Re: [R] R CMD check fails at package dependencies check on Fedora Core 5, works on other systems

From: Marc Schwartz (via MN) <mschwartz_at_mn.rr.com>
Date: Wed 20 Sep 2006 - 15:02:06 GMT

On Wed, 2006-09-20 at 13:20 +0200, Kurt Hornik wrote:
> >>>>> Marc Schwartz (via MN) writes:
>
> > On Tue, 2006-09-19 at 22:16 +1000, Robert King wrote:
> >> Here is another thing that might help work out what is happening. If I
> >> use --no-install, ade4 actually fails as well, in the same way as zipfR.
> >>
> >> [Desktop]$ R CMD check --no-install ade4
> >> * checking for working latex ... OK
> >> * using log directory '/home/rak776/Desktop/ade4.Rcheck'
> >> * using Version 2.3.1 (2006-06-01)
> >> * checking for file 'ade4/DESCRIPTION' ... OK
> >> * this is package 'ade4' version '1.4-1'
> >> * checking if this is a source package ... OK
> >> * checking package directory ... OK
> >> * checking for portable file names ... OK
> >> * checking for sufficient/correct file permissions ... OK
> >> * checking DESCRIPTION meta-information ... ERROR
> >>
> >> [Desktop]$ R CMD check --no-install zipfR
> >> * checking for working latex ... OK
> >> * using log directory '/home/rak776/Desktop/zipfR.Rcheck'
> >> * using Version 2.3.1 (2006-06-01)
> >> * checking for file 'zipfR/DESCRIPTION' ... OK
> >> * checking extension type ... Package
> >> * this is package 'zipfR' version '0.6-0'
> >> * checking if this is a source package ... OK
> >> * checking package directory ... OK
> >> * checking for portable file names ... OK
> >> * checking for sufficient/correct file permissions ... OK
> >> * checking DESCRIPTION meta-information ... ERROR
>
> > <snip>
>
> > Robert,
>
> > I tried the process last night (my time) using the initial instructions
> > on my FC5 system with:
>
> > $ R --version
> > R version 2.3.1 Patched (2006-08-06 r38829)
> > Copyright (C) 2006 R Development Core Team
>
>
> > I could not replicate the problem.
>
> > However, this morning, with your additional communication:
>
> > $ R CMD check --no-install zipfR_0.6-0.tar.gz
> > * checking for working latex ... OK
> > * using log directory '/home/marcs/Downloads/zipfR.Rcheck'
> > * using Version 2.3.1 Patched (2006-08-06 r38829)
> > * checking for file 'zipfR/DESCRIPTION' ... OK
> > * checking extension type ... Package
> > * this is package 'zipfR' version '0.6-0'
> > * checking if this is a source package ... OK
> > * checking package directory ... OK
> > * checking for portable file names ... OK
> > * checking for sufficient/correct file permissions ... OK
> > * checking DESCRIPTION meta-information ... OK
> > * checking top-level files ... OK
> > * checking index information ... OK
> > * checking package subdirectories ... OK
> > * checking R files for syntax errors ... OK
> > * checking R files for library.dynam ... OK
> > * checking S3 generic/method consistency ... OK
> > * checking replacement functions ... OK
> > * checking foreign function calls ... OK
> > * checking Rd files ... OK
> > * checking Rd cross-references ... WARNING
> > Warning in grep(pattern, x, ignore.case, extended, value, fixed,
> > useBytes) :
> > input string 70 is invalid in this locale
> > * checking for missing documentation entries ... WARNING
> > Warning in grep(pattern, x, ignore.case, extended, value, fixed,
> > useBytes) :
> > input string 70 is invalid in this locale
> > All user-level objects in a package should have documentation entries.
> > See chapter 'Writing R documentation files' in manual 'Writing R
> > Extensions'.
> > * checking for code/documentation mismatches ... OK
> > * checking Rd \usage sections ... OK
> > * checking DVI version of manual ... OK
>
> > WARNING: There were 2 warnings, see
> > /home/marcs/Downloads/zipfR.Rcheck/00check.log
> > for details
>
>
>
> > So I am wondering if this raises the possibility of a locale issue on
> > your FC5 system resulting in a problem reading DESCRIPTION files? It
> > may be totally unrelated, but one never knows I suppose. Mine is:
>
> > $ locale
> > LANG=en_US.UTF-8
> > LC_CTYPE="en_US.UTF-8"
> > LC_NUMERIC="en_US.UTF-8"
> > LC_TIME="en_US.UTF-8"
> > LC_COLLATE="en_US.UTF-8"
> > LC_MONETARY="en_US.UTF-8"
> > LC_MESSAGES="en_US.UTF-8"
> > LC_PAPER="en_US.UTF-8"
> > LC_NAME="en_US.UTF-8"
> > LC_ADDRESS="en_US.UTF-8"
> > LC_TELEPHONE="en_US.UTF-8"
> > LC_MEASUREMENT="en_US.UTF-8"
> > LC_IDENTIFICATION="en_US.UTF-8"
> > LC_ALL=
>
>
> > HTH,
>
> > Marc Schwartz
>
> That's a bug in tools:::Rd_aliases (it needs to preprocess the Rd lines,
> which re-encodes if necessary and possible).
>
> I'll commit a fix later today.
>
> Thanks for spotting this.
>
> Best
> -k

Thanks for noting this Kurt!

Regards,

Marc



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