I'm a Windows user. A few weeks ago I installed R and Rstudio along with many packages. Today there was a message that new packages were not installed.
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/src/contrib:
cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/src/contrib/PACKAGES'
I reinstalled R but this did not solve the problem.
Warning in install.packages :
InternetOpenUrl failed: 'Can not connect to server'
This is something that pops up in R and RStudio only once in a while. RStudio changes quite a few settings, and the option "repos" is one of them. On Windows, the following is added
EDIT: It's not RStudio adding this extra repository. The repository is kindly provided by Dr. Brian Ripley for packages that for some reason can't be made available on CRAN (license, not building out of the box, requiring additional software, ...). This is called "CRANextra" in the settings:
> getOption("repos")
CRAN CRANextra
"https://cran.rstudio.com/" "http://www.stats.ox.ac.uk/pub/RWin"
attr(,"RStudio")
[1] TRUE
So RStudio tries to access a specific repository when run on Windows, but that repository has had some connection issues in the past; it isn't always reachable, and when it's not, the warnings you report are issued.
You can get this warning to stop by resetting this option:
options(repos = "https://cran.rstudio.com") # or a repo of your choice.
Which allows you to install packages without the warning:
> install.packages("fortunes")
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/fortunes_1.5-4.zip'
Content type 'application/zip' length 202721 bytes (197 KB)
downloaded 197 KB
package ‘fortunes’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\Joris\AppData\Local\Temp\Rtmpu0febg\downloaded_packages
Even when this warning is displayed, packages still get installed from the rstudio CRAN mirror. The warning is reported as a bug, and RStudio has promised to tackle it soon.
EDIT: More information on the CRANextra repository in R FAQ (last paragraph):
Some CRAN packages that do not build out of the box on Windows,
require additional software, or are shipping third party libraries for
Windows cannot be made available on CRAN in form of a Windows binary
packages. Nevertheless, some of these packages are available at the
“CRAN extras” repository at https://www.stats.ox.ac.uk/pub/RWin/
kindly provided by Brian D. Ripley. Note that this repository is a
default repository for recent versions of R for Windows.
In the mean while R Studio fixes the bug, a temporal solution for not having to especifie the CRAN repository every time we start an R session, is to edit your "Rprofile.site" file and add this line
options(repos = getOption("repos")["CRAN"])
That way every time an R session is started the CRANextra repository ("http://www.stats.ox.ac.uk/pub/RWin") is removed automatically. Just remember to delete or comment with # this line after the bug is solved.
I was facing similar issue and the fix that worked for me is that, in RStudio I've opened tools -> Global Options -> Packages -> Primary CRAN Repository -> Set Global.
Also make sure you're not using installed.packages this happens to a lot of people because of RStudio typing suggestions.
You need to use install.packages("<package_name>")
Related
EDIT: see edit in end.
I have a R package in github and I'm using devtools::install_github to install it, which also install dependency packages.
Recently this process will install httpuv as source package, but compiling it in Mac meet errors with automake (something like this). I installed automake, then there was error with clang: error: unsupported option '-fopenmp'.
The issue and the possible solutions 1 2 seemed to be quite complicated. I think the CRAN version of httpuv probably will work for me, and I don't want my users to go through so many errors and fixing compiler errors.
I'd like to just install all dependency packages from CRAN in binary. For some packages that do need the more up to date version, I have specified it in my package description with remote section.
I checked install_github, then install, then install.packages. It seemed that the default behavior for binary vs source package is
An alternative (and the current default) is "both" which means ‘use
binary if available and current, otherwise try source’. The action if
there are source packages which are preferred but may contain code
which needs to be compiled is controlled by
getOption("install.packages.compile.from.source").
My getOption("install.packages.compile.from.source") is interactive. This is actually a preferred behavior for me. However I never see the interactive prompt.
I tried to give a type = "binary" parameter in install_github, but it doesn't seem to work, maybe it's not passed to every dependency package install?
