Re: [Rd] Error message library()
BTW: an ever more intuitive solution (IMHO) would be to auto-complete package names in library( ... Deepayan?;) That is non-intrusive and in line with the general use of R. (Simon) This is indeed a long wanted feature and to my surprise it actually already exists!!! (seems that Deepayan did not tell anybody about it ;) ) The help page ?completion in the utils package explains how to enable it: utils::rc.settings(ipck=TRUE) It simply worked on my Ubuntu box -- and directly went in my .Rprofile :) Hope this helps. Renaud -- Renaud Gaujoux Computational Biology - University of Cape Town South Africa __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Error message library()
On Oct 28, 2011, at 6:49 AM, Renaud Gaujoux wrote: BTW: an ever more intuitive solution (IMHO) would be to auto-complete package names in library( ... Deepayan?;) That is non-intrusive and in line with the general use of R. (Simon) This is indeed a long wanted feature and to my surprise it actually already exists!!! (seems that Deepayan did not tell anybody about it ;) ) The help page ?completion in the utils package explains how to enable it: utils::rc.settings(ipck=TRUE) Oh, well, the fact that it's off by default defeats the purpose, since the users that would benefit from it most are unlikely to mess with local configuration files... But thanks for finding it! Simon It simply worked on my Ubuntu box -- and directly went in my .Rprofile :) Hope this helps. Renaud -- Renaud Gaujoux Computational Biology - University of Cape Town South Africa __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Error message library()
On Fri, Oct 28, 2011 at 6:49 AM, Renaud Gaujoux ren...@mancala.cbio.uct.ac.za wrote: BTW: an ever more intuitive solution (IMHO) would be to auto-complete package names in library( ... Deepayan?;) That is non-intrusive and in line with the general use of R. (Simon) This is indeed a long wanted feature and to my surprise it actually already exists!!! (seems that Deepayan did not tell anybody about it ;) ) The help page ?completion in the utils package explains how to enable it: utils::rc.settings(ipck=TRUE) It simply worked on my Ubuntu box -- and directly went in my .Rprofile :) Hope this helps. Also in terms of what exists now, on Windows the Packages Load Package menu on Rgui provides a gui interface to library() from which one chooses the package from a list so one can't ask for one that does not exist. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Error message library()
On Oct 28, 2011, at 12:02 PM, Gabor Grothendieck wrote: On Fri, Oct 28, 2011 at 6:49 AM, Renaud Gaujoux ren...@mancala.cbio.uct.ac.za wrote: BTW: an ever more intuitive solution (IMHO) would be to auto- complete package names in library( ... Deepayan?;) That is non-intrusive and in line with the general use of R. (Simon) This is indeed a long wanted feature and to my surprise it actually already exists!!! (seems that Deepayan did not tell anybody about it ;) ) The help page ?completion in the utils package explains how to enable it: utils::rc.settings(ipck=TRUE) It simply worked on my Ubuntu box -- and directly went in my .Rprofile :) Hope this helps. Also in terms of what exists now, on Windows the Packages Load Package menu on Rgui provides a gui interface to library() from which one chooses the package from a list so one can't ask for one that does not exist. On a Mac with R.app the same facility exists which I how I check to see if a package is available in one of four forms (mac-binary, mac- source, Bioc-binary, Bioc-source). -- David Winsemius, MD West Hartford, CT __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Error message library()
On 10/26/11 5:49 AM, Milan Bouchet-Valat nalimi...@club.fr wrote: Le mercredi 26 octobre 2011 à 09:46 +, ONKELINX, Thierry a écrit : When one tries to load a non-installed package you get the error: Error in library(xyz) : there is no package called 'xyz' I noticed on several occasions that this puzzles beginners. Therefore I suggest to change the error description in: Error in library(xyz) : there is no package called 'xyz' installed on this machine. Check the name of the package or use install.packages(xyz) to install it. Couldn't R even directly ask for installing if it exists on CRAN? Like: Error in library(xyz) : package 'xyz' is not installed on this machine. Do you want to install it? [Y/n] I'd agree the message should be reworded, but prompting is overkill for normal users. Error in library(xyz) : package 'xyz' is not installed. Nonetheless, Kevin Wright's function is interesting. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Error message library()
On Wed, Oct 26, 2011 at 5:46 AM, ONKELINX, Thierry thierry.onkel...@inbo.be wrote: Dear all, When one tries to load a non-installed package you get the error: Error in library(xyz) : there is no package called 'xyz' I noticed on several occasions that this puzzles beginners. Therefore I suggest to change the error description in: Error in library(xyz) : there is no package called 'xyz' installed on this machine. Check the name of the package or use install.packages(xyz) to install it. Best regards, Perhaps it could report where it looked and couldn't find it: There is no package called 'xyz' in C:/R/win-library/2.13 and C:/R/R-2.13.2/library -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Error message library()
Le jeudi 27 octobre 2011 à 13:45 -0400, Gabor Grothendieck a écrit : Perhaps it could report where it looked and couldn't find it: There is no package called 'xyz' in C:/R/win-library/2.13 and C:/R/R-2.13.2/library I think it would be even more scary for beginners, and advanced users probably know how to find their library path. Regards __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Error message library()
