[BioC] makeProbePackage problems?

Matthew Hannah Hannah at mpimp-golm.mpg.de
Fri Feb 6 13:58:28 MET 2004

Hi again,

I've now decided to see how GCRMA performs, I got and installed R-devel and latest BioC (In parallel to R 1.8, so 
I have r1081 and r1090dev folders in my R directory- but assume this is not the problem?) When I tried to use it I 
found there is no probe package for the arabidopsis ATH1-121501 chip. I downloaded ATH1-121501_probe_tab.zip
from netaffx, changed it to a .gz using win-gz, put it into the matchprobes>data folder and followed the matchprobes 
vignette and ?makeProbePackage help.

I tried this-
filename <- file.path(.path.package("matchprobes"), "data", "ATH1-121501_probe_tab.gz")
outdir <- tempdir()
me <- "Matt Hannah <hannah at NOSPAM>"
makeProbePackage("ATH1-121501", datafile = gzfile(filename, open = "r"), outdir = outdir, maintainer = me, version
 = "0.0.1", force = TRUE)

And got this error-
Importing the data.
Creating package in C:\TEMP\Rtmp11933/ath1121501probe 
Existing C:\TEMP\Rtmp11933/ath1121501probe was removed.
Writing the data.
Checking the package.
Error in makeProbePackage("ATH1-121501", datafile = gzfile(filename, open = "r"),  : 
        Expected but did not find the log-file ath1121501probe.Rcheck/00check.log after R CMD check
In addition: Warning message: 
C:\PROGRA~1\R\RW1090~1/bin/R not found 

If I add ...check = FALSE) then I suppress the error message but is the ProbePackage ok? Do I just copy the folders
from the temp dir to the R library to use it? Does the other warning message matter?


Dr. Matt Hannah
Max-Planck Institute of Molecular Plant Physiology
Am Mühlenburg 1
14476 Golm

+ 49 (331) 567 8255 (phone)
+ 49 (331) 567 8250 (fax)

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