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Annotation of OpenXM/src/R/r-packages/note.txt, Revision 1.8

1.8     ! takayama    1: $OpenXM: OpenXM/src/R/r-packages/note.txt,v 1.7 2016/10/28 02:27:39 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:
1.7       takayama   66: make clean
1.4       takayama   67: R CMD check hgm --use-valgrind
                     68: more hgm.Rcheck/hgm-Ex.Rout
                     69: Example of an error (Note that there is no error message in *.log)
                     70: ==14813== Conditional jump or move depends on uninitialised value(s)
                     71: ==14813==    at 0xCA20170: mh_t (jack-n.c:1361)
                     72:   for (i=0; i<=M_m; i++) {
                     73:     -- snip
                     74:     serror = myabs((partial_sum[i]-partial_sum[i-1])/partial_sum[i-1]);
                     75:   }
                     76:   partial_sum[-1] is accessed!
                     77:
                     78: As to details, search "valgrind" in R-exts.pdf
                     79:
                     80: * R CMD check hgm --use-gct
1.5       takayama   81:
                     82: * Note on building R package: @s/2015/04/05-hgm-r-package-memo.txt
                     83:
1.6       takayama   84: ;;
                     85: 2016.02.15  testdata.
                     86: c<-hgm.p2wishart(m=4,n1=50,n2=100,beta=c(1,2,4,8),q0=0.5,q=30,autoplot=1);
                     87:   output is wrong.
                     88: 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))
                     89:   output is correct.
                     90: 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)
                     91:   crashed, but by commented out todo in mh.c, it works. See @s/2016/02
                     92:
1.8     ! takayama   93: ;;
        !            94: http://kbroman.org/pkg_primer/pages/cran.html
        !            95:
        !            96: R CMD check hgm --as-cran
        !            97:
        !            98: