David Mathog wrote:
In the land of dominoes...
The NCBI added another character or two to the allowed
list of letters that can be stored in BLAST databases
Yeah ... breaks my parsers every now and then ...
which
broke my software that interfaces with those database
:)
which
broke every program I use that reads sequence data through that interface.
You should see what they did to the code itself. Just go try to build
it in a non-GCC linux environment on x86_64. It will complain, badly.
I have patches for that in my latest RPMs
(http://downloads.scalableinformatics.com/downloads/ncbi/). Annoying.
That sort of change happens once or twice a year and so is par for the
Progress ...
course. What is unusual this time is that when I tried to rebuild the
first one of these PVM based applications (hmmer 2.3.2 package by Sean
Eddy) the linker was very unhappy with the static pvm library:
/usr/common/pvm3/lib/LINUX/libpvm3.a(lpvmpack.o): In function `pvm_vpackf':
lpvmpack.c:(.text+0x36d4): undefined reference to `__ctype_b'
lpvmpack.c:(.text+0x36f8): undefined reference to `__ctype_b'
lpvmpack.c:(.text+0x3728): undefined reference to `__ctype_b'
lpvmpack.c:(.text+0x3747): undefined reference to `__ctype_b'
/usr/common/pvm3/lib/LINUX/libpvm3.a(lpvmpack.o): In function
`pvm_vunpackf':
lpvmpack.c:(.text+0x3bb8): undefined reference to `__ctype_b'
/usr/common/pvm3/lib/LINUX/libpvm3.a(lpvmpack.o):lpvmpack.c:(.text+0x3bd7):
more undefined references to `__ctype_b' follow
collect2: ld returned 1 exit status
make: *** [afetch] Error 1
In the spirit of leaving well enough alone the hmm applications have not
been modified in 3 years, and libpvm3.a has not been
Been modified by some :) to make them go faster. Also there is a nice
MPI version out now (no PVM vs MPI here, just pointing it out) at
http://code.google.com/p/mpihmmer/ . Dev team are good guys :)
touched since Oct 2002. Apparently that library must now be rebuilt.
The source was PVM 3.4.4, it seems in the last 5 years they've released
3.4.5, so I guess it's time to update to that.
Anybody else seen this particular PVM/linker issue?
I think this could be due to some libs being built with older glibc/gcc
bits. Library mismatch is best guess.
If so, is there anything else that needs to be done beyond
rebuilding PVM (applications and library)?
Possibly any dependencies.
--
Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: [EMAIL PROTECTED]
web : http://www.scalableinformatics.com
http://jackrabbit.scalableinformatics.com
phone: +1 734 786 8423
fax : +1 866 888 3112
cell : +1 734 612 4615
_______________________________________________
Beowulf mailing list, Beowulf@beowulf.org
To change your subscription (digest mode or unsubscribe) visit
http://www.beowulf.org/mailman/listinfo/beowulf
