Sorry to all those who responded, but I am not getting my point across.
I have read the "Writing R Extensions" document and DO have the
suggested directory structure, and I have the data files in the
data directory. One data file is really an .RData file, one _cannot_ be.
I am even having trouble with the .RData data file.
Most of the confusion is that people are giving me suggestions that
work when the package is already installed and R knows about the
package PATH (for lack of a better concept). My problem is that
during the "check" sequence, the existing R PATH does _not_ contain
the data to be data()'d or load()'d, EVEN THOUGH the data IS
IN the <package>/data directory (or so it seems to me).
to wit (from within R):
> system("pwd")
/home/thoar/R> system("ls -l")
total 10
drwxr-xr-x 5 thoar cgdcas 512 Jan 9 16:44
RadioSonde> system("ls -lR RadioSonde")
RadioSonde:
total 10
-rw-r--r-- 1 thoar cgdcas 750 Jan 9 16:32 DESCRIPTION
-rw-r--r-- 1 thoar cgdcas 758 Jan 9 16:44 INDEX
drwxr-xr-x 2 thoar cgdcas 512 Jan 9 14:20 R
drwxr-xr-x 2 thoar cgdcas 512 Jan 9 16:44 data
drwxr-xr-x 2 thoar cgdcas 512 Jan 4 16:43 man
RadioSonde/R:
total 106
-rw-r--r-- 1 thoar cgdcas 2433 Jan 9 11:54 getsonde.R
-rw-r--r-- 1 thoar cgdcas 701 Jan 9 14:13 plot.wind.R
-rw-r--r-- 1 thoar cgdcas 2115 Jan 9 14:10 plotsonde.R
-rw-r--r-- 1 thoar cgdcas 439 Jan 4 16:43 satlft.R
-rw-r--r-- 1 thoar cgdcas 11171 Jan 9 14:17 skewt.axis.R
-rw-r--r-- 1 thoar cgdcas 21188 Jan 4 16:43 skewt.data.R
-rw-r--r-- 1 thoar cgdcas 146 Jan 4 16:43 skewt.lines.R
-rw-r--r-- 1 thoar cgdcas 116 Jan 4 16:43 skewt.points.R
-rw-r--r-- 1 thoar cgdcas 251 Jan 4 16:43 skewtx.R
-rw-r--r-- 1 thoar cgdcas 212 Jan 4 16:43 skewty.R
-rw-r--r-- 1 thoar cgdcas 4346 Jan 9 10:40 station.symbol.R
-rw-r--r-- 1 thoar cgdcas 3977 Jan 4 16:43 wobf.R
RadioSonde/data:
total 256
-rw-r--r-- 1 thoar cgdcas 179 Jan 9 16:44 00Index
-rw-r--r-- 1 thoar cgdcas 63216 Jan 4 16:43 ExampleSonde.txt
-rw-r--r-- 1 thoar cgdcas 65718 Jan 9 13:19 sample.sonde.RData
RadioSonde/man:
total 58
-rw-r--r-- 1 thoar cgdcas 5222 Jan 10 09:05 ExampleSonde.Rd
-rw-r--r-- 1 thoar cgdcas 372 Jan 9 12:29 RadioSonde-internal.Rd
-rw-r--r-- 1 thoar cgdcas 4294 Jan 10 09:05 getsonde.Rd
-rw-r--r-- 1 thoar cgdcas 1775 Jan 10 09:03 plot.wind.Rd
-rw-r--r-- 1 thoar cgdcas 2710 Jan 10 09:06 plotsonde.Rd
-rw-r--r-- 1 thoar cgdcas 2383 Jan 9 15:33 sample.sonde.Rd
-rw-r--r-- 1 thoar cgdcas 2680 Jan 10 09:06 skewt.axis.Rd
-rw-r--r-- 1 thoar cgdcas 1175 Jan 10 09:24 skewt.lines.Rd
-rw-r--r-- 1 thoar cgdcas 1157 Jan 10 09:24 skewt.points.Rd
-rw-r--r-- 1 thoar cgdcas 1873 Jan 10 09:24
station.symbol.Rd> data("ExampleSonde.txt")
Warning message:
Data set `ExampleSonde.txt' not found in:
data("ExampleSonde.txt")> data("sample.sonde.RData")
Warning message:
Data set `sample.sonde.RData' not found in:
data("sample.sonde.RData")
# PLEASE NOTE: There exists no "RadioSonde" package at this point!
All
# the pieces are there, but thats about it.
# sample.sonde.Rdata was created by
save(<yadda>,<yadda>,ascii=TRUE)
# When I use a different LOAD:
> load("RadioSonde/data/sample.sonde.RData")
>
# R does EXACTLY as expected! However, this is clearly not an appropriate
# example once the package is installed!
# I have commented out all my examples save one:
\examples{
load("sample.sonde.RData")
}
When I try to "check" it, it bombs:
0[230]2 sunray2:~/R > R CMD check RadioSonde
* checking for working latex ... OK
* using log directory `/home/thoar/R/RadioSonde.Rcheck'
Installing source package `RadioSonde' ...
