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

[Henrik Bengtsson]

On Wed, Sep 12, 2012 at 12:37 PM, Simon Urbanek
<simon.urbanek at 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 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. 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
>>
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