, Alan -- Alan Wilter SOUSA da SILVA, DSc Senior 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 -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ 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] Error in installing guile20
Well, I gave a try, I copied from stable to local and appended /sw/fink/dists/local/main/finkinfo/languages/guile20.patch with lines from https://gist.github.com/rahulg/ baa500e84136f0965e9ade2fb36b90ba but, alas, it didn't work. Alan On 30 September 2016 at 09:18, Alan <alanwil...@gmail.com> wrote: > Hi there, > > Same problem here. I know Fink has ways of patching files ... if pointed > how to do this, I can give a try. > > Thanks, > > Alan > > On 29 September 2016 at 16:41, Joakim Kjellsson < > joakim.kjells...@gmail.com> wrote: > >> Hi >> >> I’ve been trying to install ffmpeg via fink, which requires guile20. >> However, I run into the following error: >> >> */usr/include/stdio.h:277:7: **note: *'tmpnam' has been explicitly >> marked deprecated here >> char*tmpnam(char *); >> * ^* >> 1 warning generated. >> CC libguile_2.0_la-net_db.lo >> CC libguile_2.0_la-socket.lo >> CC libguile_2.0_la-regex-posix.lo >> CCLD libguile-2.0.la >> Undefined symbols for architecture x86_64: >> "_clock_getcpuclockid", referenced from: >> _scm_init_stime in libguile_2.0_la-stime.o >> ld: symbol(s) not found for architecture x86_64 >> clang: *error: *linker command failed with exit code 1 (use -v to see >> invocation) >> make[3]: *** [libguile-2.0.la] Error 1 >> make[2]: *** [all] Error 2 >> >> The specs are the following: >> Package manager version: 0.41.0 >> Distribution version: selfupdate-rsync Thu Sep 29 16:16:58 2016, 10.12, >> x86_64 >> Trees: local/main stable/main >> Xcode.app: 8.0 >> Xcode command-line tools: 8.0.0.0.1.1472435881 >> Max. Fink build jobs: 1 >> >> After some time on google I found that the bug is because Apple have >> changed something in a “clock” routine and that this patch >> https://gist.github.com/rahulg/baa500e84136f0965e9ade2fb36b90ba >> fixes it. >> However, I have no idea where to put this fix or if it could be put into >> the main version on fink. >> Any help here is much appreciated. >> >> All the best >> Joakim >> >> ---- >> -- >> >> ___ >> 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 >> >> > > > -- > Alan Wilter SOUSA da SILVA, DSc > Senior 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 > -- Alan Wilter SOUSA da SILVA, DSc Senior 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] Error in installing guile20
Hi there, Same problem here. I know Fink has ways of patching files ... if pointed how to do this, I can give a try. Thanks, Alan On 29 September 2016 at 16:41, Joakim Kjellsson <joakim.kjells...@gmail.com> wrote: > Hi > > I’ve been trying to install ffmpeg via fink, which requires guile20. > However, I run into the following error: > > */usr/include/stdio.h:277:7: **note: *'tmpnam' has been explicitly marked > deprecated here > char*tmpnam(char *); > * ^* > 1 warning generated. > CC libguile_2.0_la-net_db.lo > CC libguile_2.0_la-socket.lo > CC libguile_2.0_la-regex-posix.lo > CCLD libguile-2.0.la > Undefined symbols for architecture x86_64: > "_clock_getcpuclockid", referenced from: > _scm_init_stime in libguile_2.0_la-stime.o > ld: symbol(s) not found for architecture x86_64 > clang: *error: *linker command failed with exit code 1 (use -v to see > invocation) > make[3]: *** [libguile-2.0.la] Error 1 > make[2]: *** [all] Error 2 > > The specs are the following: > Package manager version: 0.41.0 > Distribution version: selfupdate-rsync Thu Sep 29 16:16:58 2016, 10.12, > x86_64 > Trees: local/main stable/main > Xcode.app: 8.0 > Xcode command-line tools: 8.0.0.0.1.1472435881 > Max. Fink build jobs: 1 > > After some time on google I found that the bug is because Apple have > changed something in a “clock” routine and that this patch > https://gist.github.com/rahulg/baa500e84136f0965e9ade2fb36b90ba > fixes it. > However, I have no idea where to put this fix or if it could be put into > the main version on fink. > Any help here is much appreciated. > > All the best > Joakim > > > -- > > ___ > 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 > > -- Alan Wilter SOUSA da SILVA, DSc Senior 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] Where to find fink_0.41.0-101_darwin-x86_64.deb ?
Trying to follow http://www.finkproject.org/download/10.12-upgrade.php?phpLang=en Thanks, Alan -- Alan Wilter SOUSA da SILVA, DSc Senior 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] Fink upgrade for Sierra
Yep, using Sierra and then I tried: fink reinstall fink Use 'fink reinstall fink' to switch distributions from 10.11 to 10.12. Information about 9827 packages read in 5 seconds. WARNING: your info file index has not been updated for 16 days. You should run 'fink selfupdate' to get the latest package descriptions. The following package will be reinstalled: fink Reading buildlock packages... /sw/bin/dpkg-lockwait -i /sw/var/cache/apt/archives/fink_0.39.5-101_darwin-x86%5f64.deb (Reading database ... 241941 files and directories currently installed.) Preparing to replace fink 0.39.5-101 (using .../fink_0.39.5-101_darwin-x86%5f64.deb) ... Unpacking replacement fink ... Setting up fink (0.39.5-101) ... Checking system... i386-apple-darwin16.0.0 Use of uninitialized value $gcc in regexp compilation at /sw/lib/perl5/Fink/Services.pm line 1364. Use of uninitialized value $gcc in concatenation (.) or string at /sw/lib/perl5/Fink/Bootstrap.pm line 164. This system was not released at the time this Fink release was made. Prerelease versions of Mac OS X might work with Fink, but there are no guarantees. Use of uninitialized value $distroot in string eq at /sw/lib/fink/ postinstall.pl line 164. Use of uninitialized value $distroot in concatenation (.) or string at /sw/lib/fink/postinstall.pl line 196. ln -s /sw/fink/10.12 Use of uninitialized value $distroot in concatenation (.) or string at /sw/lib/fink/postinstall.pl line 203. ln -s 10.12 /sw/fink/dists Use of uninitialized value $selfupdatetree in concatenation (.) or string at /sw/lib/fink/postinstall.pl line 236. /bin/mkdir -p /sw/fink/dists/local/injected/finkinfo/update-packages mkdir: /sw/fink/dists/local/injected/finkinfo/update-packages: Not a directory ### execution of /bin/mkdir failed, exit code 1 ERROR: couldn't create directory /sw/fink/dists/local/injected/finkinfo/update-packages /sw/bin/dpkg: error processing fink (--install): subprocess post-installation script returned error exit status 1 Errors were encountered while processing: fink ### execution of /sw/bin/dpkg-lockwait failed, exit code 1 Failed: can't install package fink-0.39.5-101 Is there a remedy or should I install Fink from scratch again? Many thanks, Alan -- Alan Wilter SOUSA da SILVA, DSc Senior 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] I need npm, which fink package to install?
Thanks Alexander On 20 July 2016 at 17:46, Alexander Hansen <alexanderk.han...@gmail.com> wrote: > > > > On Jul 20, 2016, at 08:44, Alan <alanwil...@gmail.com> wrote: > > > > Thanks Alexander, > > > > So no 'npm' in Fink, right? > > > > Right. As best as I can tell, we’ve never had it. > > > > -- Alan Wilter SOUSA da SILVA, DSc Senior 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 -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev___ 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] I need npm, which fink package to install?
Thanks Alexander, So no 'npm' in Fink, right? On 20 July 2016 at 17:41, Alexander Hansen <alexanderk.han...@gmail.com> wrote: > > > On Jul 20, 2016, at 07:57, Alan <alanwil...@gmail.com> wrote: > > > > I see several node... > > > > Which one would contain npm? > > > > Thanks, > > > > Alan > > > > -- > > Alan Wilter SOUSA da SILVA, DSc > > Senior 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 > > ——— > > None of them. > > -- Alan Wilter SOUSA da SILVA, DSc Senior 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 -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev___ 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] I need npm, which fink package to install?
I see several node... Which one would contain npm? Thanks, Alan -- Alan Wilter SOUSA da SILVA, DSc Senior 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 -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev___ 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 7.1
I got this message after updating to Xcode 7.1: WARNING: Xcode.app version (7.1) and Xcode Command Line Tools version (7.0) I can’t find a way of updating command line. Thanks, Alan -- Alan Wilter SOUSA da SILVA, DSc Senior 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 7.1
I have 10.11 (not 10.11.1 yet). I will wait my fink finishes updating (taking ages as it has to compile from source) and then I will do the upgrade to 10.11.1 and again fink update. In another iMac, where everything is updated, I didn’t have this issue. Thanks, Alan On 22 October 2015 at 13:40, Alexander Hansen <alexanderk.han...@gmail.com> wrote: > > > On Oct 22, 2015, at 03:34, Alan <alanwil...@gmail.com> wrote: > > > > I got this message after updating to Xcode 7.1: > > > > WARNING: Xcode.app version (7.1) and Xcode Command Line Tools version > (7.0) > > > > I can’t find a way of updating command line. > > > > Thanks, > > > > Alan > > > > > > > > -- > > Alan Wilter SOUSA da SILVA, DSc > > Senior 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 > > What OS version? On 10.11 I had the updated command-line tools show up in > the App Store at the same time as the 10.11.1 update and the Xcode 7.1 > update. > > Try “sudo xcode-select --install” > > -- > Alexander Hansen, Ph.D. > Fink User Liaison > > -- Alan Wilter SOUSA da SILVA, DSc Senior 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] command line tools in El Capitan
Use App Store, search Xcode. Download it. Then start Xcode app, accept the T Cmd lines should be installed. I am afraid one cannot use Fink anymore without full Xcode installation. Alan On 2 October 2015 at 16:47, PNM <p...@minoofar.com> wrote: > I get this error from xcodebuild: > xcodebuild: error: invalid option '—install' > > I’m denied access to the link below because, the error says, I haven’t > agreed to the terms of service or I don’t have access to this resource with > my free membership. > > Are the command line tools in beta, or is Apple requiring the annual $99 > payment to have access to this? > > It’s not showing up in the list of downloadable resources in my developer > account. I can download 10.10 command line tools for Xcode 7.1 beta, but > not 10.11. > > Well, at this point, it doesn’t seem like a fink problem, but your help is > appreciated. > > Payam > > > "The United States is a nation of laws: badly written and randomly > enforced." > Frank Zappa > > On Oct 2, 2015, at 08:24, Alexander Hansen <alexanderk.han...@gmail.com> > wrote: > > > > > On Oct 2, 2015, at 08:16, PNM <p...@minoofar.com> wrote: > > > > Where do you find command line tools? In the download tab of XCode > preferences, or in the downloads section the developer web site? I cannot > find it in either place. > > > > Thank you. > > > > Payam > > --- > > "Every science engenders some pseudo-science, inspiring eccentrics to > explore freakish by-ways; astronomy has its parodists in astrology, > chemistry used to have them in alchemy."--Stanislaw Lem, Solaris > > > > My recollection is that the ability download the command-line tools via > Xcode.app went away in 10.9. > > I see it in the downloads section of the developer web site. The URL > shows up as: > > > http://adcdownload.apple.com/Developer_Tools/Command_Line_Tools_OS_X_10.11_for_Xcode_7/Command_Line_Tools_OS_X_10.11_for_Xcode_7.dmg > > > You might also try “sudo xcodebuild --install” and see what that does. > > -- > 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 > > -- 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] 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] 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] 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
[Fink-users] where’s /sw/bin/ls ?
