[R-SIG-Mac] R packages on Mac

Federico Calboli f.calboli at imperial.ac.uk
Wed Jan 23 14:33:02 CET 2013 

On 23 Jan 2013, at 11:27, Ivan Calandra <ivan.calandra at u-bourgogne.fr> wrote:

> It happened to me that when I clicked on the "install dependencies" checkbox, it basically installed every possible package.

Never had this issue

> I remember it happened with doBy, where it installed tens of packages. The problem is likely because it installs the dependencies of the dependencies of the dependencies and so on. It might be fixed by now.

If package A depends on B, and B depends on C, it seems logical that, to avoid breaking B, A depends on C as well. If the behaviour has changed it might be due to fewer dependencies in general.  In addition, unless you are using Raspberry PI, any modern hard drive (HDD or SSD) should be able to accommodate a non trivial percentage of all CRAN and Bioconductor packages without batting an eyelid.

BW

F




> But this has never happened with install.packages() so I don't try to use the package installer anymore.
> 
> Ivan
> 
> --
> Ivan CALANDRA
> Université de Bourgogne
> UMR CNRS/uB 6282 Biogéosciences
> 6 Boulevard Gabriel
> 21000 Dijon, FRANCE
> +33(0)3.80.39.63.06
> ivan.calandra at u-bourgogne.fr
> http://biogeosciences.u-bourgogne.fr/calandra
> 
> Le 23/01/13 12:18, Federico Calboli a écrit :
>> On 23 Jan 2013, at 11:07, Ivan Calandra <ivan.calandra at u-bourgogne.fr> wrote:
>> 
>>> Hi again,
>>> 
>>> It probably won't be of any help for now, but you might need it in the future: I used to install packages from the package installer. Then I realized that it often messed up with dependencies.
>> I notice there is a nice 'install dependencies' checkbox on the GUI package installer.  It has always worked for me.
>> 
>> BW
>> 
>> F
>> 
>> 
>> 
>> 
>>> That's why the best way to install packages and their dependencies on Mac is to run install.packages("package") in the console.
>>> 
>>> I hope you'll be able to fix your problem soon
>>> Ivan
>>> 
>>> --
>>> Ivan CALANDRA
>>> Université de Bourgogne
>>> UMR CNRS/uB 6282 Biogéosciences
>>> 6 Boulevard Gabriel
>>> 21000 Dijon, FRANCE
>>> +33(0)3.80.39.63.06
>>> ivan.calandra at u-bourgogne.fr
>>> http://biogeosciences.u-bourgogne.fr/calandra
>>> 
>>> Le 23/01/13 11:59, Ross Tinsley a écrit :
>>>> Hi Ivan
>>>> 
>>>> In R I was going to the Packages and Data menu then clicking on Packages Installer option. From there I selected CRAN sources and used that to search for the below libraries (I also ticked the option to install dependencies). Some such as Amelia did install but others one didn't. Prof Brian has given some suggestions so I will follow up on those first, as I think my overall install is not correct just yet.
>>>> 
>>>> Will get back to you all on how I get on.
>>>> 
>>>> Thanks
>>>> 
>>>> Ross
>>>> *
>>>> Dr Ross Tinsley*
>>>> Head of Research | Editor IHTSJ
>>>> International Hospitality and Tourism Research Centre
>>>> *HTMi* | Hotel and Tourism Management Institute | Switzerland
>>>> 
>>>> 
>>>> On 23 Jan 2013, at 11:43, Ivan Calandra <ivan.calandra at u-bourgogne.fr <mailto:ivan.calandra at u-bourgogne.fr>> wrote:
>>>> 
>>>>> Hi!
>>>>> 
>>>>> Not sure it will help you, but in the R.app, have you run install.packages("name of package") first? What is the error when you type library(name of package)?
>>>>> 
>>>>> HTH,
>>>>> Ivan
>>>>> 
>>>>> --
>>>>> Ivan CALANDRA
>>>>> Université de Bourgogne
>>>>> UMR CNRS/uB 6282 Biogéosciences
>>>>> 6 Boulevard Gabriel
>>>>> 21000 Dijon, FRANCE
>>>>> +33(0)3.80.39.63.06
>>>>> ivan.calandra at u-bourgogne.fr <mailto:ivan.calandra at u-bourgogne.fr>
>>>>> http://biogeosciences.u-bourgogne.fr/calandra
>>>>> 
>>>>> Le 23/01/13 11:27, Ross Tinsley a écrit :
>>>>>> Originally posted this on the standard mailing list and it was suggested that I post here on SIG Mac list. Have also included Beren's response who emphasised using the R.app GUI, however I am doing this as my first step. The below error message turns up there as well. Am stuck on the 'make' command and how to make that work.
>>>>>> 
>>>>>> Here are the commands in R I am trying to run.
>>>>>> 
>>>>>> library(Amelia)
>>>>>> library(Hmisc)
>>>>>> library(polycor)
>>>>>> library(psych)
>>>>>> library(qgraph)
>>>>>> library(lavaan)
>>>>>> library(semTools)
>>>>>> library(paran)
>>>>>> library(nFactors)
>>>>>> library(GPArotation)
>>>>>> library(sem)
>>>>>> library(polycor)
>>>>>> library(rrcov)
>>>>>> 
>>>>>> Thanks for any help.
>>>>>> 
>>>>>> 
>>>>>> Hello all
>>>>>> 
