recent acedb update problems

Richard Durbin rd at sanger.ac.uk
Sun Sep 7 10:08:42 EST 1997



There have been several messages about problems with the recent acedb
updates.  If you don't want to read the details in the rest of this
message, my brief response is that as far as I can see now, none of
these reflect systematic bugs/errors in the release.

[1] Erich Schwarz says that he left his acedb unusable, and warns
non-Unix jocks from installing.  His problem appears to have been that
he used the wrong version of the program, solaris rather than sun.  Of
course overwriting the bin/ directory with one built for a different
operating system left things unworkable.  This is not a problem with
the release.
  In detail, so that others don't have the same difficulty, Sun
Microsystems made a new, incompatible version of their operating
system SunOS a few years ago, which they called Solaris. Unfortunately
they also give Solaris SunOS release numbers.  The cutoff version
number is 4.2 -- all SunOS versions before that should use
bin.sun.4_5d.tar.Z, and all versions after should use
bin.solaris.4_5e.tar.Z.  To find out which version you have type
"uname -sr".  e.g.
	islay[rd]137: uname -sr
	SunOS 4.1.3
or
	ics-sparc1[rd]98: uname -sr
	SunOS 5.5
The first is old sunos, the second solaris.

[2] Paul Muhlrad had problems with the physical map.  The small contig
of one clone at the left end of I is our fault, a data problem; please
ignore it.  The zooming problem looks like a code problem.  I can not
reproduce it here, even with the same version of the program.  I have
written Paul asking for more information, and given we can fix it, and
the problem looks like it is not specific to Paul's installation, I
will email the newsgroup with the fix.

[3] Keith from domainuser at domain.user (where?) had some installation
difficulty that ended up with his files in LOST+FOUND.  Although it is
not clear what happened, it looks to me like a system or network
problem.  That sort of thing happens when something on the network
crashes.  We have done many successful installations on all sorts of
platforms, and know of very many more, and I can't possibly see how
the installation script would itself put things in LOST+FOUND.

I should also add that Andrew Spence has had problems loading the
updates on a Linux machine (segmentation fault loading the update).  I
know at least one other person who has loaded them successfully under
Linux.  Maybe there are Linux version differences?

Overall, I am not yet aware of a reproducible problem with the release
made on Thursday/Friday, except Paul's data error.  If anyone has had
similar, or different problems to any of the above, can they please
write to me and/or Jean.  It is helpful to everyone if we know about
bugs, and it is worth asking a direct question first, because we may
be able to fix your problem, and your own diagnosis may be incorrect
and create unnecessary alarm if sent to whole newsgroup.

Richard Durbin

PS I have also had encouragement to get the macace code back and get
macace up to date, and am pursuing that.



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