I finally had to upgrade to Yosemite, did a clean Fink install (all fine), but alas, I have now idea which package installs /sw/bin/ls. 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 -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://pubads.g.doubleclick.net/gampad/clk?id=154624111iu=/4140/ostg.clktrk___ 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] aria2c missing lib
aria2c ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/RELEASE.metalink dyld: Library not loaded: /sw/lib/libnettle.4.dylib Referenced from: /sw/bin/aria2c Reason: image not found [1]37315 trace trap aria2c Then I did fink install nettle4a-shlibs and this sorted the issue. Package manager version: 0.37.0 Distribution version: selfupdate-rsync Wed Jul 9 13:36:10 2014, 10.9, x86_64 Trees: local/main stable/main -- 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 -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft___ 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] Issue with xcode
This issue re-emerged again: Information about 10048 packages read in 2 seconds. Can't resolve dependency xcode.app (= 4.6) for package kde4-buildenv-4.13.1-1 (no matching packages/versions found) Exiting with failure. Package manager version: 0.37.0 Distribution version: selfupdate-rsync Wed Jul 2 19:08:46 2014, 10.9, x86_64 Trees: local/main stable/main And now I have fink bin diet enabled. Thanks, Alan On 2 June 2014 16:09, Alan alanwil...@gmail.com wrote: Many thanks! (bin enabled) Alan On 2 June 2014 15:49, Alexander Hansen alexanderk.han...@gmail.com wrote: On 6/2/14, 7:15 AM, Alan wrote: Hi I have only the “xcode command line” installed. How do I sort the issue below? Information about 9742 packages read in 1 seconds. Can't resolve dependency xcode.app (= 4.6) for package qt4-base-mac-4.8.6-2 (no matching packages/versions found) Exiting with failure. Package manager version: 0.36.4.1 Distribution version: selfupdate-rsync Mon Jun 2 15:08:51 2014, 10.9, x86_64 Trees: local/main stable/main 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 You're either going to need to install the full Xcode to build qt4*-mac, or to enable the binary distribution via fink configure. -- Alexander Hansen, Ph.D. Fink User Liaison My package updates: http://finkakh.wordpress.com/ -- 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 -- 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 -- Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft___ 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] Issue with xcode
Hi I have only the “xcode command line” installed. How do I sort the issue below? Information about 9742 packages read in 1 seconds. Can't resolve dependency xcode.app (= 4.6) for package qt4-base-mac-4.8.6-2 (no matching packages/versions found) Exiting with failure. Package manager version: 0.36.4.1 Distribution version: selfupdate-rsync Mon Jun 2 15:08:51 2014, 10.9, x86_64 Trees: local/main stable/main 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 -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech___ 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] Issue with xcode
Many thanks! (bin enabled) Alan On 2 June 2014 15:49, Alexander Hansen alexanderk.han...@gmail.com wrote: On 6/2/14, 7:15 AM, Alan wrote: Hi I have only the “xcode command line” installed. How do I sort the issue below? Information about 9742 packages read in 1 seconds. Can't resolve dependency xcode.app (= 4.6) for package qt4-base-mac-4.8.6-2 (no matching packages/versions found) Exiting with failure. Package manager version: 0.36.4.1 Distribution version: selfupdate-rsync Mon Jun 2 15:08:51 2014, 10.9, x86_64 Trees: local/main stable/main 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 You're either going to need to install the full Xcode to build qt4*-mac, or to enable the binary distribution via fink configure. -- Alexander Hansen, Ph.D. Fink User Liaison My package updates: http://finkakh.wordpress.com/ -- 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 -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech___ 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] Can’t install rpy2
fink install rpy2-py27 Information about 8381 packages read in 1 seconds. Can't resolve dependency r-base215-dev for package rpy2-py27-2.2.2-5 (no matching packages/versions found) Exiting with failure. Package manager version: 0.36.3.1 Distribution version: selfupdate-rsync Wed Feb 12 10:15:25 2014, 10.9, x86_64 Trees: local/main stable/main No recognized Xcode.app installed Xcode command-line tools: 5.0.1.0.1.1382131676 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 -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151iu=/4140/ostg.clktrk___ 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] Can’t install rpy2
Many thanks! It did work indeed, with this: diff /sw/fink/dists/stable/main/finkinfo/sci/rpy2-py.info/sw/fink/dists/local/main/finkinfo/ rpy2-py.info 5,6c5,6 Revision: 5 Description: Python module to access R (2.15) functions --- Revision: 5.1 Description: Python module to access R (3.0) functions 13,14c13,14 BuildDepends: fink (= 0.24.12-1), r-base215-dev, r-base Depends: python%type_pkg[python], r-base215, numpy-py%type_pkg[python] (= 1.3.0-7) --- BuildDepends: fink (= 0.24.12-1), r-base30-dev, r-base Depends: python%type_pkg[python], r-base30, numpy-py%type_pkg[python] (= 1.3.0-7) 22c22 SetLDFLAGS: -L%p/Library/Frameworks/R.framework/Versions/2.15/Resources/lib -undefined dynamic_lookup --- SetLDFLAGS: -L%p/Library/Frameworks/R.framework/Versions/3.0/Resources/lib -undefined dynamic_lookup 26c26 %p/bin/python%type_raw[python] setup.py build --r-home=%p/Library/Frameworks/R.framework/Versions/2.15/Resources --- %p/bin/python%type_raw[python] setup.py build --r-home=%p/Library/Frameworks/R.framework/Versions/3.0/Resources and don’t forget rpy2-py.patch. Alan On 12 February 2014 19:49, Hanspeter Niederstrasser f...@snaggledworks.comwrote: On 2/12/2014 5:17 AM, Alan wrote: fink install rpy2-py27 Information about 8381 packages read in 1 seconds. Can't resolve dependency r-base215-dev for package rpy2-py27-2.2.2-5 (no matching packages/versions found) Exiting with failure. Package manager version: 0.36.3.1 Distribution version: selfupdate-rsync Wed Feb 12 10:15:25 2014, 10.9, x86_64 Trees: local/main stable/main No recognized Xcode.app installed Xcode command-line tools: 5.0.1.0.1.1382131676 Passing this on to the rpy2 maintainer. r-base215 has been excluded from OS X 10.9, but rpy2 might work with r-base-3.0. You can copy the file /sw/fink/dists/10.7/stable/ main/finkinfo/sci/rpy2-py.info to /sw/fink/dists/local/main/finkinfo, increase the Revision: field to 5.1, and change all instances of r-base215 to r-base30, then try to rebuild rpy2-py27. If it works, please post back to the list (and to the Maintainer), so that rpy2 can be updated to use the newer rpy2. Baba: rpy2 upstream is also now at 2.3.0, which is newer than our version. 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 -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151iu=/4140/ostg.clktrk___ 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] Failed: phase installing: test-deep-pm5162-0.112-1failed
Thanks a lot, it’s all fine now. Alan On 21 January 2014 13:58, Daniel Macks dma...@netspace.org wrote: On Tue, 21 Jan 2014 12:47:03 +, Alan alanwil...@gmail.com wrote: Installing /sw/src/fink.build/root-test-deep-pm5162-0.112-1/sw/share/ man/man3/Test::Deep::NoTest.3pm Appending installation info to /sw/src/fink.build/root-test- deep-pm5162-0.112-1/sw/lib/perl5/5.16.2/darwin-thread- multi-2level/perllocal.pod mv /sw/src/fink.build/root-test-deep-pm5162-0.112-1/sw/share/man /sw/src/fink.build/root-test-deep-pm5162-0.112-1/sw/lib/perl5/5.16.2 sudo -u fink-bld [ENV] sh -c /tmp/fink.VPZ1W /bin/mkdir -p /sw/src/fink.build/root-test-deep-pm5162-0.112-1/sw/share/ podfiles/5.16.2 for i in `find /sw/src/fink.build/root-test-deep-pm5162-0.112-1/sw -name perllocal.pod`; do /bin/cat $i | sed -e s,/sw/src/fink.build/root- test-deep-pm5162-0.112-1/sw/lib/perl5,/sw/lib/perl5, /sw/src/fink.build/root-test-deep-pm5162-0.112-1/sw/share/ podfiles/5.16.2/perllocal.test-deep-pm5162.pod; /bin/rm -rf $i; done; /usr/bin/install -d -m 700 /sw/src/fink.build/root-test- deep-pm5162-0.112-1/sw/share/doc/test-deep-pm5162 /bin/cp -r CHANGES /sw/src/fink.build/root-test- deep-pm5162-0.112-1/sw/share/doc/test-deep-pm5162/ cp: CHANGES: No such file or directory I just uploaded revision -2, which should fix this (case-sensitivity change) and also a different mistake in the COPYRIGHT file. dan -- Daniel Macks dma...@netspace.org -- 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ 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] Which X11 with Mavericks?
Hi, I am in process to install Fink 0.36 and then I screen popup asking me to install X11 from Xquartz. Then a link take me to http://xquartz.macosforge.org/landing/ But I don’t see maverick option there. What should I do please? 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 -- November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231iu=/4140/ostg.clktrk___ 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] fink install rpy2-py27 ?
Thanks a lot, it did work, but I have to copy rpy2-py.patch as well. Cheers, Alan On 11 October 2013 18:28, Hanspeter Niederstrasser f...@snaggledworks.comwrote: On 10/11/2013 10:02 AM, Alan wrote: Failed: no package found for specification 'rpy2-py27'! Using Package manager version: 0.35.2 Distribution version: selfupdate-rsync Thu Oct 10 14:00:42 2013, 10.8, x86_64 Trees: local/main stable/main local/injected Thanks in advance, For some reason, rpy2-py* was limited to only 10.7 and below. I've added the rpy2 maintainer so he can advance it if needed. If you want to test it yourself, copy the file /sw/fink/dists/stable/main/**finkinfo/sci/rpy2-py.info to /sw/fink/dists/local/main/**finkinfo and remove the entire Distribution: 10.7, 10.6, 10.5, 10.4 line and then try rebuilding rpy2-py27. If it does work, please let us know so we can make it available for newer OS X versions. 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 -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60134071iu=/4140/ostg.clktrk___ 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] fink install rpy2-py27 ?
Failed: no package found for specification 'rpy2-py27'! Using Package manager version: 0.35.2 Distribution version: selfupdate-rsync Thu Oct 10 14:00:42 2013, 10.8, x86_64 Trees: local/main stable/main local/injected Thanks in advance, 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 -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60134071iu=/4140/ostg.clktrk___ 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] fink with Xcode 5
On 22 September 2013 11:01, jean-francois jean-francois.don...@irap.omp.euwrote: i recently updated to Xcode5 (including command tools) and noticed that the self-update task does not complete properly, BTW, how to update Xcode 5 command tools? It asked me for dev account, which I thought I had, but now apparently I have to pay $99? Can someone elaborate here please? 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 -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/22/13. http://pubads.g.doubleclick.net/gampad/clk?id=64545871iu=/4140/ostg.clktrk___ 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] Fink and cx_Oracle
Thanks for your suggestion. Indeed, I tried but didn't work. I am wondering if there's anyone in Fink list that uses Fink python 64 bits and cx_Oracle. Alan On 2 July 2013 18:50, Alexander Hansen alexanderk.han...@gmail.com wrote: On 7/1/13 7:01 AM, Alan wrote: Hi there, I am trying to install cx_Oracle in my fink python 2.7. Details: Fink: Package manager version: 0.34.8 Distribution version: selfupdate-rsync Thu Jun 6 12:26:46 2013, 10.8, x86_64 Trees: local/main stable/main local/injected Python: Python 2.7.5 (default, May 30 2013, 21:19:08) [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin Mac OSX 10.8.4 Since cx_Oracle is not in Fink, I tried: /sw/bin/easy_install-2.7 -U cx_Oracle Searching for cx-Oracle Reading http://pypi.python.org/simple/**cx_Oracle/http://pypi.python.org/simple/cx_Oracle/ Reading http://starship.python.net/**crew/atuininghttp://starship.python.net/crew/atuining Reading http://cx-oracle.sourceforge.**nethttp://cx-oracle.sourceforge.net Best match: cx-Oracle 5.1.2 Downloading http://prdownloads.**sourceforge.net/cx-oracle/cx_** Oracle-5.1.2.tar.gz?downloadhttp://prdownloads.sourceforge.net/cx-oracle/cx_Oracle-5.1.2.tar.gz?download Processing cx_Oracle-5.1.2.tar.gz Writing /tmp/easy_install-3x7DYB/cx_**Oracle-5.1.2/setup.cfg Running cx_Oracle-5.1.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-3x7DYB/cx_**Oracle-5.1.2/egg-dist-tmp-**IiFGbT error: Setup script exited with error: $MACOSX_DEPLOYMENT_TARGET mismatch: now 10.3 but 10.8 during configure I've tried all I can to understand this mismatch for no avail. Using /usr/bin/easy_install-2.7 and all goes fine. Many thanks in advance, Alan -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 Have you tried e.g. export MACOSX_DEPLOYMENT_TARGET=10.8 before using /sw/bin/easy_install ? -- Alexander Hansen, Ph.D. Fink User Liaison My package updates: http://finkakh.wordpress.com/ -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev___ 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] Fink and cx_Oracle
Hi there, I am trying to install cx_Oracle in my fink python 2.7. Details: Fink: Package manager version: 0.34.8 Distribution version: selfupdate-rsync Thu Jun 6 12:26:46 2013, 10.8, x86_64 Trees: local/main stable/main local/injected Python: Python 2.7.5 (default, May 30 2013, 21:19:08) [GCC 4.2.1 Compatible Apple LLVM 4.2 (clang-425.0.28)] on darwin Mac OSX 10.8.4 Since cx_Oracle is not in Fink, I tried: /sw/bin/easy_install-2.7 -U cx_Oracle Searching for cx-Oracle Reading http://pypi.python.org/simple/cx_Oracle/ Reading http://starship.python.net/crew/atuining Reading http://cx-oracle.sourceforge.net Best match: cx-Oracle 5.1.2 Downloading http://prdownloads.sourceforge.net/cx-oracle/cx_Oracle-5.1.2.tar.gz?download Processing cx_Oracle-5.1.2.tar.gz Writing /tmp/easy_install-3x7DYB/cx_Oracle-5.1.2/setup.cfg Running cx_Oracle-5.1.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-3x7DYB/cx_Oracle-5.1.2/egg-dist-tmp-IiFGbT error: Setup script exited with error: $MACOSX_DEPLOYMENT_TARGET mismatch: now 10.3 but 10.8 during configure I've tried all I can to understand this mismatch for no avail. Using /usr/bin/easy_install-2.7 and all goes fine. Many thanks in advance, Alan -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev___ 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] Gromacs again
Hi, I followed the issues with GMX 4.6 and waited. So today I gave a try and got this: [skip] make [ 0%] Building NVCC (Device) object src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o [ 0%] Building NVCC (Device) object src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o Scanning dependencies of target gpu_utils [ 0%] Building CXX object src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/dummy.cpp.o Linking CXX static library libgpu_utils.a /usr/bin/ranlib: file: libgpu_utils.a(dummy.cpp.o) has no symbols /usr/bin/ranlib: file: libgpu_utils.a(dummy.cpp.o) has no symbols [ 0%] Built target gpu_utils [ 0%] Building NVCC (Device) object src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o /sw/src/fink.build/gromacs-4.6-2/gromacs-4.6/src/gmxlib/cuda_tools/ pmalloc_cuda.cu(64): error: no instance of overloaded function cudaMallocHost matches the argument list argument types are: (void **, size_t, int) /sw/src/fink.build/gromacs-4.6-2/gromacs-4.6/src/gmxlib/cuda_tools/ pmalloc_cuda.cu(87): error: no instance of overloaded function cudaMallocHost matches the argument list argument types are: (void **, size_t, int) 2 errors detected in the compilation of /tmp/tmpxft_29fc_-4_pmalloc_cuda.cpp1.ii. CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:264 (message): Error generating file /sw/src/fink.build/gromacs-4.6-2/gromacs-4.6/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o make[2]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o] Error 1 make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 make: *** [all] Error 2 ### execution of /tmp/fink._AHcW failed, exit code 2 ### execution of /tmp/fink.9rNkw failed, exit code 2 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-gromacs-4.6-2 (Reading database ... 179750 files and directories currently installed.) Removing fink-buildlock-gromacs-4.6-2 ... Reading buildlock packages... /sw/bin/dpkg-lockwait -i /sw/fink/debs/gromacs_4.5.4-2_darwin-x86_64.deb Selecting previously deselected package gromacs. (Reading database ... 179749 files and directories currently installed.) Unpacking gromacs (from .../gromacs_4.5.4-2_darwin-x86_64.deb) ... Setting up gromacs (4.5.4-2) ... Updating the list of locally available binary packages. Failed: phase installing: gromacs-4.6-2 failed Package manager version: 0.34.5 Distribution version: selfupdate-rsync Mon Mar 4 13:32:14 2013, 10.8, x86_64 Trees: local/main stable/main local/injected Xcode.app: 4.6 Xcode command-line tools: 4.5.0.0.1.1249367152 Max. Fink build jobs: 4 -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb___ 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] Gromacs again
