From simon.urbanek at r-project.org  Fri Mar 26 15:19:20 2010
From: simon.urbanek at r-project.org (Simon Urbanek)
Date: Fri, 26 Mar 2010 10:19:20 -0400
Subject: [Rd] libgfortran [Was: R CMD install: problem quoting spaces when
	calling gzip?]
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	<CA772FCF-202F-4F2B-A9CF-9F76747EF375@gmail.com>
Message-ID: <B08921AB-EF9B-410C-BE9B-94A48A08AE5F@r-project.org>


On Mar 26, 2010, at 8:24 , jochen laubrock wrote:

> Yes, that worked, thanks a lot! Looking forward to the 2.11.0 release.
>
>> install.packages("~/Projects/R Library/potsdam/eyetrackR/ 
>> eyetrackR_0.13.tar.gz", repos = NULL, type = "source")
> * installing *source* package ?eyetrackR? ...
> ** R
> ** data
> ** demo
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices ...
> ** testing if installed package can be loaded
> * DONE (eyetrackR)
>> library(eyetrackR)
>
>> sessionInfo()
> R version 2.11.0 alpha (2010-03-26 r51420)
> x86_64-apple-darwin10.2.0
>
> locale:
> [1] de_DE.UTF-8/de_DE.UTF-8/C/C/de_DE.UTF-8/de_DE.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
> btw, this is probably known, but ... the gfortran in /usr/bin (gcc  
> version 4.2.1 (Apple Inc. build 5646)) did not work (complaining  
> about /usr/lib/libgfortran.dylib, missing required architecture  
> x86_64),


I suspect you have installed broken 3rd party Fortran at some point.  
Our apple build Fortran uses static libraries and includes all  
architectures. I would suggest removing libgfortran.dylib (and any  
other left-overs from 3rd party compilers).