>>>>>> I am a researcher in the field of tourism and have just recently installed R64 and RStudio onto my Mac (running latest OS). I am ran into some problems installing additional packages. I have looked through the General FAQs and Mac FAQS but haven't been able to find a solution.
>>>>>> 
>>>>>> I have downloaded the various packages I need from CRAN sources and while some have successfully installed others have not. I have been following the instructions on the Mac FAQ to unzip and install the downloaded packages using the command line but the results seem to indicate an error (they are installed but then don't work properly and so are subsequently uninstalled). It happens on more than one so that's why I thought it might be something generic I am doing. Here is a copy of the command line results:
>>>>>> 
>>>>>> Rosss-MacBook-Pro:~ rosstinsley$ R CMD INSTALL /private/var/folders/ld/3f2dl80154z47_864skpt2_80000gn/T/Rtmp0ittcT/downloaded_packages/Hmisc_3.10-1.tar.gz
>>>>>> * installing to library ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library’
>>>>>> * installing *source* package ‘Hmisc’ ...
>>>>>> ** package ‘Hmisc’ successfully unpacked and MD5 sums checked
>>>>>> ** libs
>>>>>> *** arch - i386
>>>>>> sh: make: command not found
>>>>>> ERROR: compilation failed for package ‘Hmisc’
>>>>>> * removing ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Hmisc’
>>>>>> Rosss-MacBook-Pro:~ rosstinsley$ R CMD INSTALL /private/var/folders/ld/3f2dl80154z47_864skpt2_80000gn/T/Rtmp0ittcT/downloaded_packages/acepack_1.3-3.2.tar.gz
>>>>>> * installing to library ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library’
>>>>>> * installing *source* package ‘acepack’ ...
>>>>>> ** package ‘acepack’ successfully unpacked and MD5 sums checked
>>>>>> ** libs
>>>>>> *** arch - i386
>>>>>> sh: make: command not found
>>>>>> ERROR: compilation failed for package ‘acepack’
>>>>>> * removing ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/acepack’
>>>>>> Rosss-MacBook-Pro:~ rosstinsley$ R CMD INSTALL /private/var/folders/ld/3f2dl80154z47_864skpt2_80000gn/T/Rtmp0ittcT/downloaded_packages/arm_1.6-01.02.tar.gz
>>>>>> * installing to library ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library’
>>>>>> ERROR: dependency ‘lme4’ is not available for package ‘arm’
>>>>>> * removing ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/arm’
>>>>>> Rosss-MacBook-Pro:~ rosstinsley$ R CMD INSTALL /private/var/folders/ld/3f2dl80154z47_864skpt2_80000gn/T/Rtmp0ittcT/downloaded_packages/chron_2.3-43.tar.gz
>>>>>> * installing to library ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library’
>>>>>> * installing *source* package ‘chron’ ...
>>>>>> ** package ‘chron’ successfully unpacked and MD5 sums checked
>>>>>> ** libs
>>>>>> *** arch - i386
>>>>>> sh: make: command not found
>>>>>> ERROR: compilation failed for package ‘chron’
>>>>>> * removing ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/chron’
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> Berend's response:
>>>>>> 
>>>>>> 1. This belongs on the R-SIG-Mac mailing list
>>>>>> 
>>>>>> 2. Why don't you use the R.app GUI to install the binary versions of the required packages? Much easier.
>>>>>> 
>>>>>> 3. The message:  "sh: make: command not found" means that you don't have make installed.
>>>>>> Most likely you don't have other required tools installed.
>>>>>> If you use the R.app GUI you don't really need tall those tools.
>>>>>> 
>>>>>> Advice: use R.app to install and if needed get the Xcode tools but only if you intend to compile your own packages.
>>>>>> 
>>>>>> Berend
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> [[alternative HTML version deleted]]
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> _______________________________________________
>>>>>> R-SIG-Mac mailing list
>>>>>> R-SIG-Mac at r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> _______________________________________________
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>> 
>> --
>> Federico C. F. Calboli
>> Neuroepidemiology and Ageing Research
>> Imperial College, St. Mary's Campus
>> Norfolk Place, London W2 1PG
>> 
>> Tel +44 (0)20 75941602   Fax +44 (0)20 75943193
>> 
>> f.calboli [.a.t] imperial.ac.uk
>> f.calboli [.a.t] gmail.com
>> 
>> 
> 
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--
Federico C. F. Calboli
Neuroepidemiology and Ageing Research
Imperial College, St. Mary's Campus
Norfolk Place, London W2 1PG

Tel +44 (0)20 75941602   Fax +44 (0)20 75943193

f.calboli [.a.t] imperial.ac.uk
f.calboli [.a.t] gmail.com

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