[R-SIG-Mac] ‘package ‘XML’ is not installed for 'arch=x86_64'’

Sat Sep 29 11:58:03 CEST 2012

I bet Simon is right. Two main reasons:

1. I was following a blog post on how to set up FastRWeb on Mac OS X. This post (http://www.r-bloggers.com/setting-up-fastrweb-on-mac-os-x/) speaks about installing from sources and, even though "I think" I move to binaries prior to posting here on this issue, I can't be sure about that.
2. My understanding about multiple sub-architectures is more than poor. So, I could be sure I used the correct terms and concepts when analyzing the issue I was facing here.

I always try to stick to "official" sources of information when studying how to use a given R piece of software, but Google and other search engines put tones of other documents a couple of clicks away and is by no means easy to decide which one deserves to be followed. I think many of them can be useful when read with enough background as to be able to separate noise and information.

Please, allow me to hijack this thread to put in another, for me, related question I'm trying to work out on the list. To the best of my understanding and by following the documentation when I install R binary for Mac OS X both i386 and x86_64 are available. In fact I can easily choose among them by launching R Console by click on R or R64 "icons". But I'm not able to find the switch I must use to get the same thing when running R from the command line: I always get x86_64. I'm not able to solve this question by following R for Mac OS X FAQ or other sources of information available from CRAN.

Sorry for the noise I introduced in this list. Thanks to everybody!

