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
which broke my software that interfaces with those database which broke every program I use that reads sequence data through that interface. That sort of change happens once or twice a year and so is par for the 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 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? If so, is there anything else that needs to be done beyond rebuilding PVM (applications and library)? Thanks, David Mathog [EMAIL PROTECTED] Manager, Sequence Analysis Facility, Biology Division, Caltech _______________________________________________ Beowulf mailing list, Beowulf@beowulf.org To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf
