From bryanlepore at mail.utexas.edu  Sun Mar  5 22:38:51 2006
From: bryanlepore at mail.utexas.edu (Bryan W. Lepore)
Date: Sun Mar  5 22:39:05 2006
Subject: [Discuss] pdbc on mac osx 10.3.9
Message-ID: <Pine.OSX.4.58.0603051636130.3270@dhcp-128-83-98-87.phr.utexas.edu>

i have tried pdbc on four .ent files on mac os 10.3.9, and i get three "Bus
error"s and one "Segmentation fault", but no problems on my Linux box.

just wondering if anyone noticed that before i try fixing it.

-bryan

From bryanlepore at mail.utexas.edu  Sun Mar  5 23:37:45 2006
From: bryanlepore at mail.utexas.edu (Bryan W. Lepore)
Date: Sun Mar  5 23:37:51 2006
Subject: [Discuss] multalign on mac osx 10.3.9
In-Reply-To: <Pine.OSX.4.58.0603051636130.3270@dhcp-128-83-98-87.phr.utexas.edu>
References: <Pine.OSX.4.58.0603051636130.3270@dhcp-128-83-98-87.phr.utexas.edu>
Message-ID: <Pine.OSX.4.58.0603051729230.3270@dhcp-128-83-98-87.phr.utexas.edu>

hi again,

i built the amps package on my powerbook by choosing the BUILD linux option, and
i was sort-of surprised to see the executables seem ok except :

<prompt>% ./multalign.linux
bash: ./multalign.linux: cannot execute binary file

my g77 is GNU Fortran (GCC) 3.4.3 - i'm hoping someone could suggest a
particular place to look into fix the multalign problem.

btw, i worked around and did not fix the pdbc bus errors/segfaults.  it seems to
not dump the stderr to a file, i.e. it prints to screen, but i cannot get it to
do e.g:

pdbc > filename.log.

-bryan
From bryanlepore at mail.utexas.edu  Mon Mar  6 03:23:38 2006
From: bryanlepore at mail.utexas.edu (Bryan W. Lepore)
Date: Mon Mar  6 03:23:46 2006
Subject: [Discuss] just one more : dstamp (w/ ss gap penalties)
Message-ID: <Pine.OSX.4.58.0603052104030.3270@dhcp-128-83-98-87.phr.utexas.edu>

just let me ask one more, and i'll try to lay low for a while:

i ran stamp_clean on a ss-gap penalty multalign run, to get a .clean file,
now dstamp says

Reading block file
No terminating * in blocfile

... but there's a * at the end.  i suspect that the 14 carriage returns in my
.clean file after the "% 14 STAMP fields found:" line needs some fields, but not
sure what to put there besides the 6 that are indicated in the .blc file:

%   6 STAMP fields found: T P A G B R

i tried this with stamp 43.

-bryan
From tom at compbio.dundee.ac.uk  Mon Mar  6 10:22:07 2006
From: tom at compbio.dundee.ac.uk (Tom Walsh)
Date: Mon Mar  6 10:22:23 2006
Subject: [Discuss] multalign on mac osx 10.3.9
In-Reply-To: <Pine.OSX.4.58.0603051729230.3270@dhcp-128-83-98-87.phr.utexas.edu>
References: <Pine.OSX.4.58.0603051636130.3270@dhcp-128-83-98-87.phr.utexas.edu>
	<Pine.OSX.4.58.0603051729230.3270@dhcp-128-83-98-87.phr.utexas.edu>
Message-ID: <440C0D4F.6050109@compbio.dundee.ac.uk>

Bryan W. Lepore wrote:

>hi again,
>
>i built the amps package on my powerbook by choosing the BUILD linux option, and
>i was sort-of surprised to see the executables seem ok except :
>
><prompt>% ./multalign.linux
>bash: ./multalign.linux: cannot execute binary file
>
>my g77 is GNU Fortran (GCC) 3.4.3 - i'm hoping someone could suggest a
>particular place to look into fix the multalign problem.
>  
>
    The multalign source code is not a place for the faint-hearted. I've
had a quick look at the Linux Makefile and there's nothing in it that
looks like it should cause trouble on OS X. I'll see if I can get access
to an OS X and sort out these problems.

    Tom

From tom at compbio.dundee.ac.uk  Mon Mar  6 10:26:59 2006
From: tom at compbio.dundee.ac.uk (Tom Walsh)
Date: Mon Mar  6 10:27:23 2006
Subject: [Discuss] just one more : dstamp (w/ ss gap penalties)
In-Reply-To: <Pine.OSX.4.58.0603052104030.3270@dhcp-128-83-98-87.phr.utexas.edu>
References: <Pine.OSX.4.58.0603052104030.3270@dhcp-128-83-98-87.phr.utexas.edu>
Message-ID: <440C0E73.7060607@compbio.dundee.ac.uk>

Bryan W. Lepore wrote:

>just let me ask one more, and i'll try to lay low for a while:
>
>i ran stamp_clean on a ss-gap penalty multalign run, to get a .clean file,
>now dstamp says
>
>Reading block file
>No terminating * in blocfile
>
>... but there's a * at the end.  i suspect that the 14 carriage returns in my
>.clean file after the "% 14 STAMP fields found:" line needs some fields, but not
>sure what to put there besides the 6 that are indicated in the .blc file:
>  
>
    Send me the .clean file and I'll try to work out what's going on.

    Tom