[R-SIG-Mac] unprecedented errors at start-up

Massimo Pinto pintarello at gmail.com
Fri Jan 8 15:13:02 CET 2010 

Dear Simon and all list subscribers,

Happy New Year!

Back to a problem that I had at Christmas time, when I could not
install any new BioC packages in R. I ended up re-installing the
operating system from scratch, as you Simon suggested, with Xcode, but
got only partial success. R can now find gcc and several more programs
(see below). When I try to install Rgraphviz either from source or
from Mac Binary, again tar notifies me that it could not set the
default locale and cannot complete the installation.

Just to be sure, I also downloaded the Mac binary and the source
"tarball" and tried a manual installation:

:> install.packages("/Users/massimopinto/Downloads/Rgraphviz_1.24.0.tgz",
repos=NULL, lib="/Users/massimopinto/Library/R/2.10/library",
type="mac.binary")
tar: Failed to set default locale

but to no avail. Does this provide any extra elements as to how to proceed?
Thank you in advance,
Yours Truly
Massimo

installation log follows.
-----
During startup - Warning messages:
1: Setting LC_CTYPE failed, using "C"
2: Setting LC_TIME failed, using "C"
3: Setting LC_MESSAGES failed, using "C"
tar: Failed to set default locale
* installing *source* package 'Rgraphviz' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for whether compiler has bool... yes
configure: No --with-graphviz option was specified. Trying to find
Graphviz using other methods.
checking for pkg-config... no
checking for dotneato-config... no
configure: dotneato-config not found in PATH.
configure: Using default directory /usr/local, consider specifiying
--with-graphviz
configure: error: /usr/local/bin/dot not found.  Check Graphviz installation.
ERROR: configuration failed for package 'Rgraphviz'
* removing '/Library/Frameworks/R.framework/Versions/2.10/Resources/library/Rgraphviz'
* restoring previous
'/Library/Frameworks/R.framework/Versions/2.10/Resources/library/Rgraphviz'
------



Massimo Pinto
Post Doctoral Research Fellow
Enrico Fermi Centre and Italian Public Health Research Institute (ISS), Rome
http://claimid.com/massimopinto



