Hello.
I've developed an algorithm in R which I need to package.
The implementation uses S4 objects and it's divided in 5 files.
Everything is working fine when I load the files into the R console but when
I try to make a package I get an error that I don't quite understand.
Here's what I do:
*1.* in R console, I do and get:
> package.skeleton(name='remora')
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:
<
Calls: <Anonymous> -> code2LazyLoadDB -> sys.source ->
parse
Execution
halted
ERROR: lazy loading failed for package
'remora'
** Removing
'/home/fmm/thesis/R/src/remora.Rcheck/remora'
f...@darkmaster:~/thesis/R/src$ grep -i __C__remoraConfiguration *
f...@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
}
I'm using R version 2.8.1 (2008-12-22).
Sorry for the long email, but I don't want to miss any important
information.
Am I doing something wrong? If so, what?
How can I overcome this problem?
Thank you very much.
--
Fernando Martins
http://www.vilma-fernando.net/it/ "In Dreams Begin...
http://m6onsoftware.blogspot.com/ Responsability"
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