R
data
help
>>> Building/Updating help pages for package `RadioSonde'
Formats: text html latex example
ExampleSonde text html latex example
RadioSonde-internal text html latex
getsonde text html latex example
plot.wind text html latex example
plotsonde text html latex example
sample.sonde text html latex
skewt.axis text html latex example
skewt.lines text html latex example
skewt.points text html latex example
station.symbol text html latex example
DONE (RadioSonde)
DONE (INSTALL)
* checking for file `RadioSonde/DESCRIPTION' ... OK
* checking package directory ... OK
* checking for sufficient file permissions ... OK
* checking DESCRIPTION Package field ... OK
* checking DESCRIPTION Version field ... OK
* checking DESCRIPTION License field ... OK
* checking DESCRIPTION Description field ... OK
* checking DESCRIPTION Title field ... OK
* checking DESCRIPTION Author field ... OK
* checking DESCRIPTION Maintainer field ... OK
* checking R files for library.dynam ... OK
* checking Rd files ... OK
* checking for undocumented objects ... OK
* checking for code/documentation mismatches ... OK
* creating RadioSonde-Ex.R ... OK
* checking examples ... ERROR
* running examples failed
1[231]2 sunray2:~/R >
I don't see how, BEFORE THE PACKAGE IS BUILT, the "data",
"load", or any
other command should know to search for any "data" directories in all
directories in the current working directory. Naturally, once the package
is installed, this is not a problem. At the CHECK stage, however, there
is no .lib.loc information available for a package that does not exist.
What am I not understanding about the PATH strategy for R?
Perhaps I am not building/checking the package in the intended fashion?
I can send a TAR file of the package (~54kb) to any interested parties.
Sincerely, and I appreciate the help -- Tim
P.S. The intended [real world] data files are the result of a data
collection mechanism beyond my control and contain an aggregation of
metadata in a header and a subsequent table. They have an unknown
number of lines of "text", a unique line of text, what amounts
to
the col.names, a garbage line of text, and then the table of data.
Seems to me the .txt extension is the best descriptor for this.
All my getsonde() function does is scan() the file in as a series
of lines, parse the lines and decodes the number of lines to skip
for read.table(). Along the way I grab the col.names and convert
to lower case, and the presence of the garbage line in-between
the col.names and the data prevents a straightforward call to
read.table.
Some of my examples SHOULD show how to read a real radiosonde
datafile, not a preprocessed R dataset. So, I really need to
have sample.sonde <- getsonde("ExampleSonde.txt") as
a valid example. Simply getting data("contrived") to
work is insufficient, I think.
<The rest of this is in response to Brian Ripley's reply>
> Use data(). Have a file ExampleSonde.R in RadioSonde/data that does
> whatever is necessary to read ExampleSonde.txt. Then
> data(ExampleSonde) will work, from anywhere.
>
> I think ExampleSonde.R could just contain
>
> ExampleSonde <- getsonde("ExampleSonde.txt")
>
> BTW, assuming ExampleSonde.txt is really data, I suggect you don't give
it
> a .txt extension. data() allows that for rectangular arrays of data.
>
> See ?data for more details.
>
> --
> Brian D. Ripley, ripley at stats.ox.ac.uk
> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel: +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272860 (secr)
> Oxford OX1 3TG, UK Fax: +44 1865 272595
Hunh? RadioSonde/R/getsonde.R is the function that reads in
RadioSonde/data/ExampleSonde.txt. Are you telling me to
copy/move RadioSonde/R/getsonde.R to
RadioSonde/data/ExampleSonde.R ?
I'm sorry, but I really don't understand.
Tim
## Tim Hoar, Associate Scientist email: thoar at ucar.edu ##
## Geophysical Statistics Project phone: 303-497-1708 ##
## National Center for Atmospheric Research FAX : 303-497-1333 ##
## Boulder, CO 80307 http://www.cgd.ucar.edu/~thoar ##
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