Annotation of OpenXM/src/R/r-packages/note.txt, Revision 1.5
1.5 ! takayama 1: $OpenXM: OpenXM/src/R/r-packages/note.txt,v 1.4 2015/04/02 00:11:32 takayama Exp $
1.1 takayama 2:
3: See also OpenXM/src/hgm/note.txt
4:
5: * C source codes.
6: C sources and headers should be developed and edited in the directory
7: OpenXM/src/hgm in order to provide a standalone mode without R
8: in the OpenXM project.
9: They are copied by rsync to hgm/src from OpenXM/src/hgm/
10: See the Makefile.
11:
12: * How to develope and tests.
13: (1) Develope the system in OpenXM/src/hgm as a standalone system.
14: See OpenXM/src/hgm/so3 as an example.
15: (2) Add rsync-[projectname] to OpenXM/src/R/r-packages/Makefile
16: See the example of the project so3.
17: (3) Example in the case of hgm.
18: R CMD check hgm
19: It generates pdf documents and shared libraries.
20: hgm.Rcheck/hgm-Ex.Rout contains the result of the execution of examples
21: embedded in the documents in man.
22: hgm.Rcheck/hgm-manual.pdf is the PDF manual.
23:
24: See also http://fe.math.kobe-u.ac.jp/Movies/oxvh,
25: 2012-09-05-r-package[.mov]
26: 2013-02-06-Ropenxm[.mov]
27:
28: R CMD INSTALL hgm
29: R
30: library(hgm)
31: You can check hgm.so3nc by hand.
32: R CMD REMOVE hgm
33: It is used to remove the test library.
34:
35: R --help
1.2 takayama 36: (4) Binary build on Windows.
37: R CMD INSTALL --build hgm
38: ( Check R CMD INSTALL --help for details. )
39: or
40: R CMD build --binary hgm (perhaps, obsolete style)
1.1 takayama 41:
42: * Notes.
43: library.dynam() shows a list of shared libraries loaded.
44: dyn.load("hgm.so") can be used to load shared library by hand.
45: getwd() gets the current working directory.
46:
1.3 takayama 47:
48: * Undocumented functions which are removed temporary fro NAMESPACE. 2015.03.24
49: export(hgm.so3nc)
50: export(hgm.normalizingConstantOfFisherDistributionOnSO3)
51: export(hgm.normalizingConstantOfOrthant)
52: export(hgm.normalizingConstantOfBinghamDistribution)
53: export(hgm.z.mleDemo)
54: export(hgm.ssFB)
55:
1.1 takayama 56:
1.4 takayama 57: * Check the memory leak by valgrind and by AddressSanitizer. 2015.04.01
58: ** Valgrind
59: apt-get install valgrind
60:
61: cat >>~/.valgrindrc
62: --leak-check=full
63: --track-origins=yes
64: ctrl-D
65:
66: R CMD check hgm --use-valgrind
67: more hgm.Rcheck/hgm-Ex.Rout
68: Example of an error (Note that there is no error message in *.log)
69: ==14813== Conditional jump or move depends on uninitialised value(s)
70: ==14813== at 0xCA20170: mh_t (jack-n.c:1361)
71: for (i=0; i<=M_m; i++) {
72: -- snip
73: serror = myabs((partial_sum[i]-partial_sum[i-1])/partial_sum[i-1]);
74: }
75: partial_sum[-1] is accessed!
76:
77: As to details, search "valgrind" in R-exts.pdf
78:
79: * R CMD check hgm --use-gct
1.5 ! takayama 80:
! 81: * Note on building R package: @s/2015/04/05-hgm-r-package-memo.txt
! 82:
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