Where can I find old R packages in .zip format ?
At CRAN for example : http://cran.r-project.org/src/contrib/Archive/shapefiles
there are only sources of .tar.gz files, I have to install old version of shapefiles because some finctions have been removed.
Package sources were only ever supplied in tar.gz compressed archives. Other archives (eg .zip) were binary packages for Windows or MacOS X. CRAN doesn't keep binaries for older versions of packages nor does it keep them for Archived packages, as per its policy.
If you are looking for a pre-built binary then you will either have to build one yourself, or if you are on Windows, you could use the win-builder service to build a Windows binary for you, but you'll need to make sure you change the maintainer details so you get a response and make sure you are allowed by the licence to re-distribute the sources in the manner you are doing. Do note all the caveats on that page before submitting!
Several CRAN mirrors keep old Windows binary versions of packages in a separate directory. See if the version appropriate for your old version of R might be here:
http://cran.cnr.berkeley.edu/bin/windows/contrib
Old R CRAN binary files for Windows (in fact all files on CRAN) for specific dates are available from the Microsoft Time Machine for CRAN: https://mran.microsoft.com/timemachine
Related
We have a ubuntu linux server in our office which is a air-gapped environment. There is no internet access to external network.
However I would like to install few R packages like ggplot2, Database Connector, dplyr, Tidyverse etc. I have more than 10-15 packages to download
While I cannot write the usual command install.packages("DatabaseConnector"), I have to download the zipped folders from CRAN as shown here.
I am new to R. So, can you help me with my questions given below?
a) Why is there are no files for linux systems? I only see windows binaries and macOS binaries. Which one should I download?
b) Should I download binaries or package source? which one is easy to install?
c) When I download packages like above as zipped file from CRAN like shown here, will the dependencies be automatically downloaded as well? Or should I look at error messages and keep downloading them one by one?
d) Since I work in a Air-gapped environment, what would be the best way to do this process efficiently.
Under linux packages are always installed from source. There are no official binary packages for linux. However, your distro might offer some of them in the official repositories. Ubuntu does. However these tend to be quite old versions and usually limited to a handfull of the most important packages. So, for linux you have to download the source packages. The zip files are for windows and will not work.
You will also need to download all of the dependencies of the packages. For something like tidyverse this will be a huge number. Tracking those by hand is a lot of work. Easiest is probably to use a package like miniCRAN outside of your airgapped system to build a selective copy of CRAN. You can specify the packages you want and the package will download all dependencies. You can then copy the downloaded directories to your server, point install.packages in the right direction and install as usually using install.packages. For details see https://andrie.github.io/miniCRAN/articles/miniCRAN-introduction.html.
You might also run into the problem that your system does not have all of the depencies needed to build all of the packages. Under ubuntu you need for example to install libxml2-dev to be able to install the xml package. For that you need to use the package manager of ubuntu. How to do that on an airgapped system is another issue
I want to install a package that is listed in https://cran.r-project.org/web/packages/available_packages_by_name.html as available in CRAN, but when I check in R the install packages menu or the available.packages() command, I can't see the package there.
Do I need to do something different to install those packages? Why aren't those packages available?
The packages I'm interested on are WikipediR ( https://cran.r-project.org/web/packages/WikipediR/index.html ), WikidataR and WikipediaR.
If it matters, I'm using R 2.15.0 in Windows XP.
See the documentation for ?available.packages...
By default, the return value includes only packages whose version and
OS requirements are met by the running version of R, and only gives
information on the latest versions of packages.
In other words... your R 2.15 is likely too old for the package you are looking to download.
You can try to download the package source manually add the package to the package library usually found somewhere like "win-library/2.15/" but like Cory mentioned it is likely that the older version of R does not support the package build.
The advice given so far is a bit incomplete although I do agree you need to update your R version if you want to use these packages. Looks like they don't need compilation so you might have been able to either install from a local copy or drop R code in, but critically they depend on httr which requires R 3.0.0 or above. They were released only relatively recently, so there will be no Windows binaries from back in 2012. (Your copy of R is from 30-Mar-2012.) Look in the DESCRIPTION file which is presented in a nice web format at the CRAN/package listing:
https://cran.r-project.org/web/packages/WikidataR/index.html
Imports: httr, jsonlite, WikipediR
Suggests: testthat, knitr, pageviews
# only one version of these two
https://cran.r-project.org/src/contrib/Archive/WikidataR/WikidataR_1.0.0.tar.gz
https://cran.r-project.org/src/contrib/Archive/WikipediaR/WikipediaR_1.0.tar.gz
# pick one of these
https://cran.r-project.org/src/contrib/Archive/WikipediR/
When I install the packages in R, sometimes it is used by devtools::install_github(). other times it is used by install.packages().
Could I ask what is the essential difference between them?
