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Annotation of OpenXM/src/R/r-packages/note.txt, Revision 1.9

1.9     ! takayama    1: $OpenXM: OpenXM/src/R/r-packages/note.txt,v 1.8 2016/10/30 01:10:18 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)
1.9     ! takayama   31:         You can check hgm.ncso3 by hand.
1.1       takayama   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:
1.9     ! takayama   42: (5) make copy-web-hgm
        !            43:    hgm_x.yz.tar.gz
        !            44:    [cran submit package] search ==> http://cran.r-project.org/submit.html
        !            45:
1.1       takayama   46: * Notes.
                     47:     library.dynam()   shows a list of shared libraries loaded.
                     48:     dyn.load("hgm.so") can be used to load shared library by hand.
                     49:     getwd() gets the current working directory.
                     50:
1.3       takayama   51:
                     52: * Undocumented functions which are removed temporary fro NAMESPACE. 2015.03.24
                     53: export(hgm.so3nc)
                     54: export(hgm.normalizingConstantOfFisherDistributionOnSO3)
                     55: export(hgm.normalizingConstantOfOrthant)
                     56: export(hgm.normalizingConstantOfBinghamDistribution)
                     57: export(hgm.z.mleDemo)
                     58: export(hgm.ssFB)
                     59:
1.1       takayama   60:
1.4       takayama   61: * Check the memory leak by valgrind and by AddressSanitizer. 2015.04.01
                     62: ** Valgrind
                     63: apt-get install valgrind
                     64:
                     65: cat >>~/.valgrindrc
                     66: --leak-check=full
                     67: --track-origins=yes
                     68: ctrl-D
                     69:
1.7       takayama   70: make clean
1.4       takayama   71: R CMD check hgm --use-valgrind
                     72: more hgm.Rcheck/hgm-Ex.Rout
                     73: Example of an error (Note that there is no error message in *.log)
                     74: ==14813== Conditional jump or move depends on uninitialised value(s)
                     75: ==14813==    at 0xCA20170: mh_t (jack-n.c:1361)
                     76:   for (i=0; i<=M_m; i++) {
                     77:     -- snip
                     78:     serror = myabs((partial_sum[i]-partial_sum[i-1])/partial_sum[i-1]);
                     79:   }
                     80:   partial_sum[-1] is accessed!
                     81:
                     82: As to details, search "valgrind" in R-exts.pdf
                     83:
                     84: * R CMD check hgm --use-gct
1.5       takayama   85:
                     86: * Note on building R package: @s/2015/04/05-hgm-r-package-memo.txt
                     87:
1.6       takayama   88: ;;
                     89: 2016.02.15  testdata.
                     90: c<-hgm.p2wishart(m=4,n1=50,n2=100,beta=c(1,2,4,8),q0=0.5,q=30,autoplot=1);
                     91:   output is wrong.
                     92: 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))
                     93:   output is correct.
                     94: 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)
                     95:   crashed, but by commented out todo in mh.c, it works. See @s/2016/02
                     96:
1.8       takayama   97: ;;
                     98: http://kbroman.org/pkg_primer/pages/cran.html
                     99:
                    100: R CMD check hgm --as-cran
                    101:
                    102: