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1. Memory leak is fixed in jack-n.c
2. An error handling is added for R.

$OpenXM: OpenXM/src/R/r-packages/note.txt,v 1.4 2015/04/02 00:11:32 takayama Exp $

See also OpenXM/src/hgm/note.txt

* C source codes.
 C sources and headers should be developed and edited in the directory
 OpenXM/src/hgm in order to provide a standalone mode without R
 in the OpenXM project.
 They are copied by rsync to hgm/src from OpenXM/src/hgm/
 See the Makefile.

* How to develope and tests.
(1) Develope the system in OpenXM/src/hgm as a standalone system.
    See OpenXM/src/hgm/so3 as an example.
(2) Add rsync-[projectname] to OpenXM/src/R/r-packages/Makefile
    See the example of the project so3.
(3) Example in the case of hgm.
    R CMD check hgm
        It generates pdf documents and shared libraries.
        hgm.Rcheck/hgm-Ex.Rout contains the result of the execution of examples
        embedded in the documents in man.
        hgm.Rcheck/hgm-manual.pdf is the PDF manual.

    See also http://fe.math.kobe-u.ac.jp/Movies/oxvh,
       2012-09-05-r-package[.mov]
       2013-02-06-Ropenxm[.mov] 

    R CMD INSTALL hgm
        R
        library(hgm)
        You can check hgm.so3nc by hand.
    R CMD REMOVE hgm
        It is used to remove the test library.
   
    R --help
(4) Binary build on Windows.
    R CMD INSTALL --build hgm
    ( Check R CMD INSTALL --help for details. )
   or
    R CMD build --binary hgm  (perhaps, obsolete style) 

* Notes.
    library.dynam()   shows a list of shared libraries loaded.
    dyn.load("hgm.so") can be used to load shared library by hand.
    getwd() gets the current working directory.


* Undocumented functions which are removed temporary fro NAMESPACE. 2015.03.24
export(hgm.so3nc)
export(hgm.normalizingConstantOfFisherDistributionOnSO3)
export(hgm.normalizingConstantOfOrthant)
export(hgm.normalizingConstantOfBinghamDistribution)
export(hgm.z.mleDemo)
export(hgm.ssFB)

 
* Check the memory leak by valgrind and by AddressSanitizer. 2015.04.01
** Valgrind
apt-get install valgrind

cat >>~/.valgrindrc
--leak-check=full
--track-origins=yes
ctrl-D

R CMD check hgm --use-valgrind
more hgm.Rcheck/hgm-Ex.Rout
Example of an error (Note that there is no error message in *.log)  
==14813== Conditional jump or move depends on uninitialised value(s)
==14813==    at 0xCA20170: mh_t (jack-n.c:1361)
  for (i=0; i<=M_m; i++) {
    -- snip
    serror = myabs((partial_sum[i]-partial_sum[i-1])/partial_sum[i-1]);
  }
  partial_sum[-1] is accessed!

As to details, search "valgrind" in R-exts.pdf

* R CMD check hgm --use-gct