'Re: [Bioc-devel] Re-encoding failures on OS X (that always puzzled me)'

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List:       bioc-devel
Subject:    Re: [Bioc-devel] Re-encoding failures on OS X (that always puzzled me)
From:       Henrik Bengtsson <hb () biostat ! ucsf ! edu>
Date:       2012-09-12 19:49:10
Message-ID: CAFDcVCSL0jB-UCSHU8M3W9p8EqxPA1idr0hj62AHMGPntzV98g () mail ! gmail ! com
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On Wed, Sep 12, 2012 at 12:37 PM, Simon Urbanek
<simon.urbanek@r-project.org> wrote:
> Chances are that this is at least partially a problem in the BioC test farm \
> settings and partially in your declaration/use of encodings. The BioC build issue \
> is related to "en_US.utf8" not being a valid locale on OS X, what the author \
> intended was "en_US.UTF-8" - for a full list see output of locale -a That said, do \
> you have your various package versions somewhere to check the source of the \
> problem?

http://xfer.aroma-project.org/tmp/20120912/aroma.light_1.27.0.tar.gz [latin1]
http://xfer.aroma-project.org/tmp/20120912/aroma.light_1.27.0-1.tar.gz [UTF-8]
http://xfer.aroma-project.org/tmp/20120912/aroma.light_1.27.0-2.tar.gz [latin2]

(it's only the latter that was built on BioC, but I don't think that
matters; they only differ by the DESCRIPTION file.)

Thanks Simon.