R's official repository for packages is located on CRAN (Comprehensive R Archive Network). The process of publishing a package there is very strict and is reachable via install.packages(). For the most part, binary packages (opposed to source code, which is not "properly translated" yet) are available and no additional tools need to be present for proper installation (see next paragraph).
GitHub is one of many webservices that offers repositories for code, incl. R code. Author can upload her or his package and if everything is in its place, the user can install a package from source via devtools::install_github(). This means you need to have a proper toolchain installed (also a distributoin of LaTeX). In Windows, this means Rtools. Linux based OS are likely to be shipped with most of the necessary tools.
My work setup relies heavily on rcom library, which is so far unavailable for R 3.x (due to licensing problems).
I'm happy to keep using the R v. 2.15.3, but the install.packages doesn't fetch new packages anymore.
Is there any way of making old R download packages on demand with something like install.packages("MASS")?
OK, this is the fallback solution:
We can always download (windows) old packages from this location on the CRAN site and unpack the ZIPs into C:\Program Files\R\R-2.15.3\library or equivalent. But it would be cool to use some form of simple R command for doing it.
It is also possible to try using different mirrors, because mirrors are not equivalent with respect to volume of archives.
At least this is how I do it on (virtual) Windows XP 32 bit.
I was trying to run code that required the R packages ‘pkgDepTools’ and ‘Rgraphviz’. I received error messages saying that neither package is available for R version 2.15.0.
A Google search turned up the following webpage RPM Pbone that seems to have the packages:
http://rpm.pbone.net/index.php3/stat/4/idpl/17802118/dir/mandrake_other/com/R-pkgDepTools-1.20.0-1-mdv2012.0.i586.rpm.html
and
http://rpm.pbone.net/index.php3/stat/4/idpl/17802080/dir/mandrake_other/com/R-Rgraphviz-1.32.0-2-mdv2012.0.i586.rpm.html
However, the files have an *.rpm extension rather than the *.tar.gz or *.zip extensions I am used to.
I am using Windows 7 and R version 2.15.0. Can I install an R package from an *.rpm file?
From Wikipedia *.rpm seems like maybe it is more for Linux:
http://en.wikipedia.org/wiki/RPM_Package_Manager
Regarding other possible solutions, I have found several earlier posts here with similar questions about installing R packages that are not available for the most recent version of R:
Bivariate Poisson Regression in R?
Package ‘GeneR’ is not available
R Venn Diagram package Venerable unavailable - alternative package?
I have installed the latest version of Rtools and the package 'devtools'. Although I know nothing about them.
There is an archived version of 'Rgraphviz' here:
http://cran.r-project.org/src/contrib/Archive/Rgraphviz/
but I cannot locate an archived version of 'pkgDepTools'.
If I can install the packages on a Windows machine using the above *.rpm files could someone please provide instructions?
If I must use Rtools to build them I might ask more questions because the instructions at the link below are challenging for me:
http://cran.r-project.org/doc/manuals/R-admin.html#Building-from-source
To be completely transparent I am hoping someone might build them for me, if that is possible. Although I recognize the experience and knowledge gained from doing it myself would probably pay off in the long run.
Thank you for any advice.
pkgDepTools and Rgraphviz are BioConductor R packages not ones hosted on CRAN. Unless you configure your R to download packages from those repos, R will report that they are not available; it can only install from repos it has been configured to install from.
To install those BioConductor packages a lite installation method is provided:
source("http://bioconductor.org/biocLite.R")
biocLite(c("pkgDepTools", "Rgraphviz"))
Further details are provided on the Install page of the BioConductor website
In general you can't use rpm packages on Windows; rpm's are the equivalent of a binary package for Linux. Any C/C++/Fortran/etc code will have been compiled for Linux not Windows. If a package really isn't available for your version of R then check if there is a reason stated on CRAN (usually Windows binaries take a few days longer to produce or there may be requirements for software not available on the CRAN Windows build machines). You can try the WinBuilder service run by Uwe Ligges to build Windows Binaries of packages for you, but if the package was on CRAN and now isn't that suggests it no longer works with current R and can not be built.
In general try a wider search for packages; the first hit in my Google search results under the search string "pkgDepTools" is the Bioconductor page for the package which includes a link to the Windows binary and instructions on how to install the package from within R.
I think this merits an answer rather than a comment.
A gentleman at Bioconductor helped me get Rgraphviz installed. The primary problem was that the version of Rgraphviz I had downloaded only seems to work with the 32-bit version of R and I was running a 64-bit version of R. I was able to install Rgraphviz in the 32-bit version of R.
I had also made an error or two in the PATH statement during some of my attempts to install Rgraphviz. However, the post above in my second comment provides the instructions for installation.
You just, it seems, cannot install the normal download version of Rgraphviz in the 64-bit version of R.
I think many of our emails back and forth are now posted on the Bioconductor forum.
I might edit this answer with more detailed instructions in the next 24-hours.