Ricardo

> ________________________________________
> From: Simon Urbanek [simon.urbanek at r-project.org]
> Sent: 29 September 2012 03:49
> To: John Maindonald
> Cc: Rodriguez Fernandez, Ricardo Julio; r-sig-mac at r-project.org
> Subject: Re: [R-SIG-Mac] ‘package ‘XML’ is not installed for 'arch=x86_64'’
>
> On Sep 28, 2012, at 9:05 PM, John Maindonald wrote:
>
>> Others may be able to give a more authoritative answer.  I doubt that
>> the method of installation was per se the difference.  I installed using
>> the Package installer, on April 6 2012.  The publication date
>> (2012-01-31 07:37:18) was the same as for the package that you
>> installed by first downloading.  You may have been unlucky that
>> something went wrong when you installed using the Package Installer.
>> Or, just possibly, a different file was temporarily on CRAN when you
>> used the package installer.
>>
>
> It think it's actually more simple than that - my guess is that  Ricardo has (apparently inadvertently)
> installed the *source* package and not the binary which is why he got only one architecture.
> The Package Installer allows the user to do either depending what the user selects.
>
> Cheers,
>Simon
>
>
>
>> John Maindonald             email: john.maindonald at anu.edu.au
>> phone : +61 2 (6125)3473    fax  : +61 2(6125)5549
>> Centre for Mathematics & Its Applications, Room 1194,
>> John Dedman Mathematical Sciences Building (Building 27)
>> Australian National University, Canberra ACT 0200.
>> http://www.maths.anu.edu.au/~johnm
>>
>> On 29/09/2012, at 10:13 AM, Ricardo.Julio.Rodriguez.Fernandez at sergas.es wrote:
>>
>>>
>>> Thanks Brian, thanks everybody. I think I can easily understand the difficulties you are speaking about:
>>> R is a huge project running in a massive amount of different, and from time to time, fancy environments.
>>> I is by no means easy to keep all packages smoothly running in all and every installation around
>>> the World! For me, maintaining CRAN is a big responsibility and of extreme difficulty!
>>>
>>> But I'm not able to understand yet what is the difference between using the R Package Installer
>>> (using CRAN repository as package repository), running in this case R Mac OS X 10.5.8  with this R installation...
>>>
>>> R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
>>> Copyright (C) 2012 The R Foundation for Statistical Computing
>>> ISBN 3-900051-07-0
>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>>
>>> And downloading XML_3.9-4.tgz from http://cran.r-project.org/web/packages/XML/index.html and installing it by submitting sudo R CMD INSTALL XML_3.93-0.tgz.
>>>
>>> The process using R Package Installer (CRAN binaries as repositoy) doesn't lead to a functional
>>> XML packages and downloading and installing it does lead to running XML packages both in i386 and x86_64 architectures.
>>>
>>> Sorry for asking once again, but, please, where am I lost with this issue?
>>>
>>> Thanks!
>>>
>>>> ________________________________________
>>>> From: r-sig-mac-bounces at r-project.org [r-sig-mac-bounces at r-project.org] On Behalf Of Prof Brian Ripley [ripley at stats.ox.ac.uk]
>>>> Sent: 28 September 2012 09:21
>>>> To: r-sig-mac at r-project.org
>>>> Subject: Re: [R-SIG-Mac] ‘package ‘XML’ is not installed for 'arch=x86_64'’
>>>>
>>>> With a package such as XML available from multiple repositories, you
>>>> have to be very precise what you are talking about.
>>>>
>>>> On CRAN, there is a source package for version 3.9-4.  That can be
>>>> compiled for multiple architectures on a Mac, and there are such
>>>> binaries on CRAN.
>>>>
>>>> It only works in a UTF-8 locale, and hence there has needed to be a
>>>> modified version for Windows, on CRANextras.
>>>>
>>>> However, the home for XML is www.omegahat.org.  There are two different
>>>> versions there, and neither work on Linux.  (3.93-0 in the Omegahat
>>>> repository and http://www.omegahat.org/RSXML/XML_3.94-0.tar.gz.)
>>>>
>>>> The CRAN team have been trying for weeks to sort this out, but the XML
>>>> maintainer is barely responsive.
>>>>
>>>> With a CRAN build of R for MacOS, you get binary packages by default,
>>>> either from the command-line or from R.app.   You get those of the
>>>> achitecture(s) which were built: this is normally both ix64 and x64_86
>>>> (and perhaps ppc) but for a few tens of packages the person in charge
>>>> (for CRAN, Simon Urbanek) needs to set up exceptions.  As packages do
>>>> change, sometimes the need to add an exception pops up unexpectedly.
>>>>
>>>
>>> On 28/09/2012 07:05, Ricardo.Julio.Rodriguez.Fernandez at sergas.es wrote:
>>>> Hi!
>>>>> ________________________________________
>>>>> From: Simon Urbanek [simon.urbanek at r-project.org]
>>>>> Sent: 28 September 2012 02:24
>>>>> To: Rodriguez Fernandez, Ricardo Julio
>>>>> Cc: r-sig-mac at r-project.org
>>>>> Subject: Re: [R-SIG-Mac] ‘package ‘XML’ is not installed for 'arch=x86_64'’
>>>>
>>>>> On Sep 27, 2012, at 6:25 PM, <Ricardo.Julio.Rodriguez.Fernandez at sergas.es> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I'm trying to confirm I understand how packages are installed and manage in R to be able to better interpret error/warning messages.
>>>>>>
>>>>>> In a Mac OS X installation of R I get this error:
>>>>>>
>>>>>>> require(XML)
>>>>>> Loading required package: XML
>>>>>> Failed with error:  ‘package ‘XML’ is not installed for 'arch=x86_64'’
>>>>>>
>>>>>> But the graphical interface R Package Installer says that version 3.9-4 is installed.
>>>>>>
>>>>>
>>>>> It is installed, but only for 32-bit and you are trying to load it in 64-bit R.
>>>>>
>>>>>
>>>>>> Please, where am I wrong?
>>>>>
>>>>> Use 32-bit R or if you want to use XML in 64-bit R, you have to compile it for 64-bit. AFAICS XML currently doesn't
>>>>> pass checks on any platform, so there are no binaries and you have to compile it from sources. If you want both 32-bit and 64-bit > you'll have to use --merge-multiarch INSTALL option or use the two-step process described in the Mac FAQ.
>>>>
>>>> Cheers,
>>>> Simon
>>>
>>> Following other replies to this thread this is what I get here after installing from the command line without switches the XML binary available at CRAN...
>>>
>>> Package: XML
>>> Version: 3.9-4
>>> ReleaseDate: 2012/01/30
>>> ...
>>> Repository: CRAN
>>> Date/Publication: 2012-01-31 07:37:18
>>> Built: R 2.15.0; universal-apple-darwin9.8.0; 2012-03-31 00:12:17 UTC; unix
>>> Archs: i386, ppc, x86_64
>>>
>>> So, it seems that i386 and x86_64 are available by installing that binary. Please, what am I misunderstanding here?
>>>
>>> Thanks for your help!
>>>
>>> Ricardo
>>>
>>>>> Thanks!
>>>>>
>>>>>
>>>>>> sessionInfo()
>>>>> R version 2.15.1 (2012-06-22)
>>>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>>>>
>>>>> 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] graphics  grDevices utils     datasets  stats     methods   base
>>>>>
>>>>> other attached packages:
>>>>> [1] foreign_0.8-50
>>>>>
>>>>> loaded via a namespace (and not attached):
>>>>> [1] tools_2.15.1
>>>>>>
>>>>>
>>>
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>>> _______________________________________________
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>>>
>>
>>
>> --
>> 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
>>
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>>
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>>

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