Re: DL damaged

2012-12-26 Thread Ryan Schmidt
On Dec 26, 2012, at 21:29, Robert Broome wrote: > Thanks for the help! > > I really appreciate it. I don't know whether to reply directly to you or > through the mailing list. We should keep the discussion on the list so that when I run out of ideas, which might already be happening now, some

Re: sudo port install tk -quartz problem (related with pymol)

2012-12-26 Thread Ryan Schmidt
On Dec 26, 2012, at 20:29, Peng Yu wrote: > On Wed, Dec 26, 2012 at 8:26 PM, Ryan Schmidt wrote: >> >> On Dec 26, 2012, at 20:22, Peng Yu wrote: >> >>> On Wed, Dec 26, 2012 at 7:22 PM, Ryan Schmidt wrote: Yeah that's weird... for the record I don't see this problem on my system. >>>

Re: sudo port install tk -quartz problem (related with pymol)

2012-12-26 Thread Peng Yu
On Wed, Dec 26, 2012 at 8:26 PM, Ryan Schmidt wrote: > > On Dec 26, 2012, at 20:22, Peng Yu wrote: > >> On Wed, Dec 26, 2012 at 7:22 PM, Ryan Schmidt wrote: >>> >>> Yeah that's weird... for the record I don't see this problem on my system. >>> So if you still see this problem after a rebuild, ple

Re: sudo port install tk -quartz problem (related with pymol)

2012-12-26 Thread Ryan Schmidt
On Dec 26, 2012, at 20:22, Peng Yu wrote: > On Wed, Dec 26, 2012 at 7:22 PM, Ryan Schmidt wrote: >> >> Yeah that's weird... for the record I don't see this problem on my system. >> So if you still see this problem after a rebuild, please attach a log of the >> build to the ticket. > > What th

Re: sudo port install tk -quartz problem (related with pymol)

2012-12-26 Thread Peng Yu
On Wed, Dec 26, 2012 at 7:22 PM, Ryan Schmidt wrote: > > On Dec 26, 2012, at 18:30, Clemens Lang wrote: > >> On Wed, Dec 26, 2012 at 08:19:23AM -0600, Peng Yu wrote: >>> $ otool -L /opt/local/bin/wish8.6 >>> /opt/local/lib:/opt/local/lib/libtk8.6.dylib (compatibility version >>> 8.6.0, curr

Re: can't write to /var/folders

2012-12-26 Thread Ryan Schmidt
On Dec 25, 2012, at 21:59, Robert Broome wrote: > I use gfortran installed via macports. I am currently at gcc46, with gcc45 > installed to support fortran-netcdf. > > When I try to compile a simple program (which has compiled on this machine > several days ago), I get: > gfortran -o sorttest

Re: DL damaged

2012-12-26 Thread Ryan Schmidt
On Dec 26, 2012, at 11:49, Robert Broome wrote: > I am getting the following error: > dyld: DYLD_ environment variables being ignored because main executable > (sudo) is setuid or setgid. You have DYLD_* environment variables set, and this message is informing you that they are being ignored wh

Re: sudo port install tk -quartz problem (related with pymol)

2012-12-26 Thread Ryan Schmidt
On Dec 26, 2012, at 18:30, Clemens Lang wrote: > On Wed, Dec 26, 2012 at 08:19:23AM -0600, Peng Yu wrote: >> $ otool -L /opt/local/bin/wish8.6 >> /opt/local/lib:/opt/local/lib/libtk8.6.dylib (compatibility version >> 8.6.0, current version 8.6.0) > > That's the problem. The part before (a

Re: sudo port install tk -quartz problem (related with pymol)

2012-12-26 Thread Clemens Lang
On Wed, Dec 26, 2012 at 08:19:23AM -0600, Peng Yu wrote: > $ otool -L /opt/local/bin/wish8.6 > /opt/local/lib:/opt/local/lib/libtk8.6.dylib (compatibility version > 8.6.0, current version 8.6.0) That's the problem. The part before (and including) the colon shouldn't be there. This might be

Re: can't write to /var/folders

2012-12-26 Thread David Nicholls
A simple work around would be to change the permissions on the executable, using either 'chown' from the command line or 'getinfo' in Finder. DN On 27/12/2012, at 4:43 AM, robert.bro...@softhome.net wrote: > I have already received helpful feedback and want to thank D. Nicholls. > when i compil

Re: matplotlib with X11

2012-12-26 Thread Adam Mercer
On Sat, Dec 22, 2012 at 2:00 PM, Corey Cooke wrote: > Does anyone know how to set up matplotlib (right now i'm using > py27-matplotlib) such that it uses X11 to draw the windows so they can be > viewed from a remote SSH session? I've tried changing the backend in > ~/.matplotlib/matplotlibrc from

Re: DL damaged

2012-12-26 Thread Lawrence Velázquez
On Dec 26, 2012, at 12:49 PM, robert.bro...@softhome.net wrote: > I am getting the following error: > dyld: DYLD_ environment variables being ignored because main executable > (sudo) is setuid or setgid. [snip] > Has anyone had any experience with this > error message and can you tell me what is

DL damaged

2012-12-26 Thread Robert . Broome
I am getting the following error: dyld: DYLD_ environment variables being ignored because main executable (sudo) is setuid or setgid. Because of an earlier misconfiguration problem that I caused, in order to run gfortran, I have to run gfortran as root. I am hoping someone will be able to help me

can't write to /var/folders

2012-12-26 Thread Robert . Broome
I have already received helpful feedback and want to thank D. Nicholls. when i compile as root, sudo gfortran etc. this works. The resulting executable is owned by root however. So as expected the problem is permissions. I don't know how to make a call to gfortran work properly as a user. Any expe

Re: sudo port install tk -quartz problem (related with pymol)

2012-12-26 Thread Peng Yu
On Wed, Dec 26, 2012 at 2:52 AM, Clemens Lang wrote: > Hi, > > On Tue, Dec 25, 2012 at 11:26:17PM -0600, Peng Yu wrote: >> Could not open /opt/local/lib:/opt/local/lib/libtk8.6.dylib: Error >> opening or reading file (referenced from /opt/local/bin/wish8.6) >> DEBUG: Marking /opt/local/bin/wish8.6

Re: Failed to install webkit-gtk

2012-12-26 Thread Ryan Schmidt
On Dec 26, 2012, at 05:57, Ryan Schmidt wrote: > I do get the same error on my Power Mac with Leopard. Would you please file a > bug report in our issue tracker? > > https://guide.macports.org/chunked/project.html And I've also reproduced it now on Leopard on Intel. _

Re: Failed to install webkit-gtk

2012-12-26 Thread Ryan Schmidt
On Dec 26, 2012, at 05:45, Eneko Gotzon Ares wrote: > On Dec 26, 2012, at 12:18 AM, Ryan Schmidt wrote: > >> I'll try to reproduce the problem on my Power Mac. > > Thank you very much for your time, Ryan, and for your knowledge... :) I do get the same error on my Power Mac with Leopard. Would

Re: sudo port install tk -quartz problem (related with pymol)

2012-12-26 Thread Clemens Lang
Hi, On Tue, Dec 25, 2012 at 11:26:17PM -0600, Peng Yu wrote: > Could not open /opt/local/lib:/opt/local/lib/libtk8.6.dylib: Error > opening or reading file (referenced from /opt/local/bin/wish8.6) > DEBUG: Marking /opt/local/bin/wish8.6 as broken what's the output of otool -L /opt/local/bin/wish8