OpenXM/src/R/r-packages/note.txt - diff

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Diff for /OpenXM/src/R/r-packages/note.txt between version 1.5 and 1.13

version 1.5, 2015/04/05 23:47:46

version 1.13, 2022/04/07 00:56:44

Line 1

$OpenXM: OpenXM/src/R/r-packages/note.txt,v 1.4 2015/04/02 00:11:32 takayama Exp $

$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

Line 28 See also OpenXM/src/hgm/note.txt

Line 43 See also OpenXM/src/hgm/note.txt

R CMD INSTALL hgm

library(hgm)

You can check hgm.so3nc by hand.

You can check hgm.ncso3 by hand.

R CMD REMOVE hgm

It is used to remove the test library.

Line 39 See also OpenXM/src/hgm/note.txt

Line 54 See also OpenXM/src/hgm/note.txt

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.

Line 63 cat >>~/.valgrindrc

Line 82 cat >>~/.valgrindrc

--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)

Line 79 As to details, search "valgrind" in R-exts.pdf

Line 99 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

--> export PATH=~/this22/R/r-devel/R/bin:$PATH on orange3m (2022.04.06)

Valgrid can be used by

valgrind ./a.out

A sample: main() { int n; if (n>0) n=0; }

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