failed to build rmblastn

[cb4github]

Dear All,

I'm attempting to build rmblastn 2.11.0 from source using the steps prescribed at http://www.repeatmasker.org/RMBlast.html.

I can furnish any log output upon request from the make command, but that log is >400MB.

Also, the configure step succeeds, yet the make step succeeds in building seemingly every executable but rmblastn.

# in ncbi-blast-2.11.0+-src/c++ directory
$ ls ReleaseMT/bin
blast_formatter    cleanup-blastdb-volumes.py  lmdb_test3     seedtop
blast_report       convert2blastmask           lmdb_test4     segmasker
blastdb_aliastool  datatool                    lmdb_test5     seqdb_demo
blastdb_convert    deltablast                  lmdbxx_sample  seqdb_perf
blastdb_path       dustmasker                  makeblastdb    tblastn
blastdbcheck       gc_cli                      makembindex    tblastx
blastdbcmd         gene_info_reader            makeprofiledb  update_blastdb.pl
blastdbcp          get_species_taxids.sh       psiblast       windowmasker
blastn             legacy_blast.pl             rpsblast       windowmasker_2.2.22_adapter.py
blastp             lmdb_test1                  rpstblastn
blastx             lmdb_test2                  run_with_lock

$ uname -a
Linux <hostname> 2.6.32-431.23.3.el6.x86_64 #1 SMP Thu Jul 31 17:20:51 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

$ lsb_release -a
LSB Version:    :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
Distributor ID: CentOS
Description:    CentOS release 6.5 (Final)
Release:    6.5
Codename:   Final

Granted our campus cluster OS is EOL, but on the few nodes with centos 7 - and I forget the details for now - I get the error message "undefined symbol: Perl_Istack_sp_ptr" when I try to run RepeatMasker.

I've also had to fix by hand 4 out of 7 patches mentioned in the download file http://www.repeatmasker.org/isb-2.11.0+-rmblast.patch.gz - as well as the fix for the hard coded sort command mentioned here https://github.com/Dfam-consortium/RepeatModeler/issues/89#issuecomment-651381066

Suggestions appreciated, and please let me know what more information I can provide, thanks.

Best, CB

[rmhubley]

Is this still a problem? You mentioned you had to "fix by hand 4 out of 7 patches", what exactly needed fixing. That sort of sets of alarm bells that you might not have the distribution that the patch is based on.