On Thu, Oct 27, 2011 at 2:10 PM, Milan Bouchet-Valat nalimi...@club.fr wrote: Le jeudi 27 octobre 2011 à 13:45 -0400, Gabor Grothendieck a écrit : Perhaps it could report where it looked and couldn't find it: There is no package called 'xyz' in C:/R/win-library/2.13 and C:/R/R-2.13.2/library I think it would be even more scary for beginners, and advanced users probably know how to find their library path. Many beginners are advanced but just don't know R. Its better to give them the information they need. With this they can discover what is there even without knowing the relevant R commands. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Error message library()
I agree: much nicer to say what went wrong than to say there is no package And many people will not know what R's paths are. Why not add in a hint about what to do, like: try running install.packages(xyz) t ggrothendieck Many beginners are advanced but just don't know R. Its better to give them the information they need. With this they can discover what is there even without knowing the relevant R commands. On Oct 27, 2011, at 7:36 PM, Gabor Grothendieck wrote: On Thu, Oct 27, 2011 at 2:10 PM, Milan Bouchet-Valat nalimi...@club.fr wrote: Le jeudi 27 octobre 2011 à 13:45 -0400, Gabor Grothendieck a écrit : Perhaps it could report where it looked and couldn't find it: There is no package called 'xyz' in C:/R/win-library/2.13 and C:/R/R-2.13.2/library I think it would be even more scary for beginners, and advanced users probably know how to find their library path. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Error message library()
Dear all, When one tries to load a non-installed package you get the error: Error in library(xyz) : there is no package called 'xyz' I noticed on several occasions that this puzzles beginners. Therefore I suggest to change the error description in: Error in library(xyz) : there is no package called 'xyz' installed on this machine. Check the name of the package or use install.packages(xyz) to install it. Best regards, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek team Biometrie Kwaliteitszorg Gaverstraat 4 9500 Geraardsbergen Belgium Research Institute for Nature and Forest team Biometrics Quality Assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Error message library()
Le mercredi 26 octobre 2011 à 09:46 +, ONKELINX, Thierry a écrit : Dear all, When one tries to load a non-installed package you get the error: Error in library(xyz) : there is no package called 'xyz' I noticed on several occasions that this puzzles beginners. Therefore I suggest to change the error description in: Error in library(xyz) : there is no package called 'xyz' installed on this machine. Check the name of the package or use install.packages(xyz) to install it. Couldn't R even directly ask for installing if it exists on CRAN? Like: Error in library(xyz) : package 'xyz' is not installed on this machine. Do you want to install it? [Y/n] Regards __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Error message library()
On Oct 26, 2011, at 6:49 AM, Milan Bouchet-Valat wrote: Le mercredi 26 octobre 2011 à 09:46 +, ONKELINX, Thierry a écrit : Dear all, When one tries to load a non-installed package you get the error: Error in library(xyz) : there is no package called 'xyz' I noticed on several occasions that this puzzles beginners. Therefore I suggest to change the error description in: Error in library(xyz) : there is no package called 'xyz' installed on this machine. Check the name of the package or use install.packages(xyz) to install it. Couldn't R even directly ask for installing if it exists on CRAN? Like: Error in library(xyz) : package 'xyz' is not installed on this machine. Do you want to install it? [Y/n] Please, no! We don't want to enter the realm of the computer assuming it knows what you want to do (which is becoming too common nowadays, unfortunately, making the interaction more and more annoying). For some users this error simply means that they mistyped the package name, so fetching CRAN repos on that behalf ranges somewhere between overkill and stupidity. If the user can't type install.packages() then I am certainly not confident that the user can use R for any reasonable data analysis. Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Error message library()
Le mercredi 26 octobre 2011 à 12:34 -0400, Simon Urbanek a écrit : Please, no! We don't want to enter the realm of the computer assuming it knows what you want to do (which is becoming too common nowadays, unfortunately, making the interaction more and more annoying). For some users this error simply means that they mistyped the package name, so fetching CRAN repos on that behalf ranges somewhere between overkill and stupidity. If we need to connect to CRAN to do that, I indeed withdraw my suggestion. I had in mind a feature that's present in Bash in some recent Linux distributions: when a program doesn't exist on the system, tell the user in what package it can be found (it also detects typos in program names). If the user can't type install.packages() then I am certainly not confident that the user can use R for any reasonable data analysis. There's certainly some truth in your statement. ;-) OTOH it seems package authors have tried raising the barrier to a quite high level, and even when knowing what you do, you can get the package names wrong. Consider for example : Snowball, but snow and snowfall rJava and rJython, but RODBC and RWeka (not to pick on Kurt at all, there are many other examples, but I'm mainly using these - great - packages) Maybe a less controversial improvement would be to ask Did you mean XXX? if a package with a very similar name is *installed*. That wouldn't require fetching information from CRAN, and would most of the time be helpful (people install packages they use). Regards __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Error message library()
