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$OpenXM: OpenXM/src/R/r-packages/note.txt,v 1.13 2022/04/07 00:56:44 takayama Exp $

See also OpenXM/src/hgm/note.txt

* R package build, reference pages.
https://cran.r-project.org/bin/macosx/tools/
* Example
  Edit files in src/hgm
  cd R/r-packages
  make rsync
  R CMD INSTALL hgm
  Start R and library(hgm)
  hgm.ncso3()

  ??hgm
  ?hgm.ncorthant

  remove.packages('hgm')   

* 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.ncso3 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) 

(5) make copy-web-hgm
   hgm_x.yz.tar.gz
   [cran submit package] search ==> http://cran.r-project.org/submit.html

* 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

make clean
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

* Note on building R package: @s/2015/04/05-hgm-r-package-memo.txt

;;
2016.02.15  testdata.
c<-hgm.p2wishart(m=4,n1=50,n2=100,beta=c(1,2,4,8),q0=0.5,q=30,autoplot=1);
  output is wrong.
c<-hgm.p2wishart(m=4,n1=50,n2=100,beta=c(1,2,4,8),q0=0.5,q=30,err=c(1e-30,1e-10),mode=c(1,1,0))
  output is correct.
c<-hgm.p2wishart(m=4,n1=50,n2=100,beta=c(1,2,4,8),q0=0.5,q=30,err=c(1e-30,1e-10),autoplot=1)
  crashed, but by commented out todo in mh.c, it works. See @s/2016/02

;;
http://kbroman.org/pkg_primer/pages/cran.html

R CMD check hgm --as-cran


;;
2020.02.06  Installing r-devel
 apt-get install subversion ccache
 apt-get install xorg-dev
 apt-get install libcurl4-openssl-dev
 apt install libpcre2-dev    (2022.04.06  this22/R orange3m)
 pushd ~/this19/R  (for example)
 svn co https://svn.r-project.org/R/trunk r-devel/R
 cd r-devel/R   and follow the INSTALL
 ./configure --without-recommended-packages  --prefix ~/this19/R
 make
 export PATH=~/this19/R/r-devel/R/bin:$PATH
 -->  export PATH=~/this22/R/r-devel/R/bin:$PATH   on orange3m (2022.04.06)


Valgrid can be used by
   valgrind ./a.out
A sample:  main() { int n;  if (n>0) n=0; }