$OpenXM: OpenXM/src/R/r-packages/note.txt,v 1.12 2022/04/06 01:03:42 takayama Exp $
See also OpenXM/src/hgm/note.txt
* R package build, reference pages.
https://cran.r-project.org/bin/macosx/tools/
* Example
Edit files in src/hgm
cd R/r-packages
make rsync
R CMD INSTALL hgm
Start R and library(hgm)
hgm.ncso3()
??hgm
?hgm.ncorthant
remove.packages('hgm')
* C source codes.
C sources and headers should be developed and edited in the directory
OpenXM/src/hgm in order to provide a standalone mode without R
in the OpenXM project.
They are copied by rsync to hgm/src from OpenXM/src/hgm/
See the Makefile.
* How to develope and tests.
(1) Develope the system in OpenXM/src/hgm as a standalone system.
See OpenXM/src/hgm/so3 as an example.
(2) Add rsync-[projectname] to OpenXM/src/R/r-packages/Makefile
See the example of the project so3.
(3) Example in the case of hgm.
R CMD check hgm
It generates pdf documents and shared libraries.
hgm.Rcheck/hgm-Ex.Rout contains the result of the execution of examples
embedded in the documents in man.
hgm.Rcheck/hgm-manual.pdf is the PDF manual.
See also http://fe.math.kobe-u.ac.jp/Movies/oxvh,
2012-09-05-r-package[.mov]
2013-02-06-Ropenxm[.mov]
R CMD INSTALL hgm
R
library(hgm)
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
;;
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
;;
2020.02.06 Installing r-devel
apt-get install subversion ccache
apt-get install xorg-dev
apt-get install libcurl4-openssl-dev
apt install libpcre2-dev (2022.04.06 this22/R orange3m)
pushd ~/this19/R (for example)
svn co https://svn.r-project.org/R/trunk r-devel/R
cd r-devel/R and follow the INSTALL
./configure --without-recommended-packages --prefix ~/this19/R
make
export PATH=~/this19/R/r-devel/R/bin:$PATH
Valgrid can be used by
valgrind ./a.out
A sample: main() { int n; if (n>0) n=0; }