Re: [R] Problem installing packages: cannot open file '/sw/Library/Frameworks/R.framework/Versions/3.2/Resources/etc/Makeconf'
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-...@r-project.org for mac install issues in future.
All the best
John
From: David Winsemius
Sent: 03 March 2016 00:31
To: John Hillier
Cc: r-help@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 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: -> 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-...@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: -> sub -> grep -> readLines -> file
> In addition: Warning message:
> In file(con, "r") :
> cannot open file
> '/sw/Library
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 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: -> 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-...@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: -> 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]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
David Winsemius
Alameda, CA, USA
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Problem installing packages: cannot open file '/sw/Library/Frameworks/R.framework/Versions/3.2/Resources/etc/Makeconf'
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).
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: -> 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
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. 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.
So, I'm thoroughly confused and have run out of ideas.
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.
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: -> 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]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