Well spotted Jack. Indeed, I thought I had disabled cuda when I moved to iMac, but it was still in my $PATH. However, it only worked after I had deleted /usr/local/cuda. Thanks, Alan On 4 March 2013 15:05, Jack Howarth howa...@bromo.med.uc.edu wrote: On Mon, Mar 04, 2013 at 07:59:03AM -0700, Alexander Hansen wrote: On 3/4/13 7:39 AM, Alan wrote: Hi, I followed the issues with GMX 4.6 and waited. So today I gave a try and got this: [skip] make [ 0%] Building NVCC (Device) object src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o [ 0%] Building NVCC (Device) object src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o Scanning dependencies of target gpu_utils [ 0%] Building CXX object src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/dummy.cpp.o Linking CXX static library libgpu_utils.a /usr/bin/ranlib: file: libgpu_utils.a(dummy.cpp.o) has no symbols /usr/bin/ranlib: file: libgpu_utils.a(dummy.cpp.o) has no symbols [ 0%] Built target gpu_utils [ 0%] Building NVCC (Device) object src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o /sw/src/fink.build/gromacs-4.6-2/gromacs-4.6/src/gmxlib/cuda_tools/ pmalloc_cuda.cu http://pmalloc_cuda.cu(64): error: no instance of overloaded function cudaMallocHost matches the argument list argument types are: (void **, size_t, int) /sw/src/fink.build/gromacs-4.6-2/gromacs-4.6/src/gmxlib/cuda_tools/ pmalloc_cuda.cu http://pmalloc_cuda.cu(87): error: no instance of overloaded function cudaMallocHost matches the argument list argument types are: (void **, size_t, int) 2 errors detected in the compilation of /tmp/tmpxft_29fc_-4_pmalloc_cuda.cpp1.ii. CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:264 (message): Error generating file /sw/src/fink.build/gromacs-4.6-2/gromacs-4.6/build/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o make[2]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o] Error 1 make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 make: *** [all] Error 2 ### execution of /tmp/fink._AHcW failed, exit code 2 ### execution of /tmp/fink.9rNkw failed, exit code 2 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-gromacs-4.6-2 (Reading database ... 179750 files and directories currently installed.) Removing fink-buildlock-gromacs-4.6-2 ... Reading buildlock packages... /sw/bin/dpkg-lockwait -i /sw/fink/debs/gromacs_4.5.4-2_darwin-x86_64.deb Selecting previously deselected package gromacs. (Reading database ... 179749 files and directories currently installed.) Unpacking gromacs (from .../gromacs_4.5.4-2_darwin-x86_64.deb) ... Setting up gromacs (4.5.4-2) ... Updating the list of locally available binary packages. Failed: phase installing: gromacs-4.6-2 failed Package manager version: 0.34.5 Distribution version: selfupdate-rsync Mon Mar 4 13:32:14 2013, 10.8, x86_64 Trees: local/main stable/main local/injected Xcode.app: 4.6 Xcode command-line tools: 4.5.0.0.1.1249367152 Max. Fink build jobs: 4 -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 I didn't see this when I built it here. You might start by updating your Xcode command-line tools (e.g. via the Xcode Preferences). I believe that Alan must have some third-party CUDA devtools installed. There is no way fink can properly support that configuration so they needed to be disabled in .cshrc/.bashrc or moved aside/deinstalled first. -- Alexander Hansen, Ph.D. Fink User Liaison My package updates: http://finkakh.wordpress.com/ -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb___ 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] failing version-requirements-pm5100
Hi there, I am using: Package manager version: 0.29.20 Distribution version: selfupdate-cvs Mon Mar 14 13:28:20 2011, 10.6, x86_64 Trees: local/main stable/main unstable/main unstable/crypto stable/crypto on a iMac with MacOSX 10.6.6 fink install version-requirements-pm5100 Information about 9819 packages read in 1 seconds. The following package will be installed or updated: version-requirements-pm5100 Reading buildlock packages... /sw/bin/dpkg-lockwait -i /sw/fink/dists/unstable/main/binary-darwin-x86_64/libs/perlmods/version-requirements-pm5100_0.101020-1_darwin-x86_64.deb (Reading database ... 229647 files and directories currently installed.) Unpacking version-requirements-pm5100 (from .../version-requirements-pm5100_0.101020-1_darwin-x86_64.deb) ... /sw/bin/dpkg: error processing /sw/fink/dists/unstable/main/binary-darwin-x86_64/libs/perlmods/version-requirements-pm5100_0.101020-1_darwin-x86_64.deb (--install): error creating directory `./sw/lib/perl5/5.10.0/darwin-thread-multi-2level/auto/Version/Requirements': No such file or directory Errors were encountered while processing: /sw/fink/dists/unstable/main/binary-darwin-x86_64/libs/perlmods/version-requirements-pm5100_0.101020-1_darwin-x86_64.deb ### execution of /sw/bin/dpkg-lockwait failed, exit code 1 Failed: can't install package version-requirements-pm5100-0.101020-1 Thanks in advance, Alan -- Alan Wilter SOUSA da SILVA, D.Sc. Bioinformatician, UniProt - PANDA, EBI-EMBL CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] failing version-requirements-pm5100
Yes, I do have case-sensitive HFS as well, oh boy... Alan On 14 March 2011 14:43, Alexander Hansen alexanderk.han...@gmail.comwrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 3/14/11 9:39 AM, Alan Wilter Sousa da Silva wrote: Hi there, I am using: Package manager version: 0.29.20 Distribution version: selfupdate-cvs Mon Mar 14 13:28:20 2011, 10.6, x86_64 Trees: local/main stable/main unstable/main unstable/crypto stable/crypto on a iMac with MacOSX 10.6.6 fink install version-requirements-pm5100 Information about 9819 packages read in 1 seconds. The following package will be installed or updated: version-requirements-pm5100 Reading buildlock packages... /sw/bin/dpkg-lockwait -i /sw/fink/dists/unstable/main/binary-darwin-x86_64/libs/perlmods/version-requirements-pm5100_0.101020-1_darwin-x86_64.deb (Reading database ... 229647 files and directories currently installed.) Unpacking version-requirements-pm5100 (from .../version-requirements-pm5100_0.101020-1_darwin-x86_64.deb) ... /sw/bin/dpkg: error processing /sw/fink/dists/unstable/main/binary-darwin-x86_64/libs/perlmods/version-requirements-pm5100_0.101020-1_darwin-x86_64.deb (--install): error creating directory `./sw/lib/perl5/5.10.0/darwin-thread-multi-2level/auto/Version/Requirements': No such file or directory Errors were encountered while processing: /sw/fink/dists/unstable/main/binary-darwin-x86_64/libs/perlmods/version-requirements-pm5100_0.101020-1_darwin-x86_64.deb ### execution of /sw/bin/dpkg-lockwait failed, exit code 1 Failed: can't install package version-requirements-pm5100-0.101020-1 Thanks in advance, Alan -- Alan Wilter SOUSA da SILVA, D.Sc. Bioinformatician, UniProt - PANDA, EBI-EMBL CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 I have the same problem. I'm using case-sensitive HFS, and I have version rather than Version: $ ls /sw64/lib/perl5/5.10.0/darwin-thread-multi-2level/auto Class Compress DevelExtUtils GDIO Locale XML share Cocoa Crypt Encode File HTML LWP URI XSLoader version - -- Alexander Hansen, Ph.D. Fink User Liaison -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (Darwin) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk1+KZUACgkQB8UpO3rKjQ/G7gCfe/dsEA0ij3rFBcxWweYW0OEN JHAAn2pF3fViy2ooL2H8P/sLxUaGtQQG =DP6a -END PGP SIGNATURE- -- Alan Wilter SOUSA da SILVA, D.Sc. Bioinformatician, UniProt - PANDA, EBI-EMBL CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] failing version-requirements-pm5100
Thanks! Alan On 14 March 2011 16:42, Alexander Hansen alexanderk.han...@gmail.comwrote: /sw/lib/perl5/5.10.0/darwin-thread-multi-2level/auto/version -- Alan Wilter SOUSA da SILVA, D.Sc. Bioinformatician, UniProt - PANDA, EBI-EMBL CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] can't update-all because libgeos3.2.2-shlibs
Thanks Alex, it worked. Alan On 11 January 2011 15:21, Alexander Hansen alexanderk.han...@gmail.comwrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 1/11/11 9:57 AM, Alan Wilter Sousa da Silva wrote: Hi there, I use fink: Package manager version: 0.29.17 Distribution version: selfupdate-cvs Tue Jan 11 14:07:18 2011, 10.6, x86_64 Trying to update-all my fink and getting: The following 5 packages will be installed or updated: django-py26 django-py27 git ppix-regexp-pm5100 vim The following additional package will be installed: gdal-shlibs Do you want to continue? [Y/n] Reading buildlock packages... /sw/bin/dpkg-lockwait -i /sw/fink/dists/unstable/main/binary-darwin-x86_64/libs/gdal-shlibs_1.7.2-4_darwin-x86_64.deb (Reading database ... 205448 files and directories currently installed.) Preparing to replace gdal-shlibs 1.7.2-4 (using .../gdal-shlibs_1.7.2-4_darwin-x86_64.deb) ... Unpacking replacement gdal-shlibs ... dpkg: dependency problems prevent configuration of gdal-shlibs: gdal-shlibs depends on libgeos3.2.2-shlibs (= 3.2.2-1); however: Version of libgeos3.2.2-shlibs on system is 3.2.2-4. /sw/bin/dpkg: error processing gdal-shlibs (--install): dependency problems - leaving unconfigured Errors were encountered while processing: gdal-shlibs ### execution of /sw/bin/dpkg-lockwait failed, exit code 1 Failed: can't install package gdal-shlibs-1.7.2-4 What can I do? Thanks in advance, Alan -- Alan Wilter SOUSA da SILVA, D.Sc. Bioinformatician, UniProt - PANDA, EBI-EMBL CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 I show a different dependency versioning: $ fink show-deps gdal-shlibs | grep geos libgeos3.2.2-shlibs (= 3.2.2-1) libgeos3.2.2 (= 3.2.2-1) libgeos3.2.2-shlibs (= 3.2.2-1) which, unfortunately, was changed without changing the revision. Using fink rebuild gdal-shlibs should work around this issue for you. - -- Alexander Hansen, Ph.D. Fink User Liaison -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (Darwin) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk0sdZcACgkQB8UpO3rKjQ9yuwCffqQAuvc6FCbbjV8Oz5Z2gO4w 38wAn0oF7jR1FgkBYGWtpqOaHYVWrrTC =ZKLk -END PGP SIGNATURE- -- Alan Wilter SOUSA da SILVA, D.Sc. Bioinformatician, UniProt - PANDA, EBI-EMBL CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- Protect Your Site and Customers from Malware Attacks Learn about various malware tactics and how to avoid them. Understand malware threats, the impact they can have on your business, and how you can protect your company and customers by using code signing. http://p.sf.net/sfu/oracle-sfdevnl___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] can't update-all because libgeos3.2.2-shlibs
Hi there, I use fink: Package manager version: 0.29.17 Distribution version: selfupdate-cvs Tue Jan 11 14:07:18 2011, 10.6, x86_64 Trying to update-all my fink and getting: The following 5 packages will be installed or updated: django-py26 django-py27 git ppix-regexp-pm5100 vim The following additional package will be installed: gdal-shlibs Do you want to continue? [Y/n] Reading buildlock packages... /sw/bin/dpkg-lockwait -i /sw/fink/dists/unstable/main/binary-darwin-x86_64/libs/gdal-shlibs_1.7.2-4_darwin-x86_64.deb (Reading database ... 205448 files and directories currently installed.) Preparing to replace gdal-shlibs 1.7.2-4 (using .../gdal-shlibs_1.7.2-4_darwin-x86_64.deb) ... Unpacking replacement gdal-shlibs ... dpkg: dependency problems prevent configuration of gdal-shlibs: gdal-shlibs depends on libgeos3.2.2-shlibs (= 3.2.2-1); however: Version of libgeos3.2.2-shlibs on system is 3.2.2-4. /sw/bin/dpkg: error processing gdal-shlibs (--install): dependency problems - leaving unconfigured Errors were encountered while processing: gdal-shlibs ### execution of /sw/bin/dpkg-lockwait failed, exit code 1 Failed: can't install package gdal-shlibs-1.7.2-4 What can I do? Thanks in advance, Alan -- Alan Wilter SOUSA da SILVA, D.Sc. Bioinformatician, UniProt - PANDA, EBI-EMBL CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- Gaining the trust of online customers is vital for the success of any company that requires sensitive data to be transmitted over the Web. Learn how to best implement a security strategy that keeps consumers' information secure and instills the confidence they need to proceed with transactions. http://p.sf.net/sfu/oracle-sfdevnl ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] fink update failed because of gdal-shlibs
Hi there, Today I did fink update and it failed with the message below: fink needs help picking an alternative to satisfy a virtual dependency. The candidates: (1) gdal-shlibs: GDAL/OGR shared libraries (2) gdal-pgsql-shlibs: GDAL/OGR shared libraries (3) gdal-mysql-shlibs: GDAL/OGR shared libraries (4) gdal-pgsql-mysql-shlibs: GDAL/OGR shared libraries Pick one: [1] Can't resolve dependency xerces-c-dev for package gdal-1.7.2-3 (no matching packages/versions found) Exiting with failure. First, I don't know which gdal to choose. Second, I have no idea what is it and why I need it. Many thanks in advance, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://p.sf.net/sfu/dev2dev-palm___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] about updating to python 2.7
Hi there, I am thinking about to update my Fink python 2.6 to 2.7. However, as I do an extensive use of many modules from numpy (which is there for 2.7) to django (which is not yet) and sometimes not all modules are available yet for python 2.7, I may need to use something like eazy_install. What I don't know is if it's safe to do in a first moment 'easy_install django' and later, when e.g. django-py27 becomes available, fink install django-py27 would overwrite my previous easy_install django installation? The clear point of using Fink for me is to be able to do 'fink update-all' and forget it. If resorting to 'easy_install' I would have more painstaking routine to keep my python modules updated, hence I want to be sure that the eventual Fink package will free me from this burden. BTW, is there a easy way to print out all the modules I have installed for python 2.6 with Fink so it would work as guide for me to update to python 2.7? Many thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] mpich2
Hi there, Have we ever had mpich for Fink? Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] failed to install pyobjc-py26
