Is this El Capitan? It's possible they don't have the gcc48 port working
yet.
Two comments:
1. This question is better off asked on the MacPorts mailing list, since
it's a problem with building a port (nothing to do with Amber).
2. If you have gcc 5.2 installed, why are you installing gcc 4.8? Why not
just use gcc 5.2 instead?
HTH,
Jason
On Fri, Oct 23, 2015 at 9:41 AM, Mochena, Mogus D. <mogus.mochena.famu.edu>
wrote:
>
>
> Dear Jason and David:
> Thank you very much for your prompt response. I was able to install
> macports. However while I was configuring, I got the error message below.
> The suggested log file is too long for Amber mailing list. Hope I am not
> taking too much of your time.
> Thanks again,
> MM
>
> from ftp://ftp.gnu.org/gnu/gcc/gcc-5.2.0
> ---> Verifying checksums for libgcc
> ---> Extracting libgcc
> ---> Applying patches to libgcc
> ---> Configuring libgcc
> ---> Building libgcc
>
>
>
> ---> Staging libgcc into destroot
> ---> Installing libgcc .5.2.0_0
> ---> Activating libgcc @5.2.0_0
> ---> Cleaning libgcc
> ---> Fetching archive for gcc48
> ---> Attempting to fetch gcc48-4.8.5_0.darwin_15.x86_64.tbz2 from
> http://packages.macports.org/gcc48
> ---> Attempting to fetch gcc48-4.8.5_0.darwin_15.x86_64.tbz2 from
> http://nue.de.packages.macports.org/macports/packages/gcc48
> ---> Attempting to fetch gcc48-4.8.5_0.darwin_15.x86_64.tbz2 from
> http://lil.fr.packages.macports.org/gcc48
> ---> Fetching distfiles for gcc48
> ---> Attempting to fetch gcc-4.8.5.tar.bz2 from
> http://mirrors.ibiblio.org/gnu/ftp/gnu/gcc/gcc-4.8.5
> ---> Verifying checksums for gcc48
> ---> Extracting gcc48
> ---> Applying patches to gcc48
> ---> Configuring gcc48
> ---> Building gcc48
> Error: org.macports.build for port gcc48 returned: command execution failed
> Please see the log file for port gcc48 for details:
>
> /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc48/gcc48/main.log
> To report a bug, follow the instructions in the guide:
> http://guide.macports.org/#project.tickets
> Error: Processing of port gcc48 failed
>
> ________________________________________
> From: Jason Swails <jason.swails.gmail.com>
> Sent: Wednesday, October 21, 2015 3:38 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Problem configuring amber14
>
> On Wed, Oct 21, 2015 at 2:11 PM, Mochena, Mogus D. <mogus.mochena.famu.edu
> >
> wrote:
>
> > I have downloaded ambertools and trying to configure following
> > instructions from amber15.pdf. My operating system is Mac O S X 10.11 (El
> > Captan). I have used Xcode 7.0.1 to get gnu compilers gcc and g++;
> gfortran
> > was not included, so I installed it separately.
> >
>
> How did you install it? Because the error you are getting is likely
> caused by how you installed gfortran. Since Amber relies on cross-linking
> Fortran and C codes, libgfortran is needed at link time to compile many
> programs. If it's not available, Amber won't work.
>
> The typical way that we recommend users get gfortran is through MacPorts.
> You can see my Mac tutorial here: http://jswails.wikidot.com/mac-os-x
>
> It's a bit dated, but getting MacPorts installed and getting gcc installed
> should still be up-to-date.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 23 2015 - 07:30:04 PDT
