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

[Henrik Bengtsson]

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 at 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