EDIT:
I found the situation is a little bit more complex:
my app specified to install shiny github version via remote in description. shiny specified to install httpuv github version in remote section too. So this is actually the intended behavior.
I'm not sure if there is a solution available, other than require CRAN version of shiny in my package.
EDIT 2: It's more complex than my previous findings.
I removed remote section in my package description, supposedly only CRAN version is needed. However install_github still install most dependencies from github.
I finally found out that I have these dependencies github version installed, so their description in my local disk have the github remote information, and install_github found this information and "upgrade" them again, even when some of them have no change.
So I need to uninstall them first, only use CRAN version.
The really problem here is that if a dependency package is already new, it should not be installed. It could be a bug of devtools.
install_github passes arguments to devtools::install, and there upgrade_dependencies= FALSE and maybe even dependencies = FALSE might be what you're after:
install_github("you/urPackage", upgrade_dependencies = FALSE)
I am on Windows 7 and I am using R Studio 0.99.902 with R3.3.1. When I am trying to install a package I get the Warnings:
Warning: unable to access index for repository http://cran.rstudio.com/src/contrib:
cannot open URL 'http://cran.rstudio.com/src/contrib/PACKAGES'
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/src/contrib:
cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/src/contrib/PACKAGES'
It is the first time I see it and I cannot solve it. Can anyone help me ?
This issue is likely caused by the package being too old or too new for your R version. For example, if a package is released during R-3.4.1, it will not be available for R-3.3.1. Packages which are removed from CRAN before your R version are also not available. The package DESCRIPTION file shows if there is a hard restriction on which R versions the package will run.
Search for the package's CRAN page and see its status. You may still be able to install the package by downloading the package source (the tar.gz file) and in RStudio selecting Install from: Package Archive File in the Tools/Install Packages... menu (or using install.packages with repos = NULL). Beware that the package is not available from CRAN for a reason; you may need to make some changes to the package for it to work correctly.
Running options(download.file.method="libcurl") then installing packages did the trick for me. You may find an answer here.
Please note that compiling from source for Windows requires the appropriate version of Rtools that is compatible with the R version you are working with. This list is available at the Rtools site:
https://cran.r-project.org/src/contrib/Archive/
If compilation from source is complicated, it is also possible to find the Windows-compiled binaries (.zip files) for older versions of R at:
https://cran-archive.r-project.org/bin/windows/contrib
This link is referenced by the ReadMe file available at the "regular" repository for Windows binaries for different versions of R, namely at:
https://cran.r-project.org/bin/windows/contrib
Once the zip file is downloaded, you can run the following R code line to install the package:
# Use repos=NULL so that the first argument is a path to the local zip file
# containing the binary package to install
# (as opposed to just the name of the package to install from the web)
install.packages("<local-path-to-downloaded-zip-file>", repos=NULL)
I'm trying to install the 'yaml' and 'stringi' packages in R-Studio, and it keeps giving me these errors:
> install.packages("stringi")
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘stringi’
These will not be installed
or
> install.packages('yaml')
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘yaml’
These will not be installed
How can I get these to install properly?
The error is due to R being unable to find a binary version of the package on CRAN, instead only finding a source version of the package and your Windows installation being unable to compile it. Usually this doesn't occur, but in this case was caused by the (temporary) outage of some of the mirrors at CRAN. If you type:
> getOption('repos')
CRAN CRANextra
"http://cran.rstudio.com" "http://www.stats.ox.ac.uk/pub/RWin"
attr(,"RStudio")
[1] TRUE
You will see that R uses "http://cran.rstudio.com" by default to look for a package to download. If you see the cran mirrors web page you can see at the top that "http://cran.rstudio.com" actually redirects you to different servers world wide (I assume according to the geo location).
When I had the above issue, I solved it by manually changing the repo to one of the urls in the link provided. I suggest you use a different country (or even continent) in case you receive the above error.