On Tue, Dec 22, 2009 at 19:22, Simon Urbanek
<simon.urbanek at r-project.org> wrote:
>
> On Dec 22, 2009, at 1:07 PM, Massimo Pinto wrote:
>
>> Thank you Simon. I have tried the changing locale option but got no
>> result. When you allude to restoring permissions, what are the files
>> that you have in mind?
>
> I meant fix permissions using Disk Utility - the usual step to take on a OS that acts funny, but I suspect you may have to re-install OS X in the end (the issue is not R-specific pretty much everything will fail on the locales as you can see from tar ...)
>
> (BTW: you don't have Xcode installed so the failed source installation is due to that which is unrelated to the locales...).
>
> Cheers,
> Simon
>
>
>> Cheers
>> Massimo
>>
>>
>> On Tue, Dec 22, 2009 at 16:44, Simon Urbanek
>> <simon.urbanek at r-project.org> wrote:
>>>
>>> On Dec 22, 2009, at 9:34 , Massimo Pinto wrote:
>>>
>>>> Greetings all
>>>>
>>>> I have left R aside for about a week and upon going back to it I have
>>>> found errors which I had not encountered before. I have upgraded to
>>>> OSX 10.6 recently and these errors may be a consequence of such
>>>> upgrade.
>>>>
>>>
>>> Seems like it. Your system locales seem to be completely messed up. Seems
>>> like Archive&Install is probably what you want to do ... I have never seen
>>> this before so I don't know why your OS broke so badly. You may try the
>>> usual restore permissions, change locale, re-install OS X etc.
>>>
>>> Cheers,
>>> Simon
>>>
>>>
>>>> A first error encountered at start-up refers to the use of my locale:
>>>>
>>>> ========
>>>>
>>>> During startup - Warning messages:
>>>> 1: Setting LC_CTYPE failed, using "C"
>>>> 2: Setting LC_COLLATE failed, using "C"
>>>> 3: Setting LC_TIME failed, using "C"
>>>> 4: Setting LC_MESSAGES failed, using "C"
>>>> [R.app GUI 1.31 (5537) i386-apple-darwin9.8.0]
>>>>
>>>> WARNING: You're using a non-UTF8 locale, therefore only ASCII
>>>> characters will work.
>>>> Please read R for Mac OS X FAQ (see Help) section 9 and adjust your
>>>> system preferences accordingly.
>>>>
>>>> ============
>>>>
>>>> when trying to install a binary package from BioConductor, using the R
>>>> GUI, I get:
>>>>
>>>> =-===========
>>>> The downloaded packages are in
>>>>
>>>>  ‘/private/var/folders/vM/vMSy+Iu8HwS2jf2eaEcYFU+++TI/-Tmp-/RtmpipsYIY/downloaded_packages’
>>>> trying URL
>>>> 'http://www.bioconductor.org/packages/2.5/bioc/bin/macosx/leopard/contrib/2.10/Rgraphviz_1.24.0.tgz'
>>>> Content type 'application/x-gzip' length 800621 bytes (781 Kb)
>>>> opened URL
>>>>
>>>> downloaded 781 Kb
>>>>
>>>> tar: Failed to set default locale
>>>> ===============================================
>>>>
>>>> similarly, when trying a source package:
>>>>
>>>> =========
>>>> trying URL
>>>> 'http://www.bioconductor.org/packages/2.5/bioc/src/contrib/Rgraphviz_1.24.0.tar.gz'
>>>> Content type 'application/x-gzip' length 571761 bytes (558 Kb)
>>>> opened URL
>>>> ==================================================
>>>> downloaded 558 Kb
>>>>
>>>> During startup - Warning messages:
>>>> 1: Setting LC_CTYPE failed, using "C"
>>>> 2: Setting LC_TIME failed, using "C"
>>>> 3: Setting LC_MESSAGES failed, using "C"
>>>> tar: Failed to set default locale
>>>> * installing *source* package 'Rgraphviz' ...
>>>> checking for gcc... no
>>>> checking for cc... no
>>>> checking for cl.exe... no
>>>> configure: error: no acceptable C compiler found in $PATH
>>>> See `config.log' for more details.
>>>> ERROR: configuration failed for package 'Rgraphviz'
>>>> * removing
>>>> '/Library/Frameworks/R.framework/Versions/2.10/Resources/library/Rgraphviz'
>>>> * restoring previous
>>>>
>>>> '/Library/Frameworks/R.framework/Versions/2.10/Resources/library/Rgraphviz'
>>>> ============================
>>>>
>>>> This situation won't change if I set the locale to
>>>>
>>>>> Sys.setlocale("LC_ALL", "en_GB.UTF-8")
>>>>
>>>> Has anyone experienced this before?
>>>> Thank you in advance
>>>> Massimo
>>>>
>>>>> sessionInfo()
>>>>
>>>> R version 2.10.1 (2009-12-14)
>>>> i386-apple-darwin9.8.0
>>>>
>>>> locale:
>>>> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>>>>
>>>> attached base packages:
>>>> [1] grid      stats     graphics  grDevices utils     datasets
>>>> methods   base
>>>>
>>>> other attached packages:
>>>> [1] graph_1.22.2
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] tools_2.10.1
>>>>
>>>> Massimo Pinto
>>>> Post Doctoral Research Fellow
>>>> Enrico Fermi Centre and Italian Public Health Research Institute (ISS),
>>>> Rome
>>>> http://claimid.com/massimopinto
>>>>
>>>> _______________________________________________
>>>> R-SIG-Mac mailing list
>>>> R-SIG-Mac at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>
>>>>
>>>
>>>
>>
>>
>
>

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