John Hillier
2016-Mar-02 18:00 UTC
[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: <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 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: <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]]
David Winsemius
2016-Mar-03 00:31 UTC
[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 directoryInstalling 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]] > > ______________________________________________ > R-help at 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
John Hillier
2016-Mar-03 15:30 UTC
[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-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 directoryInstalling 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]] > > ______________________________________________ > R-help at 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