I've developed it mainly in Windows, but when it comes to the packaging part, I've switched to Linux. This is mainly because R packaging in Windows implies to install a lot of base Linux applications and tools on Windows. For those that wish to go that road, here's what you have to do: read Making tutorial about R Packages Under Windows: A Tutorial by Peter Rossi.
For everyone else, just boot your Linux.
Before I start, I took a look at Writting R Extensions. This is the first step for all that wish to build an R extension. A fast and easy way to know how to pack, is to read the An Introduction to the R package mechanism.
My implementation uses S4 objects, and that was a problem, since I had all kinds of warnings and errors during the package tests and installation. Here's the transcriptions of the post I've sent to the R-Help list asking for help:
Here's what I do:
*1.* in R console, I do and get:
> package.skeleton(name='remora')remora-package
Creating directories ...
Creating DESCRIPTION ...
Creating Read-and-delete-me ...
Saving functions and data ...
Making help files ...
Done.
Further steps are described in './remora/Read-and-delete-me'.
Warning messages:
1: In dump(internalObjs, file = file.path(code_dir,
sprintf("%s-internal.R", :
deparse of an S4 object will not be
source()able
2: In dump(internalObjs, file = file.path(code_dir,
sprintf("%s-internal.R", :
deparse of an S4 object will not be
source()able
3: In dump(internalObjs, file = file.path(code_dir,
sprintf("%s-internal.R", :
deparse of an S4 object will not be
source()able
4: In dump(internalObjs, file = file.path(code_dir,
sprintf("%s-internal.R", :
deparse of an S4 object will not be source()able
I don't know why I get these warnings. I've followed R
implementation rules and the S4 objects work fine.
*2.* Performing the 'R CMD build remora' command I get:
* checking for file 'remora/DESCRIPTION' ... OK
* preparing 'remora':
* checking DESCRIPTION meta-information ... OK
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'remora_1.0.tar.gz'
And the remora_1.0.tar.gz file seems ok.
*
3.* Performing the 'R CMD check remora' command I get:
* checking for working pdflatex ...sh: pdflatex: not found
NO
* checking for working latex ...sh: latex: not found
NO
* using log directory '/home/fmm/thesis/R/src/remora.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: UTF-8
* checking for file 'remora/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'remora' version '1.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking for executable files ... OK
* checking whether package 'remora' can be installed ...
ERROR
Installation failed.
See '/home/fmm/thesis/R/src/remora.Rcheck/00install.out'
for details.
*4.* the log file contains:
* Installing *source* package 'remora'
...
**
R
**
data
** preparing package for lazy
loading
Error in parse(n = -1, file = file) : unexpected '<' at 745:
`.__C__remoraConfiguration` <- 746: <> -> code2LazyLoadDB
-> sys.source -> parse Execution halted
ERROR: lazy loading failed for package
'remora'
** Removing
'/home/fmm/thesis/R/src/remora.Rcheck/remora'
fmm@Darkmaster:~/thesis/R/src$ grep -i __C__remoraConfiguration *
fmm@Darkmaster:~/thesis/R/src$ grep -i __C__remoraConfiguration */*
remora.Rcheck/00install.out:745: `.__C__remoraConfiguration`
<- remoraConfiguration is a constructor for the
remoraConfiguration S4 object.
# # Class configuration definition.
# CLASS_REMORA_CONFIGURATION <- "remoraConfiguration" class_configuration
<- setClass(CLASS_REMORA_CONFIGURATION, representation(
number_clusters = "numeric", class_name = "character",
weighting_function="character", scale_variance="logical", s="numeric",
d="numeric", alfa="numeric", eta = "numeric", niter="numeric",
niter_changes="numeric", perform_sum="logical", verbose="logical"),
prototype = list(number_clusters=numeric(), class_name=character(),
weighting_function=character(), scale_variance=logical(),
s=numeric(), d=numeric(), alfa=numeric(), eta=numeric(), niter=numeric(),
niter_changes=numeric(), perform_sum=logical(), verbose=logical()))
# # Builds a Remora configuration object.
# # [...]
# remoraConfiguration <- function(number_clusters, class_name,
weighting_function = FUNCTION_REMORA_EUCLIDEAN,
scale_variance=TRUE, s_value = 0.001, d = 0.3, alfa = 0.9, eta = 0.01,
niter=-1, niter_changes=5, perform_sum = TRUE, verbose=FALSE)
{
result_configuration <- new(CLASS_REMORA_CONFIGURATION)
[...]
result_configuration
}
But, unfortunately, no help came from there...
I've never stopped the search for the answer, and I've finally found it. It's actually quite easy.
Instead of packing it from the current environment, I've just passed the package.skeleton the list of source files to build the package. Here's the small R script I've done to automate the packaging procedure for my "Remora" package:
Now it's time to go to the directory created, with the name of the package,
cat('\nPacking Remora...\n')
file_lst <- character(5)
file_lst[1] <- '/home/m6/thesis/R/src/1_classes.r'
file_lst[2] <- '/home/m6/thesis/R/src/2_common.r'
file_lst[3] <- '/home/m6/thesis/R/src/3_model.r'
file_lst[4] <- '/home/m6/thesis/R/src/4_predict.r'
file_lst[5] <- '/home/m6/thesis/R/src/5_main.r'
package.skeleton(name = "remora", force = TRUE, namespace = TRUE,
code_files = file_lst)
cat('\nDone.\n')
{package} /DESCRIPTION , the description of the package;- {package}
/NAMESPACE , the list of functions and classes to export to the user; - {package}
/ man/ {package}-package.Rd, the package help file, the \examples section must provide executable code, since R check command will execute this code; - {package}
/man/ {class_name}-class.Rd, the classes help files; - {package}
/man/ {function_name}.Rd, the functions help files;
It's only necessary to document the classes and functions that will be exported, i. e. exported in the
After the package has been created, I've tested with the "R CMD check {package}
I had to run this command with the administration role, so I prefixed it with the
Finally I've build the package with the
To install it, just use the
To uninstall just execute
./M6
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