Thanks, I am cc'ing to the new maintainer as well. I tried the new one pyobjc-py.info and got now a different error. I suspect I am missing a package that pyobjc-py26 didn't request as mandatory. gcc -L/sw/lib -bundle -L/sw/lib/python2.6/config -lpython2.6 -L/sw/lib -I/sw/include build/temp.macosx-10.6-x86_64-2.6/libffi-src/ffi.o build/temp.macosx-10.6-x86_64-2.6/libffi-src/types.o build/temp.macosx-10.6-x86_64-2.6/libffi-src/powerpc/ppc-darwin.o build/temp.macosx-10.6-x86_64-2.6/libffi-src/powerpc/ppc-darwin_closure.o build/temp.macosx-10.6-x86_64-2.6/libffi-src/powerpc/ppc-ffi_darwin.o build/temp.macosx-10.6-x86_64-2.6/libffi-src/powerpc/ppc64-darwin_closure.o build/temp.macosx-10.6-x86_64-2.6/libffi-src/x86/darwin64.o build/temp.macosx-10.6-x86_64-2.6/libffi-src/x86/x86-darwin.o build/temp.macosx-10.6-x86_64-2.6/libffi-src/x86/x86-ffi64.o build/temp.macosx-10.6-x86_64-2.6/libffi-src/x86/x86-ffi_darwin.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/OC_NSBundleHack.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/OC_PythonArray.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/OC_PythonData.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/OC_PythonDate.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/OC_PythonDictionary.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/OC_PythonEnumerator.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/OC_PythonNumber.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/OC_PythonObject.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/OC_PythonSet.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/OC_PythonString.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/OC_PythonUnicode.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/ObjCPointer.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/alloc_hack.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/block_support.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/bundle-variables.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/class-builder.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/class-list.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/closure_pool.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/corefoundation.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/formal-protocol.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/fsref.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/fsspec.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/function.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/informal-protocol.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/instance-var.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/ivar-accessor.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/libffi_support.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/method-accessor.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/method-imp.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/method-signature.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/module.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/objc-NULL.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/objc-class.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/objc-object.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/objc-runtime-compat.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/objc_super.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/objc_support.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/objc_util.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/opaque-pointer.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/parsexml.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/pointer-support.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/proxy-registry.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/pyobjc-api.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/registry.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/selector.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/socketsupport.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/struct-wrapper.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/super-call.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/toll-free-bridging.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/unicode-object.o build/temp.macosx-10.6-x86_64-2.6/Modules/objc/varlist.o -o build/lib.macosx-10.6-x86_64-2.6/objc/_objc.so -framework CoreFoundation -framework Foundation -framework Carbon -isysroot / -L/sw/lib -lxml2 -lz -lpthread -L/sw/lib -liconv -lm Undefined symbols: _PyMac_Error, referenced from: _fsref_as_path in fsref.o _fsref_from_path in fsref.o ld: symbol(s) not found collect2: ld returned 1 exit status error: command 'gcc' failed with exit status 1 I hope you can help me. Alan On Mon, May 17, 2010 at 20:23, Alexander Hansen alexanderk.han...@gmail.com wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 5/17/10 3:09 PM, Alan wrote: Thanks Alexander, you're question was the first thing I checked which gcc /usr/bin/gcc gcc -v Using built-in specs. Target: i686-apple-darwin10 Configured with: /var/tmp/gcc/gcc-5659~1/src/configure --disable-checking --enable-werror --prefix=/usr --mandir=/share
[Fink-users] failed to install pyobjc-py26
Hi there, This package has no maintainer apparently, so I am posting here. I hope someone can have a solution: gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ibuild/codegen/ -Ilibffi-src/include -I/sw/include/python2.6 -c libffi-src/src/types.c -o build/temp.macosx-10.6-x86_64-2.6/libffi-src/src/types.o -I/sw/include -DMACOSX -DAPPLE_RUNTIME -no-cpp-precomp -Wno-long-double -g -Wall -Wstrict-prototypes -Wmissing-prototypes -Wformat=2 -W -Wshadow -Wpointer-arith -Wmissing-declarations -Wnested-externs -Wno-long-long -Wno-import cc1: error: unrecognized command line option -Wno-long-double error: command 'gcc' failed with exit status 1 Mac OSX 10.6.3 Package manager version: 0.29.10 Distribution version: selfupdate-cvs Mon May 17 14:30:16 2010, 10.6, x86_64 Thanks Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] issue with numpy-py26 1.3.0-7
Thanks a lot Derek. Everything looks fine and my applications is running 100% OK. So definitely numpy 1.4.1 solved my problems. Alan On Thu, May 13, 2010 at 20:58, Derek Homeier de...@astro.physik.uni-goettingen.de wrote: Hi, Developing our application here, based on python, and we start to see this error: ValueError: can't handle version -1 of numpy.dtype pickle My partner uses MacPorts and solved this issue by updating numpy to 1.4. I was wondering if numpy 1.4 for Fink is on the way. Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 You might try checking with the maintainer (fink info numpy-py26) since he would be the one who would be responsible for handling an update. I have built and tested the updated numpy and scipy versions on my machines, feel free to copy the adapted package files to your /sw/fink/dists/local/main/finkinfo/sci and give them a try. Please note that I just modified them on my own, and Sebastien Maret, the maintainer, is not responsible for any problems you might encounter (though basically, numpy.test() and scipy.test() did not produce any errors not already present in the 1.3 and 0.7.0 versions on 10.5/6, python2.5/6, powerpc/i386/x86_64). Cheers, Derek -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] gcc45-4.5.0-1001 and openmpi-1.4.1-1000
Dear all, Is there a tentative date for releasing openmpi-1.4.1 and gcc45 at least on CVS? Thanks Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] issue with numpy-py26 1.3.0-7
Hi there, Developing our application here, based on python, and we start to see this error: ValueError: can't handle version -1 of numpy.dtype pickle My partner uses MacPorts and solved this issue by updating numpy to 1.4. I was wondering if numpy 1.4 for Fink is on the way. Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] /sw/bin/mpicc is linking to /usr/bin/gcc and not /sw/bin/gcc-4
Hi there, Trying to compile a programme here and I found out that: /sw/bin/mpicc is linking to /usr/bin/gcc and not /sw/bin/gcc-4 see: /sw/bin/mpicc -v Using built-in specs. Target: i686-apple-darwin10 Configured with: /var/tmp/gcc/gcc-5659~1/src/configure --disable-checking --enable-werror --prefix=/usr --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --with-slibdir=/usr/lib --build=i686-apple-darwin10 --program-prefix=i686-apple-darwin10- --host=x86_64-apple-darwin10 --target=i686-apple-darwin10 --with-gxx-include-dir=/include/c++/4.2.1 Thread model: posix gcc version 4.2.1 (Apple Inc. build 5659) /sw/bin/mpif77 -v Using built-in specs. Target: x86_64-apple-darwin10 Configured with: ../gcc-4.4.2/configure --prefix=/sw --prefix=/sw/lib/gcc4.4 --mandir=/sw/share/man --infodir=/sw/share/info --enable-languages=c,c++,fortran,objc,java --with-gmp=/sw --with-libiconv-prefix=/sw --with-ppl=/sw --with-cloog=/sw --with-system-zlib --x-includes=/usr/X11R6/include --x-libraries=/usr/X11R6/lib --disable-libjava-multilib --build=x86_64-apple-darwin10 --host=x86_64-apple-darwin10 --target=x86_64-apple-darwin10 Thread model: posix gcc version 4.4.2 (GCC) So my program failed to link 'mpicc ... -lgfortran ...'. Is it a correct behaviour? I don't think so. How to solve this issue? I am using Fink 64 cvs on SL 10.6.3. Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] /sw/bin/mpicc is linking to /usr/bin/gcc and not /sw/bin/gcc-4
Thanks Alexander. fink -V Package manager version: 0.29.10 Distribution version: selfupdate-cvs Thu Apr 29 12:28:58 2010, 10.6, x86_64 I circumvent this problem by replacing the call 'mpicc' by: gcc-4 -D_REENTRANT -I/sw/include -I/sw/include/openmpi -L/sw/lib/openmpi -lmpi -lopen-rte -lopen-pal -lutil I got this from 'mpicc -showme', which returns: gcc -D_REENTRANT -I/sw/include -I/sw/include/openmpi -L/sw/lib/openmpi -lmpi -lopen-rte -lopen-pal -lutil But 'gcc', is /usr/bin/gcc, and from fink describe gcc44: gcc44-4.4.2-1000: GNU Compiler Collection Version 4.4 GCC, the GNU Compiler Collection, includes front ends for C, C++, Objective-C, Objective-C++, Fortran, Java, and Ada. . C, C++, Objective C and Fortran and Java are included in this package. . The C and C++ compilers are named gcc-4 and g++-4 to avoid conflicts with gcc and g++ installed by the Apple Developer Tools dpkg -S /sw/bin/mpif77 openmpi-dev: /sw/bin/mpif77 I hope it may help you to help me. Thanks, Alan On Thu, Apr 29, 2010 at 14:17, Alexander Hansen alexanderk.han...@gmail.com wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 4/29/10 8:11 AM, Alan wrote: Hi there, Trying to compile a programme here and I found out that: /sw/bin/mpicc is linking to /usr/bin/gcc and not /sw/bin/gcc-4 see: /sw/bin/mpicc -v Using built-in specs. Target: i686-apple-darwin10 Configured with: /var/tmp/gcc/gcc-5659~1/src/configure --disable-checking --enable-werror --prefix=/usr --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --with-slibdir=/usr/lib --build=i686-apple-darwin10 --program-prefix=i686-apple-darwin10- --host=x86_64-apple-darwin10 --target=i686-apple-darwin10 --with-gxx-include-dir=/include/c++/4.2.1 Thread model: posix gcc version 4.2.1 (Apple Inc. build 5659) /sw/bin/mpif77 -v Using built-in specs. Target: x86_64-apple-darwin10 Configured with: ../gcc-4.4.2/configure --prefix=/sw --prefix=/sw/lib/gcc4.4 --mandir=/sw/share/man --infodir=/sw/share/info --enable-languages=c,c++,fortran,objc,java --with-gmp=/sw --with-libiconv-prefix=/sw --with-ppl=/sw --with-cloog=/sw --with-system-zlib --x-includes=/usr/X11R6/include --x-libraries=/usr/X11R6/lib --disable-libjava-multilib --build=x86_64-apple-darwin10 --host=x86_64-apple-darwin10 --target=x86_64-apple-darwin10 Thread model: posix gcc version 4.4.2 (GCC) So my program failed to link 'mpicc ... -lgfortran ...'. Is it a correct behaviour? I don't think so. It could be that, or something else. Without seeing more than failed to link we've no real way of knowing. How to solve this issue? I am using Fink 64 cvs on SL 10.6.3. fink -V | head -n2 is a provides more explicit information, e.g. when there's a problem with the fink package manager and need to know that version. Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 Since /sw/bin/mpicc and /sw/bin/mpif77 aren't on _my_ system, I'm not sure what package provides them to see if I can reproduce your issue. How about giving us the output from dpkg -S /sw/bin/mpicc /sw/bin/mpif77 ? - -- Alexander Hansen Fink User Liaison -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (Darwin) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkvZhuEACgkQB8UpO3rKjQ+frwCfdi16Hhchi8Abqmr7RcFODci7 faQAoIvMSpZnpeBpbzxnL/EktgEI73aG =9R69 -END PGP SIGNATURE- -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] /sw/bin/mpicc is linking to /usr/bin/gcc and not /sw/bin/gcc-4
On Thu, Apr 29, 2010 at 15:10, Alexander Hansen alexanderk.han...@gmail.com wrote: So if you replace a call to 'mpicc' with your line then your compile succeeds? Yes It seems reasonable to me that the package might need to use the same gcc for both C and Fortran. I don't run it myself, however, so I don't really have a way to test it. I second this. Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] gfortran failing to link with C code
Hi there, I am trying to compile a program and bumping is this problem: Testing mixed C/Fortran compilation: gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o testp.c gfortran -O0 -c -o testp.f.o testp.f gcc -o testp testp.c.o testp.f.o -lgfortran -framework Accelerate ld: library not found for -lgfortran collect2: ld returned 1 exit status ./configure: line 1057: ./testp: No such file or directory WARNING: Unable to compile mixed C/Fortran code. I do have gfortran and everything else from Fink, 64 bits, Mac OSX 10.6.3. However I don't understand this: dpkg -l gfortran-shlibs Desired=Unknown/Install/Remove/Purge/Hold | Status=Not/Installed/Config-files/Unpacked/Failed-config/Half-installed |/ Err?=(none)/Hold/Reinst-required/X=both-problems (Status,Err: uppercase=bad) ||/ Name Version Description +++-=-=-== un gfortran-shlibs none(no description available) I also know that probably my compilation should call gcc-4, however where's gcc_select? Any help helps, thanks a lot in advance, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] qtpfsgui-mac failed in SL 10.6.2 with Fink
Hi there, Every time there is a update for qt-mac I go and try to install qtpfsgui-mac, but for no avail so far. My system is Mac OSX 10.6.2 with Fink 64 bits. The relevant errors I guess are: [snip] g++-4.2 -headerpad_max_install_names -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.5 -arch i386 -o qtpfsgui.app/Contents/MacOS/qtpfsgui generated_obj/pfs.o generated_obj/colorspace.o generated_obj/global.o generated_obj/main.o generated_obj/options.o generated_obj/smart_scroll_area.o generated_obj/panIconWidget.o generated_obj/gamma_and_levels.o generated_obj/gang.o generated_obj/commandline.o generated_obj/mainWindow.o generated_obj/DnDOption.o generated_obj/hdrviewer.o generated_obj/luminancerange_widget.o generated_obj/histogram.o generated_obj/tonemappingDialog.o generated_obj/tonemapping_widget.o generated_obj/ldrviewer.o generated_obj/tonemapperThread.o generated_obj/loadHdrThread.o generated_obj/hdrInputLoader.o generated_obj/preferencesDialog.o generated_obj/transplant.o generated_obj/resizeDialog.o generated_obj/projectiveDialog.o generated_obj/HdrCreationManager.o generated_obj/mtb_alignment.o generated_obj/createhdr.o generated_obj/robertson02.o generated_obj/responses.o generated_obj/debevec.o generated_obj/newHdrWizard.o generated_obj/editingTools.o generated_obj/previewWidget.o generated_obj/pfsrotate.o generated_obj/pfssize.o generated_obj/pfsgamma.o generated_obj/pfspanoramic.o generated_obj/pfsinrgbe.o generated_obj/pfsoutrgbe.o generated_obj/pfsoutldrimage.o generated_obj/rgbeio.o generated_obj/pfstiff.o generated_obj/pfsinexr.o generated_obj/pfsoutexr.o generated_obj/pfstmo_ashikhmin02.o generated_obj/tmo_ashikhmin02.o generated_obj/pfstmo_drago03.o generated_obj/tmo_drago03.o generated_obj/pfstmo_durand02.o generated_obj/tmo_durand02.o generated_obj/bilateral.o generated_obj/fastbilateral.o generated_obj/pfstmo_fattal02.o generated_obj/tmo_fattal02.o generated_obj/pde.o generated_obj/pfstmo_reinhard05.o generated_obj/tmo_pattanaik00.o generated_obj/pfstmo_pattanaik00.o generated_obj/pfstmo_reinhard02.o generated_obj/tmo_reinhard02.o generated_obj/approx.o generated_obj/contrast_domain.o generated_obj/pfstmo_mantiuk06.o generated_obj/batch_dialog.o generated_obj/exif_operations.o generated_obj/moc_smart_scroll_area.o generated_obj/moc_panIconWidget.o generated_obj/moc_gamma_and_levels.o generated_obj/moc_gang.o generated_obj/moc_commandline.o generated_obj/moc_mainWindow.o generated_obj/moc_DnDOption.o generated_obj/moc_hdrviewer.o generated_obj/moc_luminancerange_widget.o generated_obj/moc_tonemappingDialog.o generated_obj/moc_tonemapping_widget.o generated_obj/moc_ldrviewer.o generated_obj/moc_tonemapperThread.o generated_obj/moc_loadHdrThread.o generated_obj/moc_hdrInputLoader.o generated_obj/moc_preferencesDialog.o generated_obj/moc_transplant.o generated_obj/moc_resizeDialog.o generated_obj/moc_projectiveDialog.o generated_obj/moc_HdrCreationManager.o generated_obj/moc_editingTools.o generated_obj/moc_previewWidget.o generated_obj/moc_newHdrWizard.o generated_obj/moc_batch_dialog.o generated_obj/qrc_icons.o -F/sw/lib/qt4-mac/lib -L/sw/lib/qt4-mac/lib -lexiv2 -lIlmImf -lImath -lHalf -lIex -lfftw3f -lm -ltiff -lIlmThread -L/sw/lib -ljpeg -lexpat -liconv -framework QtGui -framework QtCore Undefined symbols for architecture x86_64: _compress, referenced from: Imf::ZipCompressor::compress(char const*, int, int, char const*)in libIlmImf.a(ImfZipCompressor.o) Imf::Pxr24Compressor::compress(char const*, int, Imath::BoxImath::Vec2int , char const*)in libIlmImf.a(ImfPxr24Compressor.o) _uncompress, referenced from: Imf::ZipCompressor::uncompress(char const*, int, int, char const*)in libIlmImf.a(ImfZipCompressor.o) Imf::Pxr24Compressor::uncompress(char const*, int, Imath::BoxImath::Vec2int , char const*)in libIlmImf.a(ImfPxr24Compressor.o) ld: symbol(s) not found for architecture x86_64 collect2: ld returned 1 exit status [snip] __ZN7QString16codecForCStringsE$non_lazy_ptr in newHdrWizard.o QTableWidget::columnCount() const, referenced from: Ui_HdrWizardForm::setupUi(QDialog*) in newHdrWizard.o ld: symbol(s) not found for architecture i386 collect2: ld returned 1 exit status lipo: can't open input file: /var/tmp//cch1sazY.out (No such file or directory) make: *** [qtpfsgui.app/Contents/MacOS/qtpfsgui] Error 1 ### execution of make failed, exit code 2 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-qtpfsgui-mac-1.9.3-1002 (Reading database ... 149186 files and directories currently installed.) Removing fink-buildlock-qtpfsgui-mac-1.9.3-1002 ... Failed: phase compiling: qtpfsgui-mac-1.9.3-1002 failed [snip] Many thanks in advance, Alan On Wed, Dec 9, 2009 at 17:59, Alexander Hansen alexanderk.han...@gmail.comwrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 12/9/09 12:40 PM, Alan wrote: Hi there, I have Mac OSX 10.6.2 with Fink 64 bits updated by CVS and trying
