Tag: linux

When performing R packages, Linux may be the best choice 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 one has to do: read Making tutorial about R Packages Under Windows: A Tutorial by Peter Rossi.
For everyone else, just boot your Linux.

Before starting, one should take a look at Writting R Extensions. This is the first step for all that wish to build R extensions. A fast and easy way to know how to pack, is to read An Introduction to the R package mechanism.

When developing using S4 objects, packaging may become a big headache.
I’ve suffered this headache. I had all kinds of warnings and errors during the package tests and installation.

I’ve started by posting to the R-Help list asking for help. Here’s the post transcript:

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 '-> 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`

But, unfortunately, no help came from there…

In the quest for the solution I’ve found out that many others were having similar problems with S4 object packaging, but no solutions were provided.
After a lot investigation, I’ve finally found it and the solution is actually quite easy.
Instead of packing it from the current environment, I’ve just passed to the package.skeleton the list of source files to build the package. As an example, here’s the small R script I’ve done to automate the packaging procedure for my “Remora” 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')

Now it's time to go to the directory created, with the name of the package,from now on {package}, and edit the following files:

• {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;

All files under /man/ are tex files and will be compiled to provide the functions help when invoked by the user.
It's only necessary to document the classes and functions that will be exported, i. e. exported in the NAMESPACE file, since all the others will not be visible to the user. All the other .Rd files may be deleted.

After the package has been created, I've tested with the "R CMD check {package}" command. My package name is "remora", so my command was "sudo R CMD check remora".
I had to run this command with the administration role, so I prefixed it with the"sudo" command. This is a characteristic my Kubuntu installation and one may not require to perform this with administrator privilegies.

Finally I've build the package with the "R CMD build {package}" command that created the tar.gz file for distribution.

To install it, just use the "R CMD INSTALL {package}" command. I've entered R and it worked fine.
To uninstall just execute "R CMD REMOVE {package}".