All Questions
3,109
questions
716
votes
19
answers
1.0m
views
How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning?
I tried to install a package, using
install.packages("foobarbaz")
but received the warning
Warning message:
package 'foobarbaz' is not available (for R version x.y.z)
Why doesn't R think that the ...
- 120k
675
votes
12
answers
576k
views
How to unload a package without restarting R
I'd like to unload a package without having to restart R (mostly because restarting R as I try out different, conflicting packages is getting frustrating, but conceivably this could be used in a ...
- 72.3k
672
votes
8
answers
174k
views
What is the difference between require() and library()?
What is the difference between require() and library()?
- 9,564
575
votes
13
answers
687k
views
How to find out which package version is loaded in R?
I am in a process of figuring out how to use my university cluster. It has 2 versions of R installed. System wide R 2.11 (Debian 6.0) and R 2.14.2 in non-standard location.
I am trying to use MPI ...
- 11.5k
451
votes
35
answers
256k
views
Elegant way to check for missing packages and install them?
I seem to be sharing a lot of code with coauthors these days. Many of them are novice/intermediate R users and don't realize that they have to install packages they don't already have.
Is there an ...
- 32.7k
281
votes
4
answers
334k
views
Where does R store packages?
The install.packages() function in R is the automatic unzipping utility that gets and install packages in R.
How do I find out what directory R has chosen to store packages?
How can I change the ...
- 9,708
238
votes
11
answers
335k
views
How to select a CRAN mirror in R
I'm trying to install a package through the R prompt by doing the following:
install.packages('RMySQL')
But the output is as follows:
--- Please select a CRAN mirror for use in this session ---
...
- 2,589
235
votes
10
answers
149k
views
Load multiple packages at once
How can I load a bunch of packages at once with out retyping the require command over and over? I've tried three approaches all of which crash and burn.
Basically, I want to supply a vector of ...
- 109k
202
votes
19
answers
228k
views
Problems installing the devtools package
I wish to use the devtools package. I've run the following commands:
> install.packages("devtools", dependencies = TRUE)
....
> library(devtools)
Error in library(devtools) : there is no ...
- 5,879
185
votes
16
answers
226k
views
Check for installed packages before running install.packages() [duplicate]
I have an R script that is shared with several users on different computers. One of its lines contains the install.packages("xtable") command.
The problem is that every time someone runs the script, ...
- 11.2k
177
votes
12
answers
69k
views
Painless way to install a new version of R?
Andrew Gelman recently lamented the lack of an easy upgrade process for R (probably more relevant on Windows than Linux). Does anyone have a good trick for doing the upgrade, from installing the ...
- 99.7k
171
votes
10
answers
35k
views
How to organize large R programs?
When I undertake an R project of any complexity, my scripts quickly get long and confusing.
What are some practices I can adopt so that my code will always be a pleasure to work with? I'm thinking ...
- 24.7k
112
votes
6
answers
141k
views
R install.packages returns "failed to create lock directory"
I get this error when downloading the Rcpp package:
> install.packages("Rcpp", dependencies=TRUE)
Installing package(s) into ‘/home/me/src/Rlibs’ (as ‘lib’ is unspecified)
trying URL 'http://cran....
- 3,496
107
votes
2
answers
250k
views
What does "The following object is masked from 'package:xxx'" mean?
When I load a package, I get a message stating that:
"The following object is masked from 'package:xxx'
For example, if I load testthat then assertive, I get the following:
library(testthat)
...
- 120k
95
votes
6
answers
206k
views
Get the list of installed packages by user in R
How we can get the list of installed packages by user in R along with its version?
I know about the command installed.packages() which will give information about all packages (base or non-base). But ...
- 12.8k
84
votes
3
answers
106k
views
How to install multiple packages?
How would I got about installing multiple packages in R?
I tried the following code:
install.packages("EIAdata", "gdata", "ggmap", "ggplot2","gridExtra","ISOweek","kobe","lubridate","maps","MASS","...
- 1,760
82
votes
2
answers
152k
views
Function to calculate geospatial distance between two points (lat,long) using R [duplicate]
I have geocoded points in long, lat format, and I want to calculate the distance between them using R. This seems pretty straight forward, yet I can't find a function that will do it easily. I've ...