On Oct 26, 2011, at 1:05 PM, Milan Bouchet-Valat wrote: Le mercredi 26 octobre 2011 à 12:34 -0400, Simon Urbanek a écrit : Please, no! We don't want to enter the realm of the computer assuming it knows what you want to do (which is becoming too common nowadays, unfortunately, making the interaction more and more annoying). For some users this error simply means that they mistyped the package name, so fetching CRAN repos on that behalf ranges somewhere between overkill and stupidity. If we need to connect to CRAN to do that, I indeed withdraw my suggestion. I had in mind a feature that's present in Bash in some recent Linux distributions: when a program doesn't exist on the system, tell the user in what package it can be found (it also detects typos in program names). Yes, and that thing drives me crazy so the first thing I do on Ubuntu is to remove it (which is not as easy as it should due to a bug in the bash script as it turns out - another story :P). In 99% of cases it's useless since the suggestions are based on typos ... If the user can't type install.packages() then I am certainly not confident that the user can use R for any reasonable data analysis. There's certainly some truth in your statement. ;-) OTOH it seems package authors have tried raising the barrier to a quite high level, and even when knowing what you do, you can get the package names wrong. Consider for example : Snowball, but snow and snowfall rJava and rJython, but RODBC and RWeka (not to pick on Kurt at all, there are many other examples, but I'm mainly using these - great - packages) Well, seeing one of my packages on the list I have to say that there were good reasons, albeit they may not be known to the user, especially since the reasons may be obsolete by now. Maybe a less controversial improvement would be to ask Did you mean XXX? if a package with a very similar name is *installed*. That wouldn't require fetching information from CRAN, and would most of the time be helpful (people install packages they use). Yes, that could be an optional feature -- I do want to stress the *optional* in the sentence, though. BTW: an ever more intuitive solution (IMHO) would be to auto-complete package names in library( ... Deepayan? ;) That is non-intrusive and in line with the general use of R. Cheers, Simon Regards __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Error message library()
Thierry,
I agree with you and think that computers _should_ help users.
When R tells me a package does not exist, it is almost never because I
typed an incorrect package name.
Almost always it is because:
(1) I am using an old script with a new version of R and have not yet
installed a package.
(2) I am running a current script on a different machine that does not have
a package installed.
(3) I am copying some code from the web and have not yet installed a
package.
MiKTeX does a nice job of auto-installing packages in a silent manner.
I've tried to imitate that with the function below. I add this to
.Rprofile. Then use lib(pkg) to install and attach packages
automatically. The function is rough and needs improvement, but works
reasonably well.
Kevin
assign(lib,
function(p=NULL, ...){
# Why ... ?
p - substitute(p)
if(!is.null(p) !is.character(p))
p - deparse(substitute(p))
print(p)
ip - rownames(installed.packages())
# Should be more clever here and only install some of 'p'
if(!(p %in% ip)) install.packages(p)
require(p, ..., character.only=TRUE)
}, env=startup)
On Wed, Oct 26, 2011 at 4:46 AM, ONKELINX, Thierry thierry.onkel...@inbo.be
wrote:
Dear all,
When one tries to load a non-installed package you get the error:
Error in library(xyz) : there is no package called 'xyz'
I noticed on several occasions that this puzzles beginners. Therefore I
suggest to change the error description in:
Error in library(xyz) : there is no package called 'xyz' installed on this
machine. Check the name of the package or use install.packages(xyz) to
install it.
Best regards,
Thierry
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek
team Biometrie Kwaliteitszorg
Gaverstraat 4
9500 Geraardsbergen
Belgium
Research Institute for Nature and Forest
team Biometrics Quality Assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
thierry.onkel...@inbo.be
www.inbo.be
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of.
~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data.
~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
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Re: [Rd] Error message library()
Please, no! We don't want to enter the realm of the computer assuming it knows what you want to do (which is becoming too common nowadays, unfortunately, making the interaction more and more annoying). For some users this error simply means that they mistyped the package name, so fetching CRAN repos on that behalf ranges somewhere between overkill and stupidity. If the user can't type install.packages() then I am certainly not confident that the user can use R for any reasonable data analysis. In that case, maybe a better message should be: library(xyz) Error in library(xyz) : there is no package called 'xyz'. Are you sure you are smart enough to use R? ;) Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Error message library()
On Oct 26, 2011, at 4:06 PM, Hadley Wickham wrote: Please, no! We don't want to enter the realm of the computer assuming it knows what you want to do (which is becoming too common nowadays, unfortunately, making the interaction more and more annoying). For some users this error simply means that they mistyped the package name, so fetching CRAN repos on that behalf ranges somewhere between overkill and stupidity. If the user can't type install.packages() then I am certainly not confident that the user can use R for any reasonable data analysis. In that case, maybe a better message should be: library(xyz) Error in library(xyz) : there is no package called 'xyz'. Are you sure you are smart enough to use R? ;) Unfortunately we are in code freeze, so it will only make it into 2.14.0 patched ... ;) Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