[Fink-users] updating openbabel to from 2.0.2 to 2.2.3
Hi Justin, Is there any chance to get openbabel updated in Fink to version 2.2.3? Many thanks in advance, Alan -- Alan Wilter Sousa da Silva, D.Sc. PDBe group, PiMS project http://www.pims-lims.org/ EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK +44 (0)1223 492 583 (office) -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] qtpfsgui-mac failed in SL 10.6.2 with Fink
Hi there, I have Mac OSX 10.6.2 with Fink 64 bits updated by CVS and trying to install qtpfsgui-mac, without success: [snip] QTableWidget::columnCount() const, referenced from: Ui_HdrWizardForm::setupUi(QDialog*) in newHdrWizard.o ld: symbol(s) not found for architecture i386 collect2: ld returned 1 exit status lipo: can't open input file: /var/tmp//cc5prMlo.out (No such file or directory) make: *** [qtpfsgui.app/Contents/MacOS/qtpfsgui] Error 1 ### execution of make failed, exit code 2 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-qtpfsgui-mac-1.9.3-1002 (Reading database ... 142763 files and directories currently installed.) Removing fink-buildlock-qtpfsgui-mac-1.9.3-1002 ... Failed: phase compiling: qtpfsgui-mac-1.9.3-1002 failed Many thanks in advance, Alan -- Alan Wilter Sousa da Silva, D.Sc. PDBe group, PiMS project http://www.pims-lims.org/ EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK +44 (0)1223 492 583 (office) -- Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] findutils and Time Machine, two great tastes that don't go great together
On Sun, Oct 18, 2009 at 7:02 PM, monipol moni...@gmx.com wrote: Hello, Douglas. This looks like an upstream (GNU) bug. Would you please report it to them? Okay, I have reported the issue to them. |ouglas -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] findutils and Time Machine, two great tastes that don't go great together
I'm not sure where the right place to report fink package bugs is, so I'll do so here: The findutils package adds an anacron job that runs a find over all your filesystems in the wee hours of the morning in order to build the database for locate. Unfortunately, if you happen to have a Time Machine disk mounted, it seems that the find job will likely crash your Mac. I believe the reason for this is that Time Machine makes use of an interesting HFS+ capability wherein you can make hard links to directories. I'm guessing that Time Machine's extensive use of this feature causes find to rampantly eat up some sort of system resource, which when exhausted causes the system to crash. |ouglas -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] FEtk for Fink
Hi there, Can someone tell me if FEtk will be included in Fink? http://www.fetk.org/ I know that at least APBS may do use of it. Many thanks in advance. Alan -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] openmotif4 to replace openmotif3
Hi there, I have SN 10.6.1 with kernel and Fink set to 64 bits. All has been installing beautifully so far and I am even taking further. For example, for packages that asked for dependencies on openmotif3, I simply changed that for openmotif4 in their respective *.info files. For example, I did it for tetex.info and it installed and worked nicely. So I am recommending to the maintainer of tetex packages, in particular, and to others maintainers that have references to openmotif3, to review their *.info files and test it obviously. I suggested that for molmol.info and I saw today that the maintainer updated it for unstable. Molmol is working fine for me. Cheers, Alan -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] Fwd: Fink for me (10.6.1, XQuartz, 32 bit)
BTW, I am about to upgrade to SN 10.6 and I use xquartz 2.4.0. What should I do? Remove xquartz 2.4.0 or hope SN will do it for me? Many thanks, Alan On Mon, Sep 14, 2009 at 14:52, David Reiser dbrei...@earthlink.net wrote: On Sep 14, 2009, at 6:34 AM, monipol wrote: I'm not sure if Gnucash installs on 10.6/i386 (32 bits) but we've had reports from users who've installed it on 10.6/x86_64 (64 bits). I don't know about gcompris yet. Maybe other list subscribers have already tried it? Including my tests (successful on both 32 and 64 bit fink trees), I have reports of 3 successful gnucash2 installs in both 32 and 64 bits. The one failure was a 32 bit install that was an upgrade-in-place fink tree where xquartz 2.4.0 had been installed prior to the 10.6 upgrade. I started with clean fink installs after my 10.6 upgrade. Dave -- David Reiser dbrei...@earthlink.net -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] testing apbs-mpi
Sorry guys, I found another problem with apbs-mpi. It's because apbs-mpi.info is replacing /sw/bin/apbs instead of putting another binary called, e.g., /sw/bin/apbs_mpi then when running apbs (with mpi) the output dx file will be appended with -PE0, no matter what one defines in the apbs.in input file, e.g.: output.dx with apbs (with mpi) will became: output-PE0.dx and if one uses many cores then there will be output-PE1.dx and so on. This is not a problem at first for those who use apbs at command line but apbs plugin for pymol and vmd will be disrupted. Eventually, I will suggest at pymol and vmd maling list the suggestion of enabling their plugin to be able to use multi core (for abps mpi enable). But because of the very peculiar way how apbs with mpi is developed (it needs to be addressed at the apbs.in input file as well and not only by mpirun -c #cpus command as many programmes like mdrun_mpi from gromacs) this is likely not simple. Cheers, Alan On Mon, Aug 17, 2009 at 07:57, Alan alanwil...@gmail.com wrote: I think it's fixed at least with openmpi since apbs-mpi is working as expected AFAIK. Cheers, Alan On Mon, Aug 17, 2009 at 03:57, William G. Scott wgsc...@chemistry.ucsc.edu wrote: Hi Alan: Sorry, I was away in the most inaccessible part of Utah I could find. I think Jack Howarth fixed it in my absence, but if not, please let me know. Sorry for this continuing nightmare. Bill On Aug 14, 2009, at 12:35 AM, Alan wrote: Starting to answer myself, I did this test with a custom compiled version of apbs: ~/Programmes/apbs-1.1.0-source% ./configure --enable-fast --with-openmpi=/usr make all cd examples/actin-dimer /usr/bin/mpirun -c 8 ../../bin/apbs apbs-mol-parallel.in WORKED! Than I realise that --with-openmpi= flag is missing in apbs-mpi-openmpi, although it's using mpicc and mpif77, but it seems not to be enough, specially because mpi is not compatible with python as I read from the configure script. And looking better at the configure script, this mpif77/python combination only pass because '--with-openmpi' is not declared and to test to avoid this incompatibility is not checked. So, I am sorry Bill Scott, but apbs-mpi is not OK yet. HOWEVER, if I put ./configure --enable-fast --with-openmpi=/sw I got this error: [snip] checking for --with-openmpi option... /sw checking for /sw/include/mpi.h... yes checking for /sw/lib/libmpi.a... no checking for /sw/lib/libmpi.so... no checking for /sw/lib/libmpi.dylib... no configure: error: Error...Could not find OpenMPI libraries in /sw/lib Well, libmpi.dylib is in /sw/lib/openmpi and frankly after reading ./configure --help all combinations I tried and I didn't get it to work with Fink openmpi libs. Any help here would be very appreciated. Cheers, Alan On Thu, Aug 13, 2009 at 17:22, Alan alanwil...@gmail.com wrote: Hi There, So I installed apbs-mpi-openmpi and it seems to work fine but when trying this link to run in multi-core machine: http://apbs.wustl.edu/MediaWiki/index.php/How_do_I_run_a_calculation_that%27s_too_big_for_my_computer%3F I got this message and nothing done. [snip] Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e NOsh_setupCalcMGPARA: Oops! You're trying to perform an 'mg-para' (parallel) calculation NOsh_setupCalcMGPARA: with a version of APBS that wasn't compiled with MPI! NOsh_setupCalcMGPARA: Perhaps you meant to use the 'async' flag? NOsh_setupCalcMGPARA: Bailing out! [snip] Checking my apbs and libmpi is there: ldd `which apbs` /sw/bin/apbs: /System/Library/Frameworks/vecLib.framework/Versions/A/vecLib (compatibility version 1.0.0, current version 242.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.4) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib (compatibility version 1.0.0, current version 218.0.0) /sw/lib/openmpi/libmpi_f77.0.dylib (compatibility version 1.0.0, current version 1.0.0) /sw/lib/openmpi/libmpi.0.dylib (compatibility version 1.0.0, current version 1.0.0) /sw/lib/openmpi/libopen-rte.0.dylib (compatibility version 1.0.0, current version 1.0.0) /sw/lib/openmpi/libopen-pal.0.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libutil.dylib (compatibility version 1.0.0, current version 1.0.0) /sw/lib/gcc4.4/lib/libgfortran.3.dylib (compatibility version 4.0.0, current version 4.0.0) /sw/lib/gcc4.4/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) om-mpirun -c 2 apbs ... doesn't work either. Any ideas? Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Alan Wilter S. da Silva, D.Sc. - CCPN
Re: [Fink-users] testing apbs-mpi
I think it's fixed at least with openmpi since apbs-mpi is working as expected AFAIK. Cheers, Alan On Mon, Aug 17, 2009 at 03:57, William G. Scott wgsc...@chemistry.ucsc.eduwrote: Hi Alan: Sorry, I was away in the most inaccessible part of Utah I could find. I think Jack Howarth fixed it in my absence, but if not, please let me know. Sorry for this continuing nightmare. Bill On Aug 14, 2009, at 12:35 AM, Alan wrote: Starting to answer myself, I did this test with a custom compiled version of apbs: ~/Programmes/apbs-1.1.0-source% ./configure --enable-fast --with-openmpi=/usr make all cd examples/actin-dimer /usr/bin/mpirun -c 8 ../../bin/apbs apbs-mol-parallel.in WORKED! Than I realise that --with-openmpi= flag is missing in apbs-mpi-openmpi, although it's using mpicc and mpif77, but it seems not to be enough, specially because mpi is not compatible with python as I read from the configure script. And looking better at the configure script, this mpif77/python combination only pass because '--with-openmpi' is not declared and to test to avoid this incompatibility is not checked. So, I am sorry Bill Scott, but apbs-mpi is not OK yet. HOWEVER, if I put ./configure --enable-fast --with-openmpi=/sw I got this error: [snip] checking for --with-openmpi option... /sw checking for /sw/include/mpi.h... yes checking for /sw/lib/libmpi.a... no checking for /sw/lib/libmpi.so... no checking for /sw/lib/libmpi.dylib... no configure: error: Error...Could not find OpenMPI libraries in /sw/lib Well, libmpi.dylib is in /sw/lib/openmpi and frankly after reading ./configure --help all combinations I tried and I didn't get it to work with Fink openmpi libs. Any help here would be very appreciated. Cheers, Alan On Thu, Aug 13, 2009 at 17:22, Alan alanwil...@gmail.com wrote: Hi There, So I installed apbs-mpi-openmpi and it seems to work fine but when trying this link to run in multi-core machine: http://apbs.wustl.edu/MediaWiki/index.php/How_do_I_run_a_calculation_that%27s_too_big_for_my_computer%3F I got this message and nothing done. [snip] Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e NOsh_setupCalcMGPARA: Oops! You're trying to perform an 'mg-para' (parallel) calculation NOsh_setupCalcMGPARA: with a version of APBS that wasn't compiled with MPI! NOsh_setupCalcMGPARA: Perhaps you meant to use the 'async' flag? NOsh_setupCalcMGPARA: Bailing out! [snip] Checking my apbs and libmpi is there: ldd `which apbs` /sw/bin/apbs: /System/Library/Frameworks/vecLib.framework/Versions/A/vecLib (compatibility version 1.0.0, current version 242.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.4) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib (compatibility version 1.0.0, current version 218.0.0) /sw/lib/openmpi/libmpi_f77.0.dylib (compatibility version 1.0.0, current version 1.0.0) /sw/lib/openmpi/libmpi.0.dylib (compatibility version 1.0.0, current version 1.0.0) /sw/lib/openmpi/libopen-rte.0.dylib (compatibility version 1.0.0, current version 1.0.0) /sw/lib/openmpi/libopen-pal.0.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libutil.dylib (compatibility version 1.0.0, current version 1.0.0) /sw/lib/gcc4.4/lib/libgfortran.3.dylib (compatibility version 4.0.0, current version 4.0.0) /sw/lib/gcc4.4/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) om-mpirun -c 2 apbs ... doesn't work either. Any ideas? Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] testing apbs-mpi
Still, is it possible to make openmpi with a handle for xgrid? It should be as simple as openmpi-static and openmpi-shared. Of course that it's not urgent since xgrid support is broken in openmpi 1.3.x series so far. Cheers, Alan On Sat, Aug 15, 2009 at 18:35, Daniel Macks dma...@netspace.org wrote: On Sat, Aug 15, 2009 at 01:30:47PM -0400, Jack Howarth wrote: Daniel, I added static library support to openmpi because of complaints from folks trying to build static binaries via fink for distributing their programs. I would rather leave that in as my philosophy is that fink should do whatever possible to discourage users from installing their own copies of libraries in /usr/local or resorting to MacPorts. I guess it's impossible to satisfy everyone. Yup, maintainers' decision as always. Whatever works for your known major audience and is at least functional for everyone else is fine. dan -- Daniel Macks dma...@netspace.org http://www.netspace.org/~dmacks -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] testing apbs-mpi
Thanks Jack, I am using you files anyway. Excellent job. Alan On Sat, Aug 15, 2009 at 03:47, Jack Howarth howa...@bromo.med.uc.eduwrote: Alan, I have uploaded a first pass of new apbs-mpi packaging which builds apbs properly against openmpi. It probably still needs work to make compatible with the lammpi variant. The packaging is on fink tracking at... https://sourceforge.net/tracker/index.php?func=detailaid=2838001group_id=17203atid=414256 Jack -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] testing apbs-mpi
