OpenXM/src/R/r-packages/note.txt - diff

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Diff for /OpenXM/src/R/r-packages/note.txt between version 1.3 and 1.13

-version 1.3, 2015/03/24 07:49:06
+version 1.13, 2022/04/07 00:56:44
 Line 1
 Line 1
 Line 1
- $OpenXM: OpenXM/src/R/r-packages/note.txt,v 1.2 2013/02/09 02:58:14 takayama Exp $
+ $OpenXM: OpenXM/src/R/r-packages/note.txt,v 1.12 2022/04/06 01:03:42 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
-Line 28  See also OpenXM/src/hgm/note.txt
+Line 43  See also OpenXM/src/hgm/note.txt
 Line 28  See also OpenXM/src/hgm/note.txt
 Line 43  See also OpenXM/src/hgm/note.txt
      R CMD INSTALL hgm
          R
          library(hgm)
-         You can check hgm.so3nc by hand.
+         You can check hgm.ncso3 by hand.
      R CMD REMOVE hgm
          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
 Line 39  See also OpenXM/src/hgm/note.txt
 Line 54  See also OpenXM/src/hgm/note.txt
     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.
-Line 54  export(hgm.z.mleDemo)
+Line 73  export(hgm.z.mleDemo)
 Line 54  export(hgm.z.mleDemo)
 Line 73  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
+ ;;
+.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
+ ;;
+.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; }

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