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Diff for /OpenXM/src/R/r-packages/note.txt between version 1.4 and 1.12

version 1.4, 2015/04/02 00:11:32 version 1.12, 2022/04/06 01:03:42
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 $OpenXM: OpenXM/src/R/r-packages/note.txt,v 1.3 2015/03/24 07:49:06 takayama Exp $  $OpenXM: OpenXM/src/R/r-packages/note.txt,v 1.11 2020/02/06 05:58:17 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()
   
     ??hgm
     ?hgm.ncorthant
   
     remove.packages('hgm')
   
 * 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 43  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.
   
Line 39  See also OpenXM/src/hgm/note.txt
Line 54  See also OpenXM/src/hgm/note.txt
    or     or
     R CMD build --binary hgm  (perhaps, obsolete style)      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.
Line 63  cat >>~/.valgrindrc
Line 82  cat >>~/.valgrindrc
 --track-origins=yes  --track-origins=yes
 ctrl-D  ctrl-D
   
   make clean
 R CMD check hgm --use-valgrind  R CMD check hgm --use-valgrind
 more hgm.Rcheck/hgm-Ex.Rout  more hgm.Rcheck/hgm-Ex.Rout
 Example of an error (Note that there is no error message in *.log)  Example of an error (Note that there is no error message in *.log)
Line 77  Example of an error (Note that there is no error messa
Line 97  Example of an error (Note that there is no error messa
 As to details, search "valgrind" in R-exts.pdf  As to details, search "valgrind" in R-exts.pdf
   
 * R CMD check hgm --use-gct  * 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
   
   
   Valgrid can be used by
      valgrind ./a.out
   A sample:  main() { int n;  if (n>0) n=0; }
   

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