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

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Diff for /OpenXM/src/R/r-packages/note.txt between version 1.1 and 1.9

-version 1.1, 2013/02/08 03:00:32
+version 1.9, 2017/03/22 00:42:56
 Line 1
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- $OpenXM$
+ $OpenXM: OpenXM/src/R/r-packages/note.txt,v 1.8 2016/10/30 01:10:18 takayama Exp $
  See also OpenXM/src/hgm/note.txt
 Line 28  See also OpenXM/src/hgm/note.txt
 Line 28  See also OpenXM/src/hgm/note.txt
 Line 28  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.
      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
+ ;;
+.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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