Installation of EPACTS on a Macintosh

[dweek...@gmail.com]

Notes re installing EPACTS on a Macintosh OS X 10.9.4 machine

To get EPACTS to install, there were a number of things I had to adjust.
Most of these appear to be minor to me. 

I share these notes in case they might be helpful, but use at your own risk as I am not 100% certain my solutions don't have unintended side effects.

Dan Weeks


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Wouldn't compile due to errors like this:

pEmmax.cpp:2560:9: error: use of undeclared identifier 'isnanf'; did you mean 'isnan'?
          if ( isnanf(emx.tvcf.genos[j + offset]) ) {

vcfast.cpp:209:13: error: use of undeclared identifier 'isnanf'; did you mean 'isnan'?

Looks like the Macintosh has isnan() but not isnanf()

Solution: Redefine isnanf as isnan in both pEmmax.cpp and vcfast.cpp

// Fix to get it to compile on a Macintosh
#define isnanf(X) isnan(X)

------
In file included from Anno.cpp:25:
./FreqTable.h:18:13: error: void function 'remove' should not return a value
      [-Wreturn-type]
            return false;
            ^      ~~~~~

It looks like the 'remove' function is not used.

Solution: To get it to compile, I changed the function from 'void' to 'int'

-------

$ test_run_epacts.sh
mkdir: illegal option -- -
usage: mkdir [-pv] [-m mode] directory ...

The offending line appears to be:

mkdir --p out/

"--p" should be "-p" instead on a Macintosh.

Solution: Change "--p" to "-p" in test_run_epacts.sh

Note: This was also a problem in the Makefile (see below).

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Loading required package: epactsR
Error: Cannot find epactsR package at /usr/local/lib/
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘epactsR’
Execution halted

Found the package in the 'data' subdirectory of the EPACTS distribution,
but it did not compile due to this:

epacts.cpp:287:7: error: use of undeclared identifier 'isnanf'; did you mean 'isnan'?

Solution: Redefine isnanf as isnan in epacts.cpp in the epactsR package:

// Fix to get it to compile on a Macintosh
#define isnanf(X) isnan(X)

--------
Installation also was incomplete because of the "--p" in the Makefile:

mkdir --p /usr/local/lib
mkdir: illegal option -- -

Solution: Change "--p" to "-p" in the Makefile

-------
Installation then died here:

** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/usr/local/lib/epactsR/libs/epactsR.so':
  dlopen(/usr/local/lib/epactsR/libs/epactsR.so, 6): Library not loaded: libmysqlclient.18.dylib
  Referenced from: /usr/local/lib/epactsR/libs/epactsR.so
  Reason: image not found
Error: loading failed
Execution halted
ERROR: loading failed

Workaround: As

R CMD INSTALL epactsR

had worked just fine from the Terminal window, I just did a symbolic link from
/usr/local/lib to the installed epactsR package:

sudo ln -s /Library/Frameworks/R.framework/Versions/3.1/Resources/library/epactsR

and then EPACTS seems happier.

I then commented out the line in the Makefile that installs the epactsR library.


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EPACTS now gets through a lot more analyses, but then dies here:

Finished generating EPACTS Makefile
Running 5 parallel jobs of EPACTS
forkExecWait(): make -f /Users/dweeks/Temporary/out/test.gene.skat.Makefile -j 5
rm 
usage: rm [-f | -i] [-dPRrvW] file ...
       unlink file
make: *** [/Users/dweeks/Temporary/out/test.gene.skat.epacts.OK] Error 64
Error in running make -f /Users/dweeks/Temporary/out/test.gene.skat.Makefile -j 5. Exit code is 2

Looks like the Makefile has a line with just the command 'rm' on it:

$ cat /Users/dweeks/Temporary/out/test.gene.skat.Makefile
.DELETE_ON_ERROR:

all: /Users/dweeks/Temporary/out/test.gene.skat.epacts.OK

/Users/dweeks/Temporary/out/test.gene.skat.epacts.OK:
    rm 
    touch /Users/dweeks/Temporary/out/test.gene.skat.epacts.OK

Does this trace back to this:

zcat: can't stat: out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz (out/1000G_exome_chr20_example_softFiltered.calls.sites.anno.vcf.gz.Z): No such file or directory

and

zcat: can't stat: /Users/dweeks/Temporary/out/test.single.q.emmax.epacts.gz (/Users/dweeks/Temporary/out/test.single.q.emmax.epacts.gz.Z): No such file or directory

zcat on the Macintosh is looking for files that end in ".Z".

Under Linux, zcat is identical to gunzip -c, but not on the Macintosh

Solution: Replaced zcat with 'gunzip -c' whereever I could find it.

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[Hyun Min Kang]

Thanks very much. These are really helpful and I really appreciate it. I will reflect this fix in the updated version.

Thanks,

Hyun.

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[Alexander Navarini]

Dear both, 

could you possibly share a compiled version of EPACTS for mac with these changes? I tried to reproduce the steps as you described, but I am not sure I am going to get it running in a reasonable time. 

thanks very much, Alexander