I provide below some of the urls in case the link above changes:
Brazil http://nbcgib.uesc.br/mirrors/cran/
Italy http://cran.mirror.garr.it/mirrors/CRAN/
Japan http://cran.ism.ac.jp/
South Africa http://r.adu.org.za/
USA https://cran.cnr.Berkeley.edu/
You need to run the function install.packages as follows:
install.packages('<package_name>', repo='http://nbcgib.uesc.br/mirrors/cran/')
#or any other url from the list or link
One of them should then work to install a binary from an alternative mirror.
You need to install RTools to build packages like this (i.e., a source package rather than a binary). After you install Rtools, then try again to install.packages("ggplot2") and R will prompt you with:
Do you want to attempt to install these from source?
y/n:
(see the picture below)
You need to answer y and it will try to compile the package so it can be installed.
Struggled with this issue today, solved it for now by first downloading the windows binary and then installing e.g.
install.packages("https://cran.r-project.org/bin/windows/contrib/3.3/stringi_1.1.1.zip", repos =NULL)
Just go to https://cran.r-project.org/ and then R Binaries/Windows/contrib and copy the url as argument to install.packages()
Install the package from a zip file - downloadable from the r-project website.
In basic R
go to Packages
Install packages from local files.
In RStudio
go to Packages
Install packages
Install from Package Archive File.
I had this issue when using an out-of-date version of R, so no binaries were available. The simple solution was to update my version of R.
Anything worked for me, until I found out my computer had an old version of R installed. Uninstalling everything and installing the newest R version worked!
I had to download the latest version of Rtools:
Go into the downloads folder and double click it to install it.
Close and reopen any R session.
Now packages should install like normal.
However, if you still have trouble, try installing the package from source (using type="source")
Like this:
install.packages("dplyr", type="source")
Kind of embarrassing / a no-go, but since it hasn't been that long that I've moved from "pure user" to "beginner-developer", I've never actually read the CHANGELOG when a new R version came out - well until today (and I have the feeling I should make this a habbit) ;-)
Yet I'm not sure if the supposed change actually occurred since I couldn't find anything about it at a first glimpse at the CHANGELOG of R R 2.15.2:
Actual question
Is it possible that the (subdirectory) structure of package repositories changed from
./bin/windows/contrib/2.xx/
to
./src/contrib/2.xx/ or even ./src/contrib?
Or at least that the PACKAGES file now needs to live here: ./src/contrib/PACKAGES?
Background info
Up to version 2.15.1, the following path worked to install packages from my local package repository:
path.repos <- "L:/R/packages"
repos <- file.path("file://", path.repos)
Function contrib.url would take repos and expand it to the right subdirectory:
> contrib.url(repos)
[1] "file:///L:/R/packages/bin/windows/contrib/2.15"
But when I try to run install.packages(), I get the following error for R 2.15.2:
> install.packages("mypkg",
+ lib=file.path(R.home(), "library"),
+ repos=repos,
+ type="win.binary"
+ )
Error in read.dcf(file = tmpf) : cannot open the connection
In addition: Warning message:
In read.dcf(file = tmpf) :
cannot open compressed file 'L:/R/packages/src/contrib/PACKAGES', probable reason 'No such file or directory'
>
When I do the same with R 2.15.1, everything works smoothly.
Due dilligence
There are some references with respect to repositories in the CHANGELOG, but the only section I found that gives me some evidence that the supposed change occurred is this:
PACKAGE INSTALLATION
For a Windows or Mac OS X binary package install, install.packages() will check if a source package is available on the same repositories, and report if it is a later version or there is a source package but no binary package available.
Just had a look at the official documentation again and got the idea that maybe arg type is not passed along to contrib.url() correctly as it seems to me install.package() is looking at the place for type="source" packages?
This particular bug isn't the same as mine.