/Henrik

> 
> FWIW the CRAN build OS X machine uses
> R_ENCODING_LOCALES="latin1=en_US.ISO8859-1:latin2=cs_CZ.ISO8859-2:UTF-8=en_US.UTF-8"
>  
> Cheers,
> Simon
> 
> 
> 
> On Sep 12, 2012, at 3:25 PM, Henrik Bengtsson <hb@biostat.ucsf.edu> wrote:
> 
> > So, I ended up doing several rounds of trial and error to test what
> > the BioC farm would report when using:
> > 
> > Encoding: latin1
> > Encoding: latin2
> > Encoding: UTF-8
> > 
> > in the DESCRIPTION of aroma.light.  To summarize, none of them solved
> > the problem of R CMD check reporting on encoding failures.  With
> > latin1 and latin2 it was only the OSX machine that complained; latin2
> > at one more test than with latin1.  With UTF-8 there were warnings all
> > over the board and in more tests.  Details below.  I'm going back to
> > latin1 for now.
> > 
> > - - - - - - - - - - - - - - - - - - - - - - - -
> > Encoding: latin1
> > - - - - - - - - - - - - - - - - - - - - - - - -
> > ### For perceval (Mac OS X Leopard (10.5.8) / i386):
> > * checking whether package 'aroma.light' can be installed ... WARNING
> > Found the following significant warnings:
> > Warning: unable to re-encode '901.CalibrationAndNormalization.R'
> > line(s) 28,67,162
> > Warning: unable to re-encode 'normalizeCurveFit.matrix.R' line(s) 112
> > See '/Users/biocbuild/bbs-2.11-bioc/meat/aroma.light.Rcheck/00install.out'
> > for details.
> > 
> > 
> > - - - - - - - - - - - - - - - - - - - - - - - -
> > Encoding: latin2
> > - - - - - - - - - - - - - - - - - - - - - - - -
> > ### For perceval (Mac OS X Leopard (10.5.8) / i386):
> > * checking whether package 'aroma.light' can be installed ... WARNING
> > Found the following significant warnings:
> > Warning: unable to re-encode '901.CalibrationAndNormalization.R'
> > line(s) 28,67,162
> > Warning: unable to re-encode 'normalizeCurveFit.matrix.R' line(s) 112
> > See '/Users/biocbuild/bbs-2.11-bioc/meat/aroma.light.Rcheck/00install.out'
> > for details.
> > [...]
> > * checking package subdirectories ... WARNING
> > Invalid citation information in 'inst/CITATION':
> > 127:5: unexpected INCOMPLETE_STRING
> > 126:   textVersion = paste(sep="",
> > 127:     "H. Bengtsson & O. H
> > ^
> > Warning message:
> > invalid input found on input connection
> > '/Users/biocbuild/bbs-2.11-bioc/meat/aroma.light.Rcheck/00_pkg_src/aroma.light/inst/CITATION'
> >  
> > 
> > - - - - - - - - - - - - - - - - - - - - - - - -
> > Encoding: UTF-8
> > - - - - - - - - - - - - - - - - - - - - - - - -
> > ### For perceval (Mac OS X Leopard (10.5.8) / i386):
> > * checking whether package 'aroma.light' can be installed ... WARNING
> > Found the following significant warnings:
> > Warning: unable to re-encode '901.CalibrationAndNormalization.R'
> > line(s) 28,67,162
> > Warning: unable to re-encode 'normalizeCurveFit.matrix.R' line(s) 112
> > See '/Users/biocbuild/bbs-2.11-bioc/meat/aroma.light.Rcheck/00install.out'
> > for details.
> > [...]
> > * checking R files for syntax errors ... WARNING
> > Warning in Sys.setlocale("LC_CTYPE", "en_US.utf8") :
> > OS reports request to set locale to "en_US.utf8" cannot be honored
> > 
> > ### For moscato1 (Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64):
> > * checking whether package 'aroma.light' can be installed ... WARNING
> > Found the following significant warnings:
> > Warning: unable to re-encode '901.CalibrationAndNormalization.R'
> > line(s) 28,67,162
> > Warning: unable to re-encode 'normalizeCurveFit.matrix.R' line(s) 112
> > See 'D:/biocbld/bbs-2.11-bioc/meat/aroma.light.Rcheck/00install.out'
> > for details.
> > 
> > 
> > ### For lamb1 (Linux (openSUSE 12.1) / x86_64):
> > * checking whether package ‘aroma.light’ can be installed ... WARNING
> > Found the following significant warnings:
> > Warning: unable to re-encode '901.CalibrationAndNormalization.R'
> > line(s) 28,67,162
> > Warning: unable to re-encode 'normalizeCurveFit.matrix.R' line(s) 112
> > See ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/aroma.light.Rcheck/00install.out’
> > for details.
> > [...]
> > * checking package subdirectories ... WARNING
> > Invalid citation information in ‘inst/CITATION’:
> > 127:5: unexpected INCOMPLETE_STRING
> > 126:   textVersion = paste(sep="",
> > 127:     "H. Bengtsson & O. H
> > ^
> > Warning message:
> > invalid input found on input connection
> > ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/aroma.light.Rcheck/00_pkg_src/aroma.light/inst/CITATION’
> >  
> > END OF MESSAGE
> > 
> > On Fri, Sep 7, 2012 at 6:49 PM, Henrik Bengtsson <hb@biostat.ucsf.edu> wrote:
> > > Hi,
> > > 
> > > not sure if this is a Bioconductor specific problem or not (because I
> > > think I've seen it on CRAN as well), but at least it appears on the
> > > BioC farm:
> > > 
> > > For aroma.light 1.27.0 (devel) I get the following R CMD check
> > > warnings on OSX (only):
> > > 
> > > * checking whether package 'aroma.light' can be installed ... WARNING
> > > Found the following significant warnings:
> > > Warning: unable to re-encode '901.CalibrationAndNormalization.R'
> > > line(s) 28,67,162
> > > Warning: unable to re-encode 'normalizeCurveFit.matrix.R' line(s) 112
> > > See '/Users/biocbuild/bbs-2.11-bioc/meat/aroma.light.Rcheck/00install.out'
> > > for details.
> > > 
> > > See http://bioconductor.org/checkResults/devel/bioc-LATEST/aroma.light/perceval-checksrc.html
> > >  
> > > The above two files contains non-ASCII characters, e.g. ö (o with umlaut) as \
> > > in: 
> > > #   \enc{Hössjer}{Hossjer} (2006).
> > > 
> > > (If anyone wonders, these non-ASCII characters are not part of actual
> > > code, but part of in-source-code Rd documentation hidden within R
> > > comments.)
> > > 
> > > To tell R that these special characters exists, I've added the
> > > following to the aroma.light DESCRIPTION file:
> > > 
> > > Encoding: latin1
> > > 
> > > This seems to work on both Linux and Windows, but not on OSX.
> > > 
> > > Before I get into trial and error on this, does anyone why/a solution
> > > to this?  Am I doing something wrong, or is it just that "latin1" is
> > > not supported on (this particular?) OSX machine?  The 'Writing R
> > > Extensions' docs says that "Only encoding names latin1, latin2 and
> > > UTF-8 are known to be portable."  Should I use "UTF-8" instead?
> > > 
> > > Thanks,
> > > 
> > > Henrik
> > 
> > _______________________________________________
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > 
> > 
> 

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