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What steps will reproduce the problem?
When I run 

moabs -cf mytestrun.cfg

the bsmap steps seem to work fine.  when it moves to mcall though, I get

/srv/gs1/software/moabs/moabs-v1.3.0/bin/moabs: Start to execute   
[/srv/gs1/software/moabs/moabs-v1.3.0//bin/mcall  -m OX.bam    -p 4  -r 
/srv/gs1/projects/snyder/yxl/db/hu_genome37.58/Homo_sapiens_lambda.GRCh37.58.dna
.fa  --sampleName OX > moabs.mcall.OX.log]
Tue May 19 19:35:32 PDT 2015
/srv/gs1/software/moabs/moabs-v1.3.0/bin/moabs: Start to execute   
[/srv/gs1/software/moabs/moabs-v1.3.0//bin/mcall  -m BS.bam    -p 4  -r 
/srv/gs1/projects/snyder/yxl/db/hu_genome37.58/Homo_sapiens_lambda.GRCh37.58.dna
.fa  --sampleName BS > moabs.mcall.BS.log]
XR:Z or ZR:Z:, or ZS:Z: field not found, please enable -R option in bsmap
XR:Z or ZR:Z:, or ZS:Z: field not found, please enable -R option in bsmap
terminate called recursively
terminate called recursively
terminate called recursively
terminate called recursively
terminate called after throwing an instance of 'std::out_of_range'
sh: line 1: 20661 Aborted                 
/srv/gs1/software/moabs/moabs-v1.3.0//bin/mcall -m OX.bam -p 4 -r 
/srv/gs1/projects/snyder/yxl/db/hu_genome37.58/Homo_sapiens_lambda.GRCh37.58.dna
.fa --sampleName OX > moabs.mcall.OX.log
sh: line 1: 20665 Aborted                 
/srv/gs1/software/moabs/moabs-v1.3.0//bin/mcall -m BS.bam -p 4 -r 
/srv/gs1/projects/snyder/yxl/db/hu_genome37.58/Homo_sapiens_lambda.GRCh37.58.dna
.fa --sampleName BS > moabs.mcall.BS.log
/srv/gs1/software/moabs/moabs-v1.3.0/bin/moabs: Failed executing     
[/srv/gs1/software/moabs/moabs-v1.3.0//bin/mcall  -m BS.bam    -p 4  -r 
/srv/gs1/projects/snyder/yxl/db/hu_genome37.58/Homo_sapiens_lambda.GRCh37.58.dna
.fa  --sampleName BS > moabs.mcall.BS.log] with doSys exit code 34304
/srv/gs1/software/moabs/moabs-v1.3.0/bin/moabs: Failed executing     
[/srv/gs1/software/moabs/moabs-v1.3.0//bin/mcall  -m OX.bam    -p 4  -r 
/srv/gs1/projects/snyder/yxl/db/hu_genome37.58/Homo_sapiens_lambda.GRCh37.58.dna
.fa  --sampleName OX > moabs.mcall.OX.log] with doSys exit code 34304
Tue May 19 19:52:21 PDT 2015
Tue May 19 19:52:21 PDT 2015
Perl exited with active threads:
        1 running and unjoined
        0 finished and unjoined
        0 running and detached


What is the expected output? What do you see instead?
I don't expect an error.

What version of the product are you using? On what operating system?
moabs-v1.3.0
Red Hat Enterprise Linux Server release 6.3 (Santiago)

Please provide any additional information below.

What steps will reproduce the problem?
1. Using most recent Rcpp/RInside will lead an error;
2. Comping mcomp and ExactNumCI module;
3. Linux/Mac OS, clang version 3.5.0/gcc-4.6.2

What is the expected output? What do you see instead?
Compile failure.

What version of the product are you using? On what operating system?
moabs-v1.2.4

Please provide any additional information below.

1.

There is a bug in mcomp.cpp: Change line 54 into

    RInside R2;

and replace all “R.” into “R2.”, in VIM you could do

    :so%/R\./R2\./g

The reason is Rcpp/RInside already uses

    RInside R;

2.

in ./moabs-v1.2.4/src/ExactNumCI/stats.cpp a header file
 #include <iostream>
is needed.

3.

Current version (v1.4) of samtools doesn't seem to have any lib/include folder 
unless one chooses to use a pre-build version provided by Linux distribution. 
May be a script is needed to create them.