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

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?

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 at 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 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. ? (o with umlaut) as in:

#   \enc{H?ssjer}{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