Starting to answer myself, I did this test with a custom compiled version of apbs: ~/Programmes/apbs-1.1.0-source% ./configure --enable-fast --with-openmpi=/usr make all cd examples/actin-dimer /usr/bin/mpirun -c 8 ../../bin/apbs apbs-mol-parallel.in WORKED! Than I realise that --with-openmpi= flag is missing in apbs-mpi-openmpi, although it's using mpicc and mpif77, but it seems not to be enough, specially because mpi is not compatible with python as I read from the configure script. And looking better at the configure script, this mpif77/python combination only pass because '--with-openmpi' is not declared and to test to avoid this incompatibility is not checked. So, I am sorry Bill Scott, but apbs-mpi is not OK yet. HOWEVER, if I put ./configure --enable-fast --with-openmpi=/sw I got this error: [snip] checking for --with-openmpi option... /sw checking for /sw/include/mpi.h... yes checking for /sw/lib/libmpi.a... no checking for /sw/lib/libmpi.so... no checking for /sw/lib/libmpi.dylib... no configure: error: Error...Could not find OpenMPI libraries in /sw/lib Well, libmpi.dylib is in /sw/lib/openmpi and frankly after reading ./configure --help all combinations I tried and I didn't get it to work with Fink openmpi libs. Any help here would be very appreciated. Cheers, Alan On Thu, Aug 13, 2009 at 17:22, Alan alanwil...@gmail.com wrote: Hi There, So I installed apbs-mpi-openmpi and it seems to work fine but when trying this link to run in multi-core machine: http://apbs.wustl.edu/MediaWiki/index.php/How_do_I_run_a_calculation_that%27s_too_big_for_my_computer%3F I got this message and nothing done. [snip] Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e NOsh_setupCalcMGPARA: Oops! You're trying to perform an 'mg-para' (parallel) calculation NOsh_setupCalcMGPARA: with a version of APBS that wasn't compiled with MPI! NOsh_setupCalcMGPARA: Perhaps you meant to use the 'async' flag? NOsh_setupCalcMGPARA: Bailing out! [snip] Checking my apbs and libmpi is there: ldd `which apbs` /sw/bin/apbs: /System/Library/Frameworks/vecLib.framework/Versions/A/vecLib (compatibility version 1.0.0, current version 242.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.4) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib (compatibility version 1.0.0, current version 218.0.0) /sw/lib/openmpi/libmpi_f77.0.dylib (compatibility version 1.0.0, current version 1.0.0) /sw/lib/openmpi/libmpi.0.dylib (compatibility version 1.0.0, current version 1.0.0) /sw/lib/openmpi/libopen-rte.0.dylib (compatibility version 1.0.0, current version 1.0.0) /sw/lib/openmpi/libopen-pal.0.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libutil.dylib (compatibility version 1.0.0, current version 1.0.0) /sw/lib/gcc4.4/lib/libgfortran.3.dylib (compatibility version 4.0.0, current version 4.0.0) /sw/lib/gcc4.4/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) om-mpirun -c 2 apbs ... doesn't work either. Any ideas? Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] openmpi with xgrid
Yep, I did some tests and found out that to have xgrid support I need to have --disable-static. So I did in openmpi.info and it compiled and installed OK. But when I went to test... /sw/bin/om-mpirun -c 2 mpiapp [amadeus.local:38063] [[2798,0],0] ORTE_ERROR_LOG: Unknown error: 1 in file src/plm_xgrid_module.m at line 119 [amadeus.local:38063] [[2798,0],0] ORTE_ERROR_LOG: Unknown error: 1 in file src/plm_xgrid_module.m at line 153 I will bother openmpi mailing list now :-) AFAIK, you need 'sudo xgridctl c start' running if using openmpi with xgrid. I understand that many doesn't want or need this functionality but having a 'openmpi-xgrid' option in fink would be plus (at least for me). Cheers, Alan On Thu, Aug 13, 2009 at 14:18, Jack Howarth howa...@bromo.med.uc.eduwrote: The failure to build the Xgrid support appears to be related to its incompatibility with the -enable-static configure option... http://www.open-mpi.org/community/lists/users/2007/08/3900.php I would complain to upstream. -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] openmpi with xgrid
Dear all, I am looking at the fink compilation of openmpi and trying to understand that: [snip] --- MCA component plm:xgrid (m4 configuration macro) checking for MCA component plm:xgrid compile mode... static checking if C and Objective C are link compatible... yes checking for XgridFoundation Framework... yes configure: WARNING: XGrid components must be built as DSOs. Disabling checking if MCA component plm:xgrid can compile... no [snip] AFAIU I ended up with openmpi without support for xgrid, even if I modify openmpi.info to add --with-xgrid. Can someone elaborate here and tell what XGrid components must be built as DSOs. means and if it would be possible to get openmpi with xgrid support? Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] openmpi with xgrid
I believe you're right because I saw some reference to that elsewhere. I will carry some tests here. Thanks. Alan On Thu, Aug 13, 2009 at 14:18, Jack Howarth howa...@bromo.med.uc.eduwrote: The failure to build the Xgrid support appears to be related to its incompatibility with the -enable-static configure option... http://www.open-mpi.org/community/lists/users/2007/08/3900.php I would complain to upstream. -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] openmpi with xgrid
I was about to do a similar question and here it goes: Why actually openmpi in Fink is compiled with static? Alan On Thu, Aug 13, 2009 at 16:16, Daniel Macks dma...@netspace.org wrote: On Thu, Aug 13, 2009 at 09:18:30AM -0400, Jack Howarth wrote: The failure to build the Xgrid support appears to be related to its incompatibility with the -enable-static configure option... http://www.open-mpi.org/community/lists/users/2007/08/3900.php I would complain to upstream. Are the static libs useful to us (the fink world)? Most library packages in fink --disable-static because it saves a huge amount of compile time and other packages that use the libs only use the shared libs. dan -- Daniel Macks dma...@netspace.org http://www.netspace.org/~dmacks -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] testing apbs-mpi-openmpi
Hi There, So I installed apbs-mpi-openmpi and it seems to work fine but when trying this link to run in multi-core machine: http://apbs.wustl.edu/MediaWiki/index.php/How_do_I_run_a_calculation_that%27s_too_big_for_my_computer%3F I got this message and nothing done. [snip] Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e NOsh_setupCalcMGPARA: Oops! You're trying to perform an 'mg-para' (parallel) calculation NOsh_setupCalcMGPARA: with a version of APBS that wasn't compiled with MPI! NOsh_setupCalcMGPARA: Perhaps you meant to use the 'async' flag? NOsh_setupCalcMGPARA: Bailing out! [snip] Checking my apbs and libmpi is there: ldd `which apbs` /sw/bin/apbs: /System/Library/Frameworks/vecLib.framework/Versions/A/vecLib (compatibility version 1.0.0, current version 242.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.4) /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib (compatibility version 1.0.0, current version 218.0.0) /sw/lib/openmpi/libmpi_f77.0.dylib (compatibility version 1.0.0, current version 1.0.0) /sw/lib/openmpi/libmpi.0.dylib (compatibility version 1.0.0, current version 1.0.0) /sw/lib/openmpi/libopen-rte.0.dylib (compatibility version 1.0.0, current version 1.0.0) /sw/lib/openmpi/libopen-pal.0.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libutil.dylib (compatibility version 1.0.0, current version 1.0.0) /sw/lib/gcc4.4/lib/libgfortran.3.dylib (compatibility version 4.0.0, current version 4.0.0) /sw/lib/gcc4.4/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) om-mpirun -c 2 apbs ... doesn't work either. Any ideas? Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] rasmol md5 seems broken
Hi there, Updating my Fink (x86_64) and I got that: How do you want to proceed? [2] curl --connect-timeout 30 -f -L -A 'fink/0.29.99.cvs' -O http://www.bernstein-plus-sons.com/software/RasMol_2.7.5.tar.gz % Total% Received % Xferd Average Speed TimeTime Time Current Dload Upload Total SpentLeft Speed 100 9538k 100 9538k0 0 545k 0 0:00:17 0:00:17 --:--:-- 575k The checksum of the file is incorrect. The most likely cause for this is a corrupted or incomplete download Expected: 0c4a0a349c9a872a091b2ffc842f405b Actual: MD5(2f43c606775248398dc71ce559b35245) SHA1(0e307d7a789d4cd201862c317b21d5d7e67730cf) Downloading the file RasMol_2.7.5.tar.gz failed. (1) Give up (2) Retry the same mirror Failed: file download failed for RasMol_2.7.5.tar.gz of package rasmol-2.7.5-1 Maintainer cc'ed. Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] transfig for fink 64bits
Hi Dave, I am using Fink bootstrapped for 64 bits. Almost all programs I've installed so far are working fine and in 64 bits except transfig, that is compiled, installed and works but: /sw/bin% for i in `ls`; do file $i ;done | grep 386 fig2dev: Mach-O executable i386 transfig: Mach-O executable i386 Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] failed for boost-jam in fink x86_64
Hi there, I am trying to install boost1.35 in Fink bootstrapped for 64 bits. It requires boost-jam and when compiling it, it fails with: fink install boost1.35.nopython Password: Information about 9125 packages read in 1 seconds. The following package will be installed or updated: boost1.35.nopython The following 2 additional packages will be installed: boost-jam boost1.35.nopython-shlibs Do you want to continue? [Y/n] curl --connect-timeout 30 -f -L -A 'fink/0.29.99.cvs' -O http://distfiles.master.finkmirrors.net/boost-jam-3.1.16.tgz % Total% Received % Xferd Average Speed TimeTime Time Current Dload Upload Total SpentLeft Speed 100 1132k 100 1132k0 0 208k 0 0:00:05 0:00:05 --:--:-- 235k curl --connect-timeout 30 -f -L -A 'fink/0.29.99.cvs' -O http://distfiles.master.finkmirrors.net/boost_1_35_0.tar.bz2 % Total% Received % Xferd Average Speed TimeTime Time Current Dload Upload Total SpentLeft Speed 100 22.3M 100 22.3M0 0 205k 0 0:01:51 0:01:51 --:--:-- 242k Setting runtime build-lock... dpkg-deb -b /sw/src/fink.build/root-fink-buildlock-boost-jam-3.1.16-1 /sw/src/fink.build dpkg-deb: building package `fink-buildlock-boost-jam-3.1.16-1' in `/sw/src/fink.build/fink-buildlock-boost-jam-3.1.16-1_2009.08.03-08.05.59_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/src/fink.build/fink-buildlock-boost-jam-3.1.16-1_2009.08.03-08.05.59_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-boost-jam-3.1.16-1. (Reading database ... 85226 files and directories currently installed.) Unpacking fink-buildlock-boost-jam-3.1.16-1 (from .../fink-buildlock-boost-jam-3.1.16-1_2009.08.03-08.05.59_darwin-x86_64.deb) ... Setting up fink-buildlock-boost-jam-3.1.16-1 (2009.08.03-08.05.59) ... gzip -dc /sw/src/boost-jam-3.1.16.tgz | /sw/bin/tar -xf - --no-same-owner --no-same-permissions sh ./build.sh ### ### Using 'darwin' toolset. ### rm -rf bootstrap mkdir bootstrap cc -o bootstrap/jam0 command.c compile.c debug.c expand.c glob.c hash.c hdrmacro.c headers.c jam.c jambase.c jamgram.c lists.c make.c make1.c newstr.c option.c output.c parse.c pathunix.c pathvms.c regexp.c rules.c scan.c search.c subst.c timestamp.c variable.c modules.c strings.c filesys.c builtins.c pwd.c class.c native.c w32_getreg.c modules/set.c modules/path.c modules/regex.c modules/property-set.c modules/sequence.c modules/order.c execunix.c fileunix.c ./bootstrap/jam0 -f build.jam --toolset=darwin --toolset-root= clean ...found 1 target... ...updating 1 target... ...updated 1 target... ./bootstrap/jam0 -f build.jam --toolset=darwin --toolset-root= ...found 47 targets... ...updating 2 targets... [MKDIR] bin.macosxx86_64 [COMPILE] bin.macosxx86_64/bjam ...updated 2 targets... /bin/rm -rf /sw/src/fink.build/root-boost-jam-3.1.16-1 /bin/mkdir -p /sw/src/fink.build/root-boost-jam-3.1.16-1/sw /bin/mkdir -p /sw/src/fink.build/root-boost-jam-3.1.16-1/DEBIAN /usr/sbin/chown -R root:admin /sw/src/fink.build/root-boost-jam-3.1.16-1 /var/tmp/tmp.1.NlBSyb #!/bin/sh -ev case x86_64 in powerpc) machine=ppc;; i386) machine=x86;; esac mkdir /sw/src/fink.build/root-boost-jam-3.1.16-1/sw/bin cp bin.macosx$machine/* /sw/src/fink.build/root-boost-jam-3.1.16-1/sw/bin cp: cannot stat `bin.macosx/*': No such file or directory ### execution of /var/tmp/tmp.1.NlBSyb failed, exit code 1 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-boost-jam-3.1.16-1 (Reading database ... 85227 files and directories currently installed.) Removing fink-buildlock-boost-jam-3.1.16-1 ... Failed: phase installing: boost-jam-3.1.16-1 failed The solution would be be simply adding x86_64) machine=x86_64;; to the case clause. Many thanks in advance. Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] failed to install apbs
just-created
`/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vfetk.h' with
`src/fem/apbs/vfetk.h'
cp: will not overwrite just-created
`/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vpee.h' with
`src/fem/apbs/vpee.h'
cp: will not overwrite just-created
`/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./apolparm.h' with
`src/generic/apbs/apolparm.h'
cp: will not overwrite just-created
`/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./femparm.h' with
`src/generic/apbs/femparm.h'
cp: will not overwrite just-created
`/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./mgparm.h' with
`src/generic/apbs/mgparm.h'
cp: will not overwrite just-created
`/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./nosh.h' with
`src/generic/apbs/nosh.h'
cp: will not overwrite just-created
`/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./pbeparm.h' with
`src/generic/apbs/pbeparm.h'
cp: will not overwrite just-created
`/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vacc.h' with
`src/generic/apbs/vacc.h'
cp: will not overwrite just-created
`/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./valist.h' with
`src/generic/apbs/valist.h'
cp: will not overwrite just-created
`/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vatom.h' with
`src/generic/apbs/vatom.h'
cp: will not overwrite just-created
`/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vcap.h' with
`src/generic/apbs/vcap.h'
cp: will not overwrite just-created
`/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vclist.h' with
`src/generic/apbs/vclist.h'
cp: will not overwrite just-created
`/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vgreen.h' with
`src/generic/apbs/vgreen.h'
cp: will not overwrite just-created
`/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vhal.h' with
`src/generic/apbs/vhal.h'
cp: will not overwrite just-created
`/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vparam.h' with
`src/generic/apbs/vparam.h'
cp: will not overwrite just-created
`/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vpbe.h' with
`src/generic/apbs/vpbe.h'
cp: will not overwrite just-created
`/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vstring.h' with
`src/generic/apbs/vstring.h'
cp: will not overwrite just-created
`/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vunit.h' with
`src/generic/apbs/vunit.h'
cp: will not overwrite just-created
`/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vgrid.h' with
`src/mg/apbs/vgrid.h'
cp: will not overwrite just-created
`/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmgrid.h' with
`src/mg/apbs/vmgrid.h'
cp: will not overwrite just-created
`/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vopot.h' with
`src/mg/apbs/vopot.h'
cp: will not overwrite just-created
`/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vpmg.h' with
`src/mg/apbs/vpmg.h'
cp: will not overwrite just-created
`/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vpmgp.h' with
`src/mg/apbs/vpmgp.h'
### execution of /var/tmp/tmp.2.awaCJH failed, exit code 1
Removing runtime build-lock...
Removing build-lock package...
/sw/bin/dpkg-lockwait -r fink-buildlock-apbs-1.1.0-4
(Reading database ... 83144 files and directories currently installed.)
Removing fink-buildlock-apbs-1.1.0-4 ...
Failed: phase installing: apbs-1.1.0-4 failed
On Sun, Aug 2, 2009 at 02:45, William Scott wgsc...@chemistry.ucsc.eduwrote:
Hopefully it will work now. (revision 4)
On Sat, August 1, 2009 3:48 pm, Martin Costabel wrote:
William G. Scott wrote:
It turns out there is a typo on line 38 of the patch file
+sitepk...@install_dir$${prefix}/lib/python${PY_VERSION}/site-packages
should be
+sitepk...@install_dir@${prefix}/lib/python${PY_VERSION}/site-packages
This corrects the problem you found.
