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version 1.1, 2013/02/08 03:00:32 | version 1.9, 2017/03/22 00:42:56 | ||
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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 | See also OpenXM/src/hgm/note.txt | ||
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R CMD INSTALL hgm | R CMD INSTALL hgm | ||
R | R | ||
library(hgm) | library(hgm) | ||
You can check hgm.so3nc by hand. | You can check hgm.ncso3 by hand. | ||
R CMD REMOVE hgm | R CMD REMOVE hgm | ||
It is used to remove the test library. | It is used to remove the test library. | ||
R --help | 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. | * Notes. | ||
library.dynam() shows a list of shared libraries loaded. | library.dynam() shows a list of shared libraries loaded. | ||
dyn.load("hgm.so") can be used to load shared library by hand. | dyn.load("hgm.so") can be used to load shared library by hand. | ||
getwd() gets the current working directory. | 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 | |||
;; | |||
2016.02.15 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 | |||