[maker-devel] segmentation fault (core dumped) for maker running

[Hung Chih-Ming]

Hi Dr. Holt,

I just installed maker-2.26-beta  in a lunix-64 bite server with Ubuntu 12.
But when I ran maker, I got an error message show segmentation fault (see
below):

STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
程式記憶體區段錯誤 (core dumped)

I updated the three modules, AnyDBM_File, BDB::SQLlite, or BerkeleyDB. And
then I run the fix in maker/lib

"sed -i 's/qw(DB_File GDBM_File NDBM_File SDBM_File)/qw(DB_File)/' $(grep
-l 'DB_File GDBM_File NDBM_File SDBM_File' *)"

Now maker seems to work!

However, I could not follow the next step based on your response in the
google discussion group,
"You may also have to run the fix below on wherever Bioperl is installed as
well, because it contains the same (DB_File GDBM_File NDBM_File SDBM_File)
statement in the Bio::DB::Fasta module in one of the BEGIN statements."

I tried to run this fix in the folder
(/usr/local/share/perl/5.14.2/Bio/LiveSeq/IO/) containing Bioperl.pm. But
it showed:
sed: 沒有輸入檔案 (it means no input files)
I want to ask if this step is necessary? If so, what is the directory where
I should run the fix?

Thanks,

Chih-Ming


Chih-Ming Hung
Postdoctoral researcher'
Department of Life Science
National Taiwan Normal University
Taipei, Taiwan
Email: ymwur1 at gmail.com
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