However there are some additional problems in that it tries to install
the examples, doc and tools directly into /sw/share, so I need to fix
that as well.
Also, there is a problem with the source tarball. I get a checksum
mismatch (same after repeated downloads):
The checksum of the file apbs-1.1.0-source.tar.gz of package apbs-1.1.0-3
is
incorrect. The most likely cause for this is a corrupted or incomplete
download
Expected: 8b844ba848cf853da712bbbf9f2e1553
Actual: MD5(ca31ba09714e4fc9acce91e7961569cd)
SHA1(7274a3a896da551f2bb689bb32ea5c852cbd32bb)
And the patch does not apply:
sed 's|@INSTALL_DIR@|/sw/src/fink.build/root-apbs-1.1.0-3|g'
/sw/fink/dists/unstable/main/finkinfo/sci/apbs.patch | patch -p1
patching file tools/python/Makefile.in
Hunk #1 FAILED at 52.
Hunk #2 FAILED at 234.
The reason is that in the source file there is
${top_builddir}/contrib/blas/.libs/libapbsblas.a, whereas the patch file
talks about ${top_builddir}/contrib/lib/libapbsblas.a.
--
Martin
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
--
Alan Wilter S. da Silva, D.Sc
Re: [Fink-users] failed to install apbs
And I know why: where just 'cp' replace with '/bin/cp'. I guess I had problem because I use package 'coreutils' Many thansk William! Cheers, Alan On Sun, Aug 2, 2009 at 12:13, Alan alanwil...@gmail.com wrote: Really sorry, but it didn't work for me... even after a fresh install. # # make install DESTDIR=%d # install it ourselves: mkdir -p /sw/src/fink.build/root-apbs-1.1.0-4/sw/bin cp bin/apbs bin/ApbsClient.py /sw/src/fink.build/root-apbs-1.1.0-4/sw/bin/. echo '#!/sw/bin/python2.6' | /sw/src/fink.build/root-apbs-1.1.0-4/sw/bin/wsdl2py echo from ZSI.generate.commands import wsdl2py /sw/src/fink.build/root-apbs-1.1.0-4/sw/bin/wsdl2py echo wsdl2py() /sw/src/fink.build/root-apbs-1.1.0-4/sw/bin/wsdl2py chmod a+x /sw/src/fink.build/root-apbs-1.1.0-4/sw/bin/wsdl2py # mkdir -p /sw/src/fink.build/root-apbs-1.1.0-4/sw/share/apbs cp -r examples /sw/src/fink.build/root-apbs-1.1.0-4/sw/share/apbs/. cp -r tools /sw/src/fink.build/root-apbs-1.1.0-4/sw/share/apbs/. cp -r doc /sw/src/fink.build/root-apbs-1.1.0-4/sw/share/apbs/. # mkdir -p /sw/src/fink.build/root-apbs-1.1.0-4/sw/share/doc ln -s /sw/share/apbs/doc /sw/src/fink.build/root-apbs-1.1.0-4/sw/share/doc/apbs # mkdir -p /sw/src/fink.build/root-apbs-1.1.0-4/sw/lib/python2.6/site-packages/ZSI cp -r contrib/opal/ZSI/ZSI/* /sw/src/fink.build/root-apbs-1.1.0-4/sw/lib/python2.6/site-packages/ZSI/. # mkdir -p /sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs cp **/*.h /sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/. cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./maloc.h' with `contrib/maloc/src/aaa_inc/maloc/maloc.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./maloc_base.h' with `contrib/maloc/src/aaa_inc/maloc/maloc_base.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./psh.h' with `contrib/maloc/src/aaa_inc/maloc/psh.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vcom.h' with `contrib/maloc/src/aaa_inc/maloc/vcom.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vio.h' with `contrib/maloc/src/aaa_inc/maloc/vio.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmem.h' with `contrib/maloc/src/aaa_inc/maloc/vmem.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmp.h' with `contrib/maloc/src/aaa_inc/maloc/vmp.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmpi.h' with `contrib/maloc/src/aaa_inc/maloc/vmpi.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vnm.h' with `contrib/maloc/src/aaa_inc/maloc/vnm.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vset.h' with `contrib/maloc/src/aaa_inc/maloc/vset.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vsh.h' with `contrib/maloc/src/aaa_inc/maloc/vsh.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vsys.h' with `contrib/maloc/src/aaa_inc/maloc/vsys.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./maloc_base.h' with `contrib/maloc/src/base/maloc/maloc_base.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./psh.h' with `contrib/maloc/src/psh/maloc/psh.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vcom.h' with `contrib/maloc/src/psh/maloc/vcom.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmp.h' with `contrib/maloc/src/psh/maloc/vmp.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmpi.h' with `contrib/maloc/src/psh/maloc/vmpi.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vsh.h' with `contrib/maloc/src/vsh/maloc/vsh.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vio.h' with `contrib/maloc/src/vsys/maloc/vio.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vmem.h' with `contrib/maloc/src/vsys/maloc/vmem.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vnm.h' with `contrib/maloc/src/vsys/maloc/vnm.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vset.h' with `contrib/maloc/src/vsys/maloc/vset.h' cp: will not overwrite just-created `/sw/src/fink.build/root-apbs-1.1.0-4/sw/include/apbs/./vsys.h' with `contrib/maloc/src/vsys
Re: [Fink-users] failed to install apbs
Hi there,
Well, I found this:
find /sw/src/fink.build | grep site
/sw/src/fink.build/apbs-1.1.0-2/apbs-1.1.0-source/contrib/opal/ZSI/@INSTALL_DIR45643{prefix}/lib/python2.6/site-packages
Apparently, at least IMHO, variable @INSTALL_DIR@ is not correctly being
replaced in apbs.info:
sed 's|@INSTALL_DIR@|%d|g' %{PatchFile} | patch -p1
In a test, I commented out in apbs.info any reference to python, including
the patch and I got apbs deb and working.
Dear William, would be possible to you to send me your apbs.info and
apbs.patch from sw64/ as well as your apbs deb package?
Many thanks in advance.
Alan
On Fri, Jul 31, 2009 at 19:35, Alexander Hansen alexanderk.han...@gmail.com
wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
William Scott wrote:
There's something funny going on in the install script. For one thing,
it's installing files in
/sw/src/fink.build/root-apbs-1.1.0-2/sw/src/fink.build/apbs-1.1.0-2/
I also found the ordering a bit suspect:
make install DESTDIR=%d
rm -Rf **/CVS # fink validate complains if this junk is left behind.
# rm -Rf **/.svn # fink validate complains if this junk is left behind.
mkdir -p %i/share/%n
mkdir -p %i/lib
I'd have assumed that we'd want to create those directories before 'make
install'.
- --
Alexander Hansen
Fink User Liaison
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.9 (Darwin)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
iEYEARECAAYFAkpzNMMACgkQB8UpO3rKjQ9ATgCeK9rkwdv7mt61pFn/rdc4RRwu
zPEAniLUCPlwooATD+lGYN9Fd+2w6cto
=V8ih
-END PGP SIGNATURE-
I'll be happy to change anything, but in my hands it works, and
validates:
% fink -v validate apbs_1.1.0-2_darwin-x86_64.deb
apbs-dev_1.1.0-2_darwin-x86_64.deb
Validating .deb file apbs_1.1.0-2_darwin-x86_64.deb...
Package looks good!
Validating .deb file
I'm trying to find if there is a missing dependency. We have the
identical setup, apart from my /sw64 vs. his /sw.
(I've emailed him back off-list).
Bill
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
It doesn't work here (10.5.7/i386)--I get an identical error to Alan.
- --
Alexander Hansen
Fink User Liaison
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.9 (Darwin)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
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=350/
-END PGP SIGNATURE-
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http://www.bio.cam.ac.uk/~awd28
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Re: [Fink-users] failed to install apbs
Dear Alexander,
When you did a fresh install, the first package you installed was fink
install apbs and the lots of dependences (including python 2.6) came
together, right?
Looking at the error and log I have the suspicion that if I install apbs and
then during the process python 2.6 is build I will not have such a problem
as you saw by yourself.
I will test something here...
Cheers,
Alan
On Sat, Aug 1, 2009 at 15:33, Alexander Hansen
alexanderk.han...@gmail.comwrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Alan wrote:
Hi there,
Well, I found this:
find /sw/src/fink.build | grep site
/sw/src/fink.build/apbs-1.1.0-2/apbs-1.1.0-source/contrib/opal/ZSI/@INSTALL_DIR45643{prefix}/lib/python2.6/site-packages
Apparently, at least IMHO, variable @INSTALL_DIR@ is not correctly being
replaced in apbs.info:
sed 's|@INSTALL_DIR@|%d|g' %{PatchFile} | patch -p1
In a test, I commented out in apbs.info any reference to python,
including
the patch and I got apbs deb and working.
Dear William, would be possible to you to send me your apbs.info and
apbs.patch from sw64/ as well as your apbs deb package?
Many thanks in advance.
Alan
It uses the same .info and .patch files on 32bit and 64bit ; that's not
the issue.
I was able to get apbs to build correctly on a clean 32 bit tree, so the
issue is presumably interference with some other installed package.
Unfortunately when I checked, the build logs didn't show any substantive
differences until the point of failure, so it's not clear yet what the
offending package might be.
You can get a .deb yourself, as William has been good enough to provide
an unofficial binary repository:
http://finkers.wordpress.com/2009/06/01/fink-and-binary-distributions/
- --
Alexander Hansen
Fink User Liaison
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.9 (Darwin)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
iEYEARECAAYFAkp0UkMACgkQB8UpO3rKjQ8T/ACggeFPd0peqyGbFYYaE4eHUTHu
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-END PGP SIGNATURE-
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http://www.bio.cam.ac.uk/~awd28
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[Fink-users] failed to install apbs
/site-packages/ This directory does not currently exist. Please create it and try again, or choose a different installation directory (using the -d or --install-dir option). make[5]: *** [install-data-local] Error 1 make[4]: *** [install-am] Error 2 make[3]: *** [install-recursive] Error 1 make[2]: *** [install-recursive] Error 1 make[1]: *** [install-recursive] Error 1 make: *** [install-recursive] Error 1 ### execution of /var/tmp/tmp.2.h0L77s failed, exit code 2 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-apbs-1.1.0-2 (Reading database ... 123610 files and directories currently installed.) Removing fink-buildlock-apbs-1.1.0-2 ... Failed: phase installing: apbs-1.1.0-2 failed I hope you can help me to solve this issue. Thanks in advance, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] scipy-py26 x86_64 from Fink
Hi List, scipy-py26 x86_64 from Fink. Scipy-py26 worked for me, but I have to do this: # modify /sw/fink/10.4/unstable/main/finkinfo/sci/scipy-py.info: gcc43 - gcc44 fink install scipy-py26 Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] dbus in 64 bits
Hi there, When I try fink install dbus, I got that: [snip] #!/bin/sh -ev MBID=`id -u messagebus 2/dev/null || echo 0` id -u messagebus 2/dev/null || echo 0 if [ $MBID -eq 0 ]; then echo You must install the 'passwd' package for D-Bus to build properly. exit 1 fi You must install the 'passwd' package for D-Bus to build properly. [snip] Running id -u messagebus: id: messagebus: No such user So, I believe that I have to create this user, but how to do it safely? Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] povray for fink 64 bits failing
Hi List,
I tried fink install povray for fink with x86_64 and it failed. Here
goes some info:
[snip]
Supporting libraries
configure: configuring in libraries/png
configure: running /bin/sh './configure.gnu' --prefix=/sw
'--prefix=/sw' '--mandir=/sw/src/fink.build/root-povray-3.61-1002/sw/share/man'
'COMPILED_BY=Andrew Rohl as part of Fink' 'CPPFLAGS=-I/sw/include'
'LDFLAGS=-L/sw/lib' --cache-file=/dev/null --srcdir=.
configure.gnu: configuring libpng 1.2.5
configure.gnu: running ./configure --srcdir=. --cache-file=/dev/null
--prefix=/sw --prefix=/sw
--mandir=/sw/src/fink.build/root-povray-3.61-1002/sw/share/man
checking build system type... i686-apple-darwin9.7.1
checking host system type... i686-apple-darwin9.7.1
checking for a BSD-compatible install... /sw/bin/ginstall -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking for gcc... gcc
checking for C compiler default output... configure: error: C compiler
cannot create executables
See `config.log' for more details.
[snip]
Looking at twedit
/sw//src/fink.build/povray-3.61-1002/povray-3.6.1/libraries/png/config.log
[snip]
configure:2088: $? = 0
configure:2090: gcc -v /dev/null 5
Using built-in specs.
Target: i686-apple-darwin9
Configured with: /var/tmp/gcc/gcc-5493~1/src/configure
--disable-checking -enable-werror --prefix=/usr --mandir=/share/man
--enable-languages=c,objc,c++,obj-c++
--program-transform-name=/^[cg][^.-]*$/s/$/-4.0/
--with-gxx-include-dir=/include/c++/4.0.0 --with-slibdir=/usr/lib
--build=i686-apple-darwin9 --with-arch=apple --with-tune=generic
--host=i686-apple-darwin9 --target=i686-apple-darwin9
Thread model: posix
gcc version 4.0.1 (Apple Inc. build 5493)
configure:2093: $? = 0
configure:2095: gcc -V /dev/null 5
gcc-4.0: argument to `-V' is missing
configure:2098: $? = 1
configure:2122: checking for C compiler default output
configure:2125: gcc -pipe -O3 -march=i686 -mtune=i686
-minline-all-stringops -I/usr/X11/include -I/sw/include
-L/usr/X11/lib -L/sw/lib conftest.c 5
conftest.c:1: error: CPU you selected does not support x86-64 instruction set
configure:2128: $? = 1
configure: failed program was:
| #line 2101 configure
| /* confdefs.h. */
|
| #define PACKAGE_NAME libpng
| #define PACKAGE_TARNAME libpng
| #define PACKAGE_VERSION 1.2.5
| #define PACKAGE_STRING libpng 1.2.5
| #define PACKAGE_BUGREPORT
| #define PACKAGE libpng
| #define VERSION 1.2.5
| /* end confdefs.h. */
|
| int
| main ()
| {
|
| ;
| return 0;
| }
configure:2167: error: C compiler cannot create executables
See `config.log' for more details.
[snip]
Any idea of how to solve this issue? Many thanks in advance.
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
http://www.bio.cam.ac.uk/~awd28
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[Fink-users] a fix for boost-jam.info for fink 64 bits
I added x86_64) machine=x86_64;; in /sw/fink/10.4/unstable/main/finkinfo/devel/boost-jam.info See attached file. Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 boost-jam.info Description: Binary data -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] uname -m = x86_64 ?
