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Diff for /OpenXM/src/R/r-packages/note.txt between version 1.1 and 1.10

version 1.1, 2013/02/08 03:00:32 version 1.10, 2019/11/16 11:03:43
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 $OpenXM$  $OpenXM: OpenXM/src/R/r-packages/note.txt,v 1.9 2017/03/22 00:42:56 takayama Exp $
   
 See also OpenXM/src/hgm/note.txt  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()
   
 * C source codes.  * C source codes.
  C sources and headers should be developed and edited in the directory   C sources and headers should be developed and edited in the directory
  OpenXM/src/hgm in order to provide a standalone mode without R   OpenXM/src/hgm in order to provide a standalone mode without R
Line 28  See also OpenXM/src/hgm/note.txt
Line 38  See also OpenXM/src/hgm/note.txt
     R CMD INSTALL hgm      R CMD INSTALL hgm
         R          R
         library(hgm)          library(hgm)
         You can check hgm.so3nc by hand.          You can check hgm.ncso3 by hand.
     R CMD REMOVE hgm      R CMD REMOVE hgm
         It is used to remove the test library.          It is used to remove the test library.
   
     R --help      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.  * Notes.
     library.dynam()   shows a list of shared libraries loaded.      library.dynam()   shows a list of shared libraries loaded.
     dyn.load("hgm.so") can be used to load shared library by hand.      dyn.load("hgm.so") can be used to load shared library by hand.
     getwd() gets the current working directory.      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
   
   
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