This issue relates to checks install.packages() now runs before installing. As Rappster said, it tries to find a source package to compare the binary version with:
For a Windows or Mac OS X binary package install, install.packages() will check if a source package is available on the same repositories, and report if it is a later version or there is a source package but no binary package available.
So a simple way of squashing this message is creating the R/src/contrib directory and running tools::write_PACKAGES() in that directory to create (an empty) PACKAGES file.
And of course, the reason you aren't getting this message in 2.15.1 is that it doesn't do the checking (see R NEWS quote above) that 2.15.2 performs.
I have submitted a bug report of my issues. No news yet. May post it to the R mailing list as well.
I am trying to update zoo from R Forge.
install.packages("zoo", repo = "http://r-forge.r-project.org")
But I get the following error
Installing package(s) into ‘C:/REVOLU~1/R-COMM~1.3/R-212~1.2/library’
(as ‘lib’ is unspecified)
Warning in install.packages :
cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
unable to access index for repository http://r-forge.r-project.org/bin/windows/contrib/2.12
Warning in install.packages :
package ‘zoo’ is not available
I am using Revolution R Community version 4.3 (64-bit).
install.packages("zoo")
Installs a slightly dated version of zoo
To clarify #DWin's and Gabor's answers slightly more:
You are running into trouble because R-forge only builds binaries for the current (2.14 right now) and development ("2.15", but Brian Ripley will probably get mad if you refer to it that way) versions of packages. In this situation you have the following options:
Upgrade R to the current version (the best idea).
If you have good reasons you can't do that (you don't have administrative rights, you are running a critical analysis that depends on a previous version of R, you need to use Revolution R because of its extensions etc.), then you can try one of the following:
(as suggested by #jthetzel's comment above) follow the links to the binary version of the package, download the binary file (zip in the case of Windows), and try installing from the local copy (with repos=NULL, or from the appropriate menu entry). This will not work if the package depends, implicitly or explicitly, on features in the latest version of R.
try to install the source version of the package: install.packages("thispkg",repos="http://r-forge.r-project.org",type="source"). This will only work if (1) you have the tools for compiling packages from source installed (see the R manual, or (for Windows) the R for Windows FAQ, google for "Rtools", etc., or (for MacOS) the R for MacOS FAQ) or (2) the package contains only R code, not compiled C/FORTRAN code (not true in the case of the zoo package, I think).
download the source package, unpack it, modify the DESCRIPTION file so that the maintainer e-mail is your own, rebuild the source package, and upload it to the CRAN win-builder service. (If you don't modify the DESCRIPTION file then you won't be informed that the package has been built and where to download it -- you'll just annoy and confuse the maintainer of the package, who will receive the e-mail.) (This only works for Windows.)
Some of the resistance you've been getting is directed less at you than at Revolution R. There's nothing wrong (I don't think) with their making money from R, but when providing support for Revolution R adds to the workload of the R community (ordinarily we would just say "upgrade to the latest version of R" and be done with it), people get a little grumpy.
This is the weekend, .... a typical time for site maintenance. A 404 message could be telling you to either wait a few hours or use a different mirror. In this case using a browser shows that the link really does not exist but its stem does and has code only for R versions 2.14 and 2.15.
You have not given enough information to determine why "version 4.3" is not accessing a current version of "zoo" but it would seem more appropriate to contact the Revolution R people or a support group dedicated to that version than post a message on a volunteer website where they seem to have no regular representative. I'm guessing that your "version 4.3" is based on R 2.12.x and that you would get failure if you actually did find a current version. You should be providing sessionInfo() rahter than the RevoR version number. The RevoR product has a Support Forum at http://forums.revolutionanalytics.com/ . My effort to determine what version they are currently shipping are frustrated by their insistence on having every query go through their personal information gathering protocol. I was unable to find online technical specs for their currently available version of "Community version".
EDIT: It appears you have already been discussing this with Gabor. He is an undisputed authority on the behavior of "zoo". You should not be looking elsewhere for advice.