Hi There! Is there any Mac OSX Leopard out there that would return x86_64 for uname -m? I want to build packages with x86_64 (64 bits) but unless I touch *.info files in Fink it won't happen since in my computer (new MBP) I get: uname -m : i386 Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] to create python26 with arch x86_64
Hi there, I am trying to create python26 fink package with support for 64-bits. I tried 2 things in python26.info: 1) ConfigureParams: --enable-shared --with-universal-archs=all 2) ConfigureParams: --enable-shared --with-universal-archs=64-bit 1) Failed with: Writing //sw/src/fink.build/root-python26-2.6.2-2/sw/lib/python2.6/lib-dynload/Python-2.6.2-py2.6.egg-info make: *** No rule to make target `update4wayuniversal', needed by `altinstall'. Stop. ### execution of /var/tmp/tmp.2.8Yz6MS failed, exit code 2 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-python26-2.6.2-2 (Reading database ... 54434 files and directories currently installed.) Removing fink-buildlock-python26-2.6.2-2 ... Failed: phase installing: python26-2.6.2-2 failed 2) Finished fine but after fink reinstall python26 python26-shlibs I still get: file /sw/lib/python2.6/config/libpython2.6.dylib /sw/lib/python2.6/config/libpython2.6.a /sw/bin/python2.6 /sw/lib/python2.6/config/libpython2.6.dylib: Mach-O dynamically linked shared library i386 /sw/lib/python2.6/config/libpython2.6.a: current ar archive random library /sw/bin/python2.6: Mach-O executable i386 ls -tlr /sw/lib/python2.6/config/libpython2.6.dylib /sw/lib/python2.6/config/libpython2.6.a /sw/bin/python2.6 -r-xr-xr-x 1 root admin 1887480 2009-07-17 10:13 /sw/lib/python2.6/config/libpython2.6.dylib -rwxr-xr-x 1 root admin 12880 2009-07-17 10:13 /sw/bin/python2.6 -rw-r--r-- 1 root admin 6712224 2009-07-17 10:13 /sw/lib/python2.6/config/libpython2.6.a Any comment would be really appreciate, many thanks in advance. Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] make -j n
Hi List, I was wondering if would be possible to make Fink aware of a multicores system and then use make -j n for speedup compilation. Sometimes I modified the _program_.info file in order to do that, but is it possible to do that for the whole system? Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] fink x86_64 failed for python26
Hi there, So following instructions from another email I was able to get fink CVS working on my system. After doing fink selfupdate-cvs, the first thing I wanted to install was python26, so I did: fink install python26 All dependency programme compiled and installed fine but then for python26 I got it: [snip] Failed to find the necessary bits to build these modules: _tkinter bsddb185 dl imageoplinuxaudiodev ossaudiodev spwd sunaudiodev To find the necessary bits, look in setup.py in detect_modules() for the module's name. (Fink package build should have 5 missing) make: *** [sharedmods] Error 1 ### execution of /var/tmp/tmp.1.TzRHfA failed, exit code 2 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-python26-2.6.2-2 (Reading database ... 8819 files and directories currently installed.) Removing fink-buildlock-python26-2.6.2-2 ... Failed: phase compiling: python26-2.6.2-2 failed Any help appreciated, many thanks in advance, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] vncserver: couldn't find Xvnc on your PATH
Hi. Anyone know what happened to the tightvnc package ? It still installs, but Xvnc is no longer included, which makes it unsuitable for my purposes. Is there another way for me to easily get TightVNC's Xvnc installed? Can I revert to an older version of the Fink package that still has it? |oug P.S. Fink 0.24.26 on PPC PowerMac running Tiger - Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] vncserver: couldn't find Xvnc on your PATH
Alexander Hansen [EMAIL PROTECTED] wrote: On Monday 14 July 2008 13:54:18 Douglas Alan wrote: Hi. Anyone know what happened to the tightvnc package ? It still installs, but Xvnc is no longer included, which makes it unsuitable for my purposes. Is there another way for me to easily get TightVNC's Xvnc installed? Can I revert to an older version of the Fink package that still has it? |oug P.S. Fink 0.24.26 on PPC PowerMac running Tiger It looks like you might be on a set of packages that haven't been supported in two years. You can confirm this by checking in /sw/etc/fink.conf and seeing what the Distribution: line says. If it says 10.4-transitional, then there haven't been any updates there since August 2006, and anything that's broken will remain so. I apologize for the confusion. The version number I posted above was for a different installation of Fink than the one I was actually complaining about. The *real* information is Fink 0.28.5 on PPC PowerMac running Tiger (10.4.11) These are the relevant lines from my fink.conf file: Distribution: 10.4 Trees: local/main unstable/main unstable/crypto stable/main stable/crypto |oug - Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] problem with plotting with python (matplotlib) on Desktop
Hi All, I have installed matplotlib-py25 on both my Desktop (intel mac) and Macbook pro (intel) both running Leopard. During testing I found that everything worked fine on my Macbook, that is I could do a simple plot, however following the same fink install process on my Desktop I was unable to do the same simply plot. It seems as though it is not recognizing the plot command. The simple plot I'm doing is; from pylab import * plot([1,2,3,4]) show() I inputted this line by line and got an error when I inputted the second line and the error was; plot([1,2,3,4]) Traceback (most recent call last): File stdin, line 1, in module File /sw/lib/python2.5/site-packages/matplotlib/pylab.py, line 2023, in plot b = ishold() File /sw/lib/python2.5/site-packages/matplotlib/pylab.py, line 937, in ishold return gca().ishold() File /sw/lib/python2.5/site-packages/matplotlib/pylab.py, line 883, in gca ax = gcf().gca(**kwargs) File /sw/lib/python2.5/site-packages/matplotlib/pylab.py, line 893, in gcf return figure() File /sw/lib/python2.5/site-packages/matplotlib/pylab.py, line 859, in figure figManager = new_figure_manager(num, figsize=figsize, dpi=dpi, facecolor=facecolor, edgecolor=edgecolor, frameon=frameon, FigureClass=FigureClass, **kwargs) File /sw/lib/python2.5/site-packages/matplotlib/backends/ backend_tkagg.py, line 88, in new_figure_manager window = Tk.Tk() File /sw/lib/python2.5/lib-tk/Tkinter.py, line 1636, in __init__ self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use) _tkinter.TclError: couldn't connect to display localhost:0.0 Could anyone please help me with this, as I can't seem to figure out why I'm having no problems on my Macbook but having problems on the Desktop. The only think I can think of is that the Pylab.py file was become corrupted during installation, although it seems fine to me. Cheers Al - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] Manually downloading Fink packages
I'm trying to install tetex and tetex-texmf which require massive downloads (dialup). Therefore I would like to use a separate download manager for the source packages. The Fink FAQ gives instructions on locating the packages on the Internet, and then moving the downloaded packages to / sw/src where they will be picked up on a fink install. However, I have been unable to determine the specific source file name (s) making up a fink (source) package. The FAQ seems to think that one already knows the file name. Google searches don't turn up exact matching filenames with version numbers. Also the files found by Google don't seem to match the size of the downloads that the fink install is attemtping. The two URLs in the Fink FAQ where supposedly these packages are stored do not work: http://distfiles.master.finkmirrors.net/ http://us.dl.sourceforge.net/fink/direct_download/source/ Do the fink info files apply only to the binaries? And the deb files apply to the source? Thanks Alan J. Robinson - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] selfupdate fails while trying to test fink 0.26.1
kinako wrote: Hi, On Mar 13, 2007, at 9:41, Geoffrey Alan Washburn wrote: % sudo fink selfupdate why do you use `sudo` ? Habit. Ideally it shouldn't make a difference. If I'm wrong let me know, but it would be kind of unfortunate if fink couldn't be installed by root. Not to mention the fact that I've managed fink this way for quite a few years now and »sudo« has never caused a problem. - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] selfupdate fails while trying to test fink 0.26.1
Alexander K. Hansen wrote: It's usually best if you give a verbatim transcript of the error message. As the error was on a different computer from where I wrote the e-mail it wasn't straightforward at the time. This time I've attached a full log. One thing to check, though, is whether you have made sure to turn ignore permissions on volume off (if it's an external volume). It's not an external volume so that does not apply. % sudo fink selfupdate Password: rsync -az -q rsync://master.us.finkmirrors.net/finkinfo//TIMESTAMP /sw/fink/TIMESTAMP.tmp I will now run the rsync command to retrieve the latest package descriptions. rsync -rtz --delete-after --delete -q --include='10.4/' --include='10.4/stable/' --include='10.4/stable/main/' --include='10.4/stable/main/finkinfo/' --include='10.4/stable/main/finkinfo/*/' --include='10.4/stable/main/finkinfo/*' --include='10.4/stable/main/finkinfo/**/*' --include='10.4/' --include='10.4/stable/' --include='10.4/stable/crypto/' --include='10.4/stable/crypto/finkinfo/' --include='10.4/stable/crypto/finkinfo/*/' --include='10.4/stable/crypto/finkinfo/*' --include='10.4/stable/crypto/finkinfo/**/*' --include='10.4/' --include='10.4/unstable/' --include='10.4/unstable/main/' --include='10.4/unstable/main/finkinfo/' --include='10.4/unstable/main/finkinfo/*/' --include='10.4/unstable/main/finkinfo/*' --include='10.4/unstable/main/finkinfo/**/*' --include='10.4/' --include='10.4/unstable/' --include='10.4/unstable/crypto/' --include='10.4/unstable/crypto/finkinfo/' --include='10.4/unstable/crypto/finkinfo/*/' --include='10.4/unstable/crypto/finkinfo/*' --include='10.4/unstable/crypto/finkinfo/**/*' --include='VERSION' --include='DISTRIBUTION' --include='README' --exclude='**' 'rsync://master.us.finkmirrors.net/finkinfo' '/sw/fink/' /usr/bin/find '/sw/fink/10.4/stable/main' -name CVS -type d -print0 | xargs -0 /bin/rm -rf /usr/bin/find '/sw/fink/10.4/stable/crypto' -name CVS -type d -print0 | xargs -0 /bin/rm -rf /usr/bin/find '/sw/fink/10.4/unstable/main' -name CVS -type d -print0 | xargs -0 /bin/rm -rf /usr/bin/find '/sw/fink/10.4/unstable/crypto' -name CVS -type d -print0 | xargs -0 /bin/rm -rf Scanning package description files.. Information about 6926 packages read in 12 seconds. The following package will be installed or updated: fink curl -f -L -A 'fink/0.26.0' -O http://distfiles.master.finkmirrors.net/fink-0.26.3.tar.gz % Total% Received % Xferd Average Speed TimeTime Time Current Dload Upload Total SpentLeft Speed 100 1213k 100 1213k0 0 85041 0 0:00:14 0:00:14 --:--:-- 51885 Setting runtime build-lock... dpkg-deb -b /sw/src/fink.build/root-fink-buildlock-fink-0.26.3-31 /sw/src/fink.build dpkg-deb: building package `fink-buildlock-fink-0.26.3-31' in `/sw/src/fink.build/fink-buildlock-fink-0.26.3-31_2007.03.12-20.38.36_darwin-powerpc.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/src/fink.build/fink-buildlock-fink-0.26.3-31_2007.03.12-20.38.36_darwin-powerpc.deb Selecting previously deselected package fink-buildlock-fink-0.26.3-31. (Reading database ... 120851 files and directories currently installed.) Unpacking fink-buildlock-fink-0.26.3-31 (from .../fink-buildlock-fink-0.26.3-31_2007.03.12-20.38.36_darwin-powerpc.deb) ... Setting up fink-buildlock-fink-0.26.3-31 (2007.03.12-20.38.36) ... gzip -dc /sw/src/fink-0.26.3.tar.gz | /sw/bin/tar -xf - --no-same-owner --no-same-permissions make test PREFIX=/sw perl -MExtUtils::Manifest=fullcheck -e 'my($missing, $extra) = fullcheck;exit (@$missing || @$extra)' ./setup.sh /Volumes/UFS/sw/src/fink.build/fink-0.26.3-31/fink-0.26.3/t/basepath Creating fink... Creating fink-virtual-pkgs... Creating fink-instscripts... Creating fink-scanpackages... Creating pathsetup.sh... Creating FinkVersion.pm... Creating Fink.pm... Creating man pages... Creating shlibs default file... Creating postinstall script... Creating dpkg helper script... Creating lockwait wrappers... Creating g++ wrappers... cd t ./testmore.pl find . -name '*.t' | sort | PREFIX=/sw xargs /usr/bin/perl -I/Volumes/UFS/sw/src/fink.build/fink-0.26.3-31/fink-0.26.3/perlmod -MTest::Harness -e 'runtests(@ARGV)' Checking for Test::More... ./00compileok ./10features/users_groups..ok ./10features/volumeok 1/2 skipped: Could not find Owners or Permissions flag in output of `/usr/sbin/diskutil info /sw 21` ./Base/initialize..ok ./Base/param...ok ./Base/param_boolean...ok ./CLI/capture..ok
[Fink-users] selfupdate fails while trying to test fink 0.26.1
It appears to be failing on execute_nonroot_okay with error messages about sudo being unable to execute /sw/bin/env because Permission denied. I am somewhat suspecting that this may be caused by having moved my /sw directory to another volume and then creating a symlink to it. Any ideas? Thanks! - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
Re: [Fink-users] arts failling because of missing zlib for python in Fink
Thanks Martin, In my installation appears /sw/lib/python2.4/lib-dynload/zlib_failed.so I just link my working mac python zlib.so there and now it's working. Thanks again. Cheers, Alan On 28/12/06, Martin Costabel [EMAIL PROTECTED] wrote: Alan wrote: Dears, I use Mac OSX 10.4.8 Intel with Fink Package manager version: 0.26.0, Distribution version: 0.8.1.rsync i386. I cannot update 'arts' basically because python under fink does not have 'zlib'. I does. On my iMac/intel, I see /sw/lib/python2.5/lib-dynload/zlib.so which is installed by the python25 package. The same goes for python23 and python24. So, in the end, my problem is how to get fink python with module zlib (under python prompt, 'import zlib' fails). Doesn't fail for me. If it does for you, there must be something wrong with your python installation. Which python version do you have installed, and how did you install it, from the binary distribution or from source? -- Martin -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] arts failling because of missing zlib for python in Fink
Dears, I use Mac OSX 10.4.8 Intel with Fink Package manager version: 0.26.0, Distribution version: 0.8.1.rsync i386. I cannot update 'arts' basically because python under fink does not have 'zlib'. So, in the end, my problem is how to get fink python with module zlib (under python prompt, 'import zlib' fails). I would thank you very much if anyone could give any hint in this topic. Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] TIP: fixing problems with installing apache2 on 10.4
Hi all- I spent all day trying to get apache2 installed via fink on my new iMac (intel) with 10.4. I was having problems with: fink install apache2 The dependencies (particularly the mpm) were failing. I finally figured it out... Something in the configure portion of the apache-mpm-* script actually runs httpd. If the server fails to come up clean, the configure bails. However, it doesn't shut down your httpd. So, what you need to do is make sure that httpd can come up cleanly. Usually at least you'll have apache2ctl installed, so you can use stop/start to try to do this, or if need be, kill. Definitely use ps since the failure can result in apache2ctl not seeing a pid file and thus *incorrectly* reporting that apache2 isn't running. Since I was also running the built-in httpd, the apache2 one couldn't come up and that was the problem. As soon as I killed the built-in one, the orphaned (/sw/sbin/apache2), and reconfigured the apache2.conf so that it could come up, I was able to complete the install. Just wanted to post this since I wasted about 8 hours today figuring this out. Good luck, Alan - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
[Fink-users] Unrecorded dependency
It would appear that the package gucharmap requires gnome-doc-util, but doesn't know about the dependency. --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637alloc_id=16865op=click ___ Fink-users mailing list Fink-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/fink-users