- 2,450
80
votes
4
answers
81k
views
R: 2 functions with the same name in 2 different packages
I need to load to R packages : tseries and chron
Both have a function named is.weekend
I always have in my environment the function from the second package I loaded.
How can I access always the ...
- 18.3k
77
votes
8
answers
15k
views
Diagnosing R package build warning: "LaTeX errors when creating PDF version"
When building a package, I received the following warning:
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
I have no idea ...
- 72.3k
77
votes
3
answers
32k
views
How do you use multiple versions of the same R package?
In order to be able to compare two versions of a package, I need to able to choose which version of the package that I load. R's package system is set to by default to overwrite existing packages, so ...
- 120k
77
votes
2
answers
10k
views
Create an R package that depends on another R package located on GitHub
I am creating an R package on GitHub, LW1949, that depends on another R package on GitHub, jvamisc. When I try to install LW1949 using
require(devtools)
devtools::install_github("user/LW1949")
I ...
- 4,774
75
votes
13
answers
85k
views
Windows 7, update.packages problem: "unable to move temporary installation"?
I am using R 2.13.0 with windows 7, after giving my user full privileges to the R folder (as described here).
This allows me to install new packages just fine.
However, when using update.packages(), ...
- 25.1k
69
votes
2
answers
9k
views
Warning about UTF-8 with roxygen2
I have a problem about UTF-8.
After conducting roxygen2::roxygenise() for my package,
it showed the warning message 'roxygen2 requires Encoding: UTF-8'.
How can I fix it?
roxygen2::roxygenise()
&...
- 795
67
votes
9
answers
142k
views
Error in installation a R package
Please help me, I cannot install "MASS" package.
> library(MASS)
Error in library(MASS) : there is no package called ‘MASS’
I tried to install MASS package from local:
> utils:::...
- 1,390
67
votes
4
answers
29k
views
Cannot install R-forge package using install.packages
This, question, is, asked, over, and, over, and, over,
on the R-sig-finance mailing list, but I do not think it has been asked on stackoverflow.
It goes like this:
Where can I obtain the latest ...
- 49.5k
63
votes
2
answers
14k
views
Multiple functions in one .Rd file
Short version: Can I emulate the documentation of Normal in package stats using roxygen?
Long version: I'm working on a package and was trying make the documentation more readable by having a number ...
- 5,244
62
votes
2
answers
29k
views
inst and extdata folders in R Packaging
In the documentation, R suggests that raw data files (not Rdata nor Rda) should be placed in inst/extdata/
From the first paragraph in: http://cran.r-project.org/doc/manuals/R-exts.html#Data-in-...
- 44.4k
62
votes
5
answers
172k
views
R not finding package even after package installation
I have always worked with the zoo package, that I have installed a long time ago. Today, I created a new R script, and ran library(zoo) and got the following error:
> library(zoo)
Error in ...
- 8,728
61
votes
6
answers
35k
views
Listing R Package Dependencies Without Installing Packages
Is there a simple way to get a list of R package dependencies (all recursive dependencies) for a given package, without installing the package and it's dependencies? Something similar to a fake ...
- 1,780
61
votes
7
answers
52k
views
How to install dependencies when using "R CMD INSTALL" to install R packages?
I'm developing my first R package (using R 2.13, Ubuntu 10.10). Let's call it foo and let's say that the code in the R/ directory begins with the line library(bar), where bar is an existing package ...
- 33.5k
58
votes
5
answers
37k
views
Install a local R package with dependencies from CRAN mirror
I have built an R package, i.e. I have the mypackage.tar.gz file. This package depends on several other packages, all downloadable and installable from any CRAN mirror.
Now I want to install this ...
- 2,608
58
votes
2
answers
3k
views
Rd file name conflict when extending a S4 method of some other package
Actual question
How do I avoid Rd file name conflicts when
a S4 generic and its method(s) are not necessarily all defined in the same package (package containing (some of) the custom method(s) ...
- 13k
53
votes
5
answers
17k
views
Rbuildignore and Excluding Directories
I am interested in excluding two directories inst\docs and inst\examples while building and installing the package. I know that an easy way out is just to move docs and examples to the root directory ...
- 55.3k
52
votes
4
answers
54k
views
How do I install a package that has been archived from CRAN?
I typed the following in the R command line:
install.packages("RecordLinkage")
I got the following error:
Warning in install.packages :
package ‘RecordLinkage’ is not available (for R version 3....