Cheers,
Simon



> but a different gfortran located in /usr/local/bin did (gcc version  
> 4.2.3, probably from Simon Urbanek's page)
>
> On Mar 26, 2010, at 11:51 , Prof Brian Ripley wrote:
>
>> So please try 2.11.0 alpha, as I believe this is already fixed (not  
>> least, gzip is not called on that platform).  Also, I suspect  
>> setting the envir variable TAR to 'internal' would work on 2.10.1  
>> (but my Mac is at home).
>>
>> Another thing that does not work with spaces in file names is  
>> command-line completion of filenames (in R, I did not try R.app).   
>> If spaces in filenames work (other than on Windows) it is somewhat  
>> accidental.  Reports of instances where they do not, with patches  
>> against current sources, would be considered but as low priority.
>>
>> BTW, 'install' works on case-insensitive file systems, but it is  
>> likely to stop working at any time: as on Windows, 'R CMD' is being  
>> moved away from Perl/sh scripts to direct use of R.
>>
>> On Fri, 26 Mar 2010, jochen laubrock wrote:
>>
>>> I am sorry, this was from 2.10.1 on Mac OS X 10.6, so it might be  
>>> Mac-specific.
>>
>> I did try it on a Mac, but I did not try 2.10.1, since the 'upgrade  
>> before posting' request in the posting guide did apply, and we are  
>> busy enough with 2.11.0 alpha.
>>
>> The behavior is reproducible both from the shell and the GUI  
>> version of R (sessionInfo output below). It does not seem to depend  
>> on the particular package: it can be reproduced by downloading an  
>> archive of a package from CRAN to a path containing spaces and  
>> calling
>>> install.packages("path/with spaces/downloadedPackage.tar.gz",  
>>> repos = NULL, type = "source"):
>>>
>>>> print(dl <- download.packages("gam", destdir="~/Projects/R  
>>>> library/tmp"))
>>> [...] downloaded 300 Kb
>>>   [,1]  [,2]
>>> [1,] "gam" "~/Projects/R library/tmp/gam_1.01.tgz"
>>>> install.packages(dl[,2], repos = NULL, type = "source")
>>> [...]
>>> gzip: /Users/jochen/Projects/R.gz: No such file or directory
>>> gzip: library/tmp/gam_1.01.tgz: No such file or directory
>>> ERROR: cannot extract package from ?/Users/jochen/Projects/R  
>>> library/tmp/gam_1.01.tgz?
>>>
>>> # /usr/bin/R
>>>> sessionInfo()
>>> R version 2.10.1 (2009-12-14)
>>> x86_64-apple-darwin9.8.0
>>>
>>> locale:
>>> [1] de_DE.UTF-8/de_DE.UTF-8/C/C/de_DE.UTF-8/de_DE.UTF-8
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> # R.app (RAqua)
>>>> sessionInfo()
>>> R version 2.10.1 (2009-12-14)
>>> i386-apple-darwin9.8.0
>>>
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>>
>>>
>>> On Mar 26, 2010, at 10:19 , Prof Brian Ripley wrote:
>>>
>>>> You haven't told us your version of R (nor any of the other  
>>>> information requested in the posting guide).  As far as I can see  
>>>> this works in 2.11.0 alpha.
>>
>>> Does that mean that it has been re-designed to work with paths  
>>> containing spaces on Unix-alikes?
>>
>> No.  It is an unintentional side-effect of
>>
>>   o   R CMD INSTALL now uses the internal untar() in package utils:
>>       this ensures that all platforms can install bzip2- and
>>       xz-compressed tarballs.
>>
>>>>
>>>> On Fri, 26 Mar 2010, jochen laubrock wrote:
>>>>
>>>>> There appears to be a quoting problem in the way R CMD install  
>>>>> handles file names containing spaces, more specifically, in the  
>>>>> way the argument is passed through to gzip.
>>>>>
>>>>> The install.packages command
>>>>>
>>>>> (from R)
>>>>> install.packages("~/Projects/R library/bar/ 
>>>>> eyetrackR_0.13.tar.gz", repos = NULL, type = "source")
>>>>>
>>>>> expands to
>>>>>
>>>>> system("R_LIBS='/Users/foo/Library/R/2.10/library' "/Library/ 
>>>>> Frameworks/R.framework/Resources/bin/R CMD INSTALL -l '/Users/ 
>>>>> foo/Library/R/2.10/library'   '/Users/foo/Projects/R\ library/ 
>>>>> bar/eyetrackR_0.13.tar.gz'")
>>>>
>>>> So that is fine.
>>>>
>>>>>
>>>>> and gives the same error messages as the following commands from  
>>>>> Terminal.app on Mac OS X
>>>>>
>>>>> (from bash)
>>>>> R CMD install /Users/foo/Projects/R\ library/bar/ 
>>>>> eyetrackR_0.13.tar.gz
>>>>> R CMD install "~/Projects/R library/bar/eyetrackR_0.13.tar.gz"
>>>>> R CMD install '~/Projects/R library/bar/eyetrackR_0.13.tar.gz'
>>>>
>>>> the documented command is INSTALL.
>>> sorry
>>>>
>>>>> , namely (the error messages):
>>>>>
>>>>> gzip: /Users/foo/Projects/R.gz: No such file or directory
>>>>> gzip: library/bar/eyetrackR_0.13.tar.gz: No such file or directory
>>>>
>>>> Yes, and INSTALL is not designed to work with paths with spaces  
>>>> in on Unix-alikes.
>>>>
>>>>>
>>>>> The following commands do work
>>>>>
>>>>> (from R)
>>>>> setwd("~/Projects/R library/bar/")
>>>>> install.packages("eyetrackR_0.13.tar.gz", repos = NULL, type =  
>>>>> "source")
>>>>>
>>>>> (from bash)
>>>>> cd ~/Projects/R\ library/bar/
>>>>> R CMD install eyetrackR_0.13.tar.gz
>>>>>
>>>>> Interestingly, if the file is unpacked on the command line (tar  
>>>>> xzvf), then both R CMD install and install.packages work fine  
>>>>> using the quoted path name syntax, i.e.,
>>>>>
>>>>> R CMD install /Users/foo/Projects/R\ library/bar/eyetrackR
>>>>> install.packages("~/Projects/R library/bar/eyetrackR", repos =  
>>>>> NULL, type = "source")
>>>>>
>>>>> Is this a known problem?
>>>>
>>>> It is a known restriction.
>>>>
>>>>> I searched the archives, but did not find a decisive answer (only
>>>> some rather old posts suggesting not to use path names containing  
>>>> spaces--unfortunately this is not an option in the managed  
>>>> Windows environment I need to work in next week).
>>>>>
>>>>> Sorry for the long post and thanks for your time,
>>>>> Jochen
>>>>>
>>>>> ----
>>>>> Jochen Laubrock, Dept. of Psychology, University of Potsdam,
>>>>> Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
>>>>> phone: +49-331-977-2346, fax: +49-331-977-2793
>>>>>
>>>>> ______________________________________________
>>>>> R-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>>
>>>>
>>>> --
>>>> Brian D. Ripley,                  ripley at stats.ox.ac.uk
>>>> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/ 
>>>> ~ripley/
>>>> University of Oxford,             Tel:  +44 1865 272861 (self)
>>>> 1 South Parks Road,                     +44 1865 272866 (PA)
>>>> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>>>
>>>
>>
>> -- 
>> Brian D. Ripley,                  ripley at stats.ox.ac.uk
>> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
>> University of Oxford,             Tel:  +44 1865 272861 (self)
>> 1 South Parks Road,                     +44 1865 272866 (PA)
>> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>
> ----
> Jochen Laubrock, Dept. of Psychology, University of Potsdam,
> Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
> phone: +49-331-977-2346, fax: +49-331-977-2793
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>



[Rd] libgfortran [Was: R CMD install: problem quoting spaces when calling gzip?]
Simon Urbanek