[R-SIG-Mac] arules installation

Thu Dec 8 11:16:48 CET 2011

Hey it worked! Thank you *very* much. I installed XCode from my Mac DVD, then downloaded the arules source file and ran R CMD INSTALL /Users/thomas/Documents/arules_1.0-7.tar.gz in the terminal.

So should I always use the source file of the pakages in the future? How come this worked but downloading the binary didn't? The binary file is somehow tied to a version of R whereas the source file isn't? Has the binary file been complied already whereas my CMD INSTALL command compiled C code on my machine? But then why would my compiled C code be different from the compiled C code in the binary file?

Anyway, important thing is it seems to have worked, but if someone could advise on whether I should use source files in the future that would be really helpful.

Thomas
________________________________________
From: David Winsemius [dwinsemius at comcast.net]
Sent: Thursday, December 08, 2011 12:58 AM
To: R.Michael Weylandt
Cc: Thomas Chesney; r-sig-mac at r-project.org
Subject: Re: [R-SIG-Mac] arules installation

On Dec 7, 2011, at 4:35 PM, R. Michael Weylandt wrote:

> Theoretically, but I've always built packages from Terminal so I can't
> promise it. Also, there's an outside chance you'll need a Fortran
> compiler too, but I haven't looked at the source files to confirm.
>
> I'd also suggest you try your CRAN mirror one more time and make sure
> you are getting the 2.13 version: for instance, I used this link:
>
> http://lib.stat.cmu.edu/R/CRAN/bin/macosx/leopard/contrib/2.13/arules_1.0-7.tgz'
>
> I believe that the link shown on the CRAN page will automatically give
> you the current release (2.14) build.
>
> Michael
>
> 2011/12/7 Thomas Chesney <Thomas.Chesney at nottingham.ac.uk>:
>> Michael - thanks for the reply. So if I install my XCode C complier,

You would want all of the Xcode to be installed including the Fortran
complier and other support.

>> then download the latest arules source file which is:
>> arules_1.0-7.tar.gz and then run: install.packages("/Users/thomas/
>> Documents/arules_1.0-7.tar.gz", repos=NULL, type="source") it will
>> just work? (Why will that work with the latest version but the
>> latest .tgz won't?)

It should succeed that way if Xocde is properly installed. Why didn't
you try that?

AND: Why are you staying with 2.13? Why not update your R version?

>>
>> What I usually do to install a package is download the .tgz file,
>> double click to unzip it, then copy the resulting folder into
>> Library/Frameworks/R.Framework/Resources/Library.

That is only going to work for  packages that are all-R and no C/Fortran

>> I could install the latest R and then do that for arules, but then
>> I'd have to do the same for dozens of other packages (or could I
>> just copy them to another folder, update R, and then copy them to
>> R.Framework/Resources/Library saying no to any replace file popups?)

The usual recommendation is after updating R , which creates a new
Resources folder with ./library/, to copy/paste the contents of the
2.13 ../library/ into the new one and then at the R console to execute:

update.packages(checkBuilt=TRUE) # and probably also include the
ask=FALSE option

I usually forget that ask option and then have to keep typing Y<cr>.

Best;
David.

>>
>> Thomas
>>
>> ________________________________________
>> From: R. Michael Weylandt <michael.weylandt at gmail.com> [michael.weylandt at gmail.com
>> ]
>> Sent: Wednesday, December 07, 2011 1:36 PM
>> To: Thomas Chesney
>> Cc: r-sig-mac at r-project.org
>> Subject: Re: [R-SIG-Mac] arules installation
>>
>> You need a C compiler: the usual recommendation is XCode which you
>> can get off your OS X install DVD or download from Apple Developer
>> pages.
>>
>> Out of curiosity, how did you download the first time? I can still
>> get 2.13.x packages from CRAN though I haven't tried with arules
>> specifically.
>>
>> Michael
>>
>> On Dec 7, 2011, at 6:05 AM, Thomas Chesney <Thomas.Chesney at nottingham.ac.uk
>> > wrote:
>>
>>> I sent the following and got the following reply to the R-Help,
>>> and then was told I should have sent it here.
>>>
>>> On 07.12.2011 10:54, Thomas Chesney wrote:
>>>> I'm using R version 2.13.0 (2011-04-13) on Mac OS X and I get the
>>>> following error message with library(arules):
>>>>
>>>> Loading required package: Matrix
>>>> Loading required package: lattice
>>>>
>>>> Attaching package: 'Matrix'
>>>>
>>>> The following object(s) are masked from 'package:base':
>>>>
>>>>    det
>>>>
>>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>>>  unable to load shared object '/Library/Frameworks/R.framework/
>>>> Versions/2.13/Resources/library/arules/libs/i386/arules.so':
>>>>  dlopen(/Library/Frameworks/R.framework/Versions/2.13/Resources/
>>>> library/arules/libs/i386/arules.so, 6): Library not loaded: /
>>>> Library/Frameworks/R.framework/Versions/2.14/Resources/lib/
>>>> libR.dylib
>>>>  Referenced from: /Library/Frameworks/R.framework/Versions/2.13/
>>>> Resources/library/arules/libs/i386/arules.so
>>>>  Reason: image not found
>>>> In addition: Warning message:
>>>> package 'arules' was built under R version 2.14.0
>>>> Error: package/namespace load failed for 'arules'
>>>
>>> Install an arules binary that was built for your version of R
>>> (reather
>>> than a later one) or install from sources.
>>>
>>> Uwe Ligges
>>>
>>>>
>>>> The arules CRAN page says: Depends:   R (≥ 2.11.0), stats,
>>>> methods, Matrix (≥ 0.999375-38), all of which I have - anyone
>>>> know what the problem is? I'm really relunctant to update R as
>>>> its Package Installer is blocked somehow by our Firewall and
>>>> updating all the packages I use is a major hassle.
>>>>
>>>> Thank you (as always!)
>>>>
>>>> Thomas
>>>>
>>>> PS on a related note, are the package installer port settings
>>>> available somewhere and I'll send them to IT, ask them to unblock
>>>> it?
>>>
>>>
>>> -------------------------------------
>>>
>>> I tried installing from source as Prof Ligges suggested (as
>>> explained here: http://stackoverflow.com/questions/1474081/how-do-i-install-an-r-package-from-source)
>>>  but got the following error:
>>>
>>> install.packages("/Users/thomas/Documents/arules_1.0-7.tar.gz",
>>> repos=NULL, type="source")
>>> * installing *source* package 'arules' ...
>>> ** libs
>>> *** arch - i386
>>> sh: make: command not found
>>> ERROR: compilation failed for package 'arules'
>>> * removing '/Library/Frameworks/R.framework/Versions/2.13/
>>> Resources/library/arules'
>>> Warning message:
>>> In install.packages("/Users/thomas/Documents/
>>> arules_1.0-7.tar.gz",  :
>>> installation of package '/Users/thomas/Documents/
>>> arules_1.0-7.tar.gz' had non-zero exit status
>>>
>>> Why would installing from source make any difference? Prof Ripley
>>> suggested I use arules for R.13.0, which I would if I could find it.
>>>
>>> Has anyone got any advice?
>>>
>>> Thank you,
>>>
>>> Thomas
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David Winsemius, MD
West Hartford, CT