[R-pkg-devel] R-devel problem with temporary files or decompression?

Henrik Bengtsson henrik.bengtsson at ucsf.edu
Sun Jul 12 22:30:16 CEST 2015

I don't see any particular wrong with your code, so it seems like
R.utils doesn't handle your 'file' / 'tmp' pathnames correctly.
However, I cannot reproduce this (know what 'file' and 'tmp' are would
help), so I cannot fix it either.

Either way, instead of using low-level decompressFile(), you can
achieve what you want with:

rsk <- R.utils::gunzip(file, temporary=TRUE, remove=FALSE)

If you don't use temporary=TRUE, then 'rsk' with point to 'sample.rsk'
in the current directory.

(author of R.utils)

On Sun, Jul 12, 2015 at 8:45 AM, Daniel Kelley <Dan.Kelley at dal.ca> wrote:
> Uwe, thanks very much. How silly of me.  It was because my code creates full pathnames except if the first char of a filename is “/“ or “~”, etc. I have never really used windows/msdos (went from 1970s unix to OSX) and so I was being very silly. Dan.
>> On Jul 12, 2015, at 12:38 PM, Uwe Ligges <ligges at statistik.tu-dortmund.de> wrote:
>> On 12.07.2015 17:33, Daniel Kelley wrote:
>>> A data file that I’d like to use in my “oce” package is quite large, and compresses well, so I thought of putting a compressed version into inst/extdata. I want my documentation to show how to uncompress the file, partly because these files tend to compress so well that I think users might like to store them in gzipped form.
>>> Naturally, I want to test my code using R-devel in addition to the ‘release’ version that I have on my box. Since I’ve never been able to get R-devel installed properly on OSX, I thought of submitting to win-builder. I got errors as below my signature line. What I don’t understand is the “Invalid argument”, which seems to be different from the “No such file or directory” that I would expect to get if there were no file. Any ideas on how to proceed?
>>> Dan Kelley / Oceanography / Dalhousie University / Halifax NS Canada
>>>> ### ** Examples
>>>> library(oce)
>>>> ## A CTD-style rsk
>>>> if (requireNamespace("R.utils")) {
>>> +   file <- system.file("extdata", "sample.rsk.gz", package="oce")
>>> +   tmp <- tempfile(fileext=".rsk")
>>> +   R.utils::decompressFile(file, destname=tmp, ext="gz", FUN=gzfile, remove=FALSE)
>>> +   rsk <- read.rsk(tmp)
>>> +   ctd <- as.ctd(rsk)
>>> +   plot(ctdTrim(ctd))
>>> + }
>>> Loading required namespace: R.utils
>>> Warning in file(file, "r") :
>>>   cannot open file 'd:/RCompile/CRANguest/R-devel/oce.Rcheck/examples_i386/D:\temp\RtmpGUYumI\file29ac3bed3fed.rsk':
>> Apparently you have put together the location of the current path and the one of the tempfile which does not make sense.
>> So very likely a bug in your code. Surprise you do not see it on your end.
>> Best,
>> Uwe Ligges
>>> Invalid argument
>>> Error in file(file, "r") : cannot open the connection
>>> Calls: read.rsk -> file
>>> Execution halted
>>> ** running examples for arch 'x64' ... ERROR
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