[R] Problem installing packages: cannot open file '/sw/Library/Frameworks/R.framework/Versions/3.2/Resources/etc/Makeconf'

[John Hillier]

Dear David,

Thank you very much!  I am sending this mail for the record.

I am on mac OSX 10.8.5. The "standard" binary installer packages worked and fixed the problem (R-3.2.1-snowleopard.pkg, RStudio 0.99.891 - Mac OS X 10.6+ (64-bit)).  So, a caution against fink (r-base and rstudio-desktop) for installing R; I assumed it was doing exactly the same thing, but was clearly wrong.

Noted to use r-sig-mac at r-project.org for mac install issues in future.

All the best

John

________________________________________
From: David Winsemius <dwinsemius at comcast.net>
Sent: 03 March 2016 00:31
To: John Hillier
Cc: r-help at R-project.org
Subject: Re: [R] Problem installing packages: cannot open file '/sw/Library/Frameworks/R.framework/Versions/3.2/Resources/etc/Makeconf'

> On Mar 2, 2016, at 10:00 AM, John Hillier <J.Hillier at lboro.ac.uk> wrote:
>
>
> Dear All,
>
>
> I am a relative newbie to R, and am struggling to install packages on my laptop (although I have managed to on my desktop and a borrowed departmental laptop).
>

The words "my laptop" is rather uninformative. Based on the path below I guessing OSX.
>
> I have tried various packages with the same result. Illustration for
>
>> install.packages("outliers")
>
>
> .... leads to .....
>
>
> Error in file(con, "r") : cannot open the connection
> Calls: <Anonymous> -> sub -> grep -> readLines -> file
> In addition: Warning message:
> In file(con, "r") :
>  cannot open file '/sw/Library/Frameworks/R.framework/Versions/3.2/Resources/etc/Makeconf': No such file or directory

Installing R inside /sw/.. directory is not a standard location. What does this return:

Sys.getenv( "R_HOME" )

On my version of OSX 10.11 with R installed from the "standard" binary installer package, it returns
[1] "/Library/Frameworks/R.framework/Resources"

>
> I have tried in both the R environment on command line, and in RStudio, with the same result, and reinstalled and updated both r-base and rstudio-desktop via fink.

fink ,,,, That's probably the reason (again if this is a Mac.) The default installation location is not being chosen. I don't understand why you are not using the binary installer. I've never seen anyone use fink for installation on a Mac but have heard of attempts with MacPorts and homebrew. Simon Urbanek says if you use one of those package installers you are "on your own".  That's a route you should only consider if you have serious NIX-skills.

>  Both using a CRAN mirror and using a download (outliers_0.14.tar.gz) seem to produce the same result, and I think they're both working as the output says 'downloaded' (see below)
>
>
>> install.packages("outliers")
> Installing package into �
> (as � is unspecified)
> --- Please select a CRAN mirror for use in this session ---
> trying URL 'https://mirrors.ebi.ac.uk/CRAN/src/contrib/outliers_0.14.tar.gz'
> Content type 'application/x-gzip' length 15090 bytes (14 KB)
> ==================================================
> downloaded 14 KB
>
>
>> From looking aroud on the web it seems that the message "In file(con, "r") : cannot open file" just means that R cannot find a file it thinks it needs. However, I've looked in /sw/Library/Frameworks/R.framework/Versions/3.2/Resources/etc/ both on this machine and the other laptop that is able to install packages, and 'Makeconf' is not in ether of them.

I do have a copy of that program in:

/Library/Frameworks/R.framework/Versions/3.2/Resources/etc/Makeconf


>
>
> So, I'm thoroughly confused and have run out of ideas.

The correct place to post questions about Mac installations is:

r-sig-mac at r-project.org

>Please help.
>
>
> I hope that this is something simple that I'm missing.  If so, a pointer to a manual page or instructions would be gratefully received.

https://cran.rstudio.com/bin/macosx/

>
>
> John
>
>
> p.s - Full output in sequence in case it's useful.
>
>
>> install.packages("outliers")
> Installing package into �
> (as � is unspecified)
> --- Please select a CRAN mirror for use in this session ---
> trying URL 'https://mirrors.ebi.ac.uk/CRAN/src/contrib/outliers_0.14.tar.gz'
> Content type 'application/x-gzip' length 15090 bytes (14 KB)
> ==================================================
> downloaded 14 KB
>
> Error in file(con, "r") : cannot open the connection
> Calls: <Anonymous> -> sub -> grep -> readLines -> file
> In addition: Warning message:
> In file(con, "r") :
>  cannot open file '/sw/Library/Frameworks/R.framework/Versions/3.2/Resources/etc/Makeconf': No such file or directory
>
> The downloaded source packages are in
>        �
> Warning message:
> In install.packages("outliers") :
>  installation of package � had non-zero exit status
>
>
>
>
>
> -------------------------
> Dr John Hillier
> Senior Lecturer - Physical Geography
> Loughborough University
> 01509 223727
>
>       [[alternative HTML version deleted]]
>
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David Winsemius
Alameda, CA, USA