today I compiled io_lib and staden from current SVN and ran into trouble when executing gap5 (gap4 seems to run just fine):
load libgap5.so => couldn't load file "libgap5.so": /package/sequencer/StadenPackage/current/bin/../lib/staden/libgap5.so: undefined symbol: scram_put_seq
invalid command name "load_alignment_matrix"
"load_alignment_matrix [keylget gap5_defs ALIGNMENT.MATRIX_FILE]"
(file "/package/sequencer/StadenPackage/current/bin/../share/staden/tcl/gap5/gap5.tcl" line 675)
Any idea what is going wrong here?
Same error when using tg_index to convert SAM to gap5:
tg_index.bin: symbol lookup error: /package/sequencer/StadenPackage/svn_2013-11-01/lib/staden/libgap5.so: undefined symbol: scram_open
Problem solved. There was a wrong (custom) LD_LIBRARY_PATH set pointing to an old installation of io_lib :-(
Sorry for the noise ..
No problem - it's no noise at all since SourceForge stopped notifying us of any discussions or bug reports. I wish I knew how to reenable these, other than the really obvious email subscription feature which doesn't do anything. Grr
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