- 1,221
52
votes
7
answers
36k
views
How to tell what packages you have used in R
I have a very long R script with many if statements and exception cases. As i've been going, if been importing and testing libraries as I've gone and haven't really documented them very well. The ...
- 1,374
48
votes
2
answers
5k
views
Writing robust R code: namespaces, masking and using the `::` operator
Short version
For those that don't want to read through my "case", this is the essence:
What is the recommended way of minimizing the chances of new packages breaking existing code, i.e. of making ...
- 13k
47
votes
5
answers
13k
views
No visible binding for global variable Note in R CMD check
I noticed in checking a package that I obtain notes "no visible binding for global variable" when I use functions like subset that use verbatim names of list elements as arguments.
For example with a ...
- 47.3k
45
votes
5
answers
21k
views
NAMESPACE not generated by roxygen2. Skipped. - Confusion with Hadley book
I am trying to make a package but when I run document() it prints NAMESPACE not generated by roxygen2. Skipped. I am trying to use ggplot2,XML, R6 packages in my functions. I am importing them in the ...
- 2,199
45
votes
1
answer
2k
views
Must R Packages Unload Dynamic Libraries When They Unload?
From Hadley's C best practices:
Like with C++, whenever you use C code in your package, you should unload the DLL when the package is unloaded:
.onUnload <- function (libpath) {
library.dynam....
- 52.4k
43
votes
4
answers
18k
views
R create reference manual with R CMD check
I am writing an R package and would like to make a pdf reference manual of all functions in the package. I understood from here that R CMD check automatically creates a reference manual.
Here I read ...
- 13.2k
43
votes
5
answers
97k
views
R "stats" citation for a scientific paper
I analyzed my data using R package ‘stats’ (version 2.15.3). A reviewer asked me the right citation of this package and not only the common
R Core Team (2012). R: A language and environment for ...
- 7,644
43
votes
2
answers
107k
views
How to uninstall R and RStudio with all packages, settings and everything else?
I messed up something and there is a problem with tidyverse. Tried to find a solution but spend lots of time without result.
How to uninstall R and RStudio with all packages, settings and everything ...
- 6,590
43
votes
1
answer
12k
views
What constitutes a good package name according to CRAN? [closed]
I'm searching a good name for a R package I want to send to the CRAN. I didn't find any information about good practice in R package namming. There is a post about how to analyze packages names but it ...
- 1,042
41
votes
7
answers
4k
views
"import as" in R
Is there a way to import a package with another name in R, the way you might with import as in Python, e.g. import numpy as np? I've been starting to use package::function lately to avoid conflicts ...
- 13.5k
39
votes
2
answers
10k
views
In R, what does "loaded via a namespace (and not attached)" mean?
In R, what does it mean for a package to be "loaded via a namespace (and not attached)" in sessionInfo()?
Edit:
For example:
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-apple-...
- 8,154
38
votes
6
answers
73k
views
Loading an R Package from a Custom directory
If I download an "package-name".tar.gz file from CRAN website, gunzip and untar it into a custom directory, how do I load that package from within R? I cannot extract the file in the R installation ...
- 1,079
38
votes
2
answers
14k
views
R: what's the proper way to overwrite a function from a package?
I am using a R package, in which there are 2 functions f1 and f2 (with f2 calling f1)
I wish to overwrite function f1.
Since R 2.15 and the mandatory usage of namespace in packages, if I just ...
- 18.3k
37
votes
2
answers
16k
views
How do I show the source code of an S4 function in a package?
I used the packages topGO in R to analyze gene enrichment with the following code:
sampleGOdata <- new("topGOdata", description = "Simple session", ontology = "BP",
allGenes =...
- 5,825
37
votes
12
answers
72k
views
Installing R Packages Error in readRDS(file) : error reading from connection
Whenever I try to install any package in R on Ubuntu 14.04, I'm getting the following error:
Error in readRDS(file) : error reading from connection
I already tried the methods given here but could ...
- 23.6k
37
votes
2
answers
5k
views
NOTE in R CRAN Check: No repository set, so cyclic dependency check skipped
As of R 3.1.0 I get the following R check:
* checking package dependencies ... NOTE
No repository set, so cyclic dependency check skipped
I tried this advice: https://twitter.com/phylorich/status/...
- 109k