I want to submit a package to CRAN. In the CRAN repository policy
it states that
"Packages for which R CMD check gives an ‘ERROR’ when a new R x.y.0 version is released will be archived".
It also says "Please ensure that R CMD check --as-cran has been run on the tarball to be uploaded before submission".
Running R CMD check --as cran on my tarball gives me the warning:
Warning: unknown option ‘--as-cran’
I am running R version 2.14.1 on Ubuntu 12.04.2 LTS. Can I build a source package using this version or do I have to use R 3.0?
And why does R CMD check --as-cran not work for me?
The document you link to says:
Please ensure that R CMD check --as-cran has been run on the tarball
to be uploaded before submission. This should be done with the current
release of R or (preferably) R-devel or R-patched.
So, right now, you should use R-3.0.1 and also test against the R-devel branch (if possible).
From the current October 2015 CRAN policy:
"Please ensure that R CMD check --as-cran has been run on the tarball to be uploaded before submission. This should be done with the current version of R-devel (or if that is not possible and explained in the submission, current R-patched or the current release of R.)"
This, I believe is a change from the policy described in the original accepted answer.
docker/rocker is a way to achieve this fairly easily without mucking up your development environment.
I think it is correct to build with the latest release version, but test with R-devel and the latest release.
You can try the new starfox/r-devel container available at https://hub.docker.com/r/starfox/r-devel/. It contains already some packages, which will make your release more convenient. There is also a guide how to use it.
Disclaimer: I am the maintainer of both, the container and the guide.
Related
I came across a package that is not available on CRAN. I tried to install the package using:
Packages & Data > Package Installer > Local Binary Package > At User
Level > [FileName.tgz] > Install...
This didn't work and I am now trying to use the R CMD INSTALL command. However, it seems I need to run that command in the command line interface but I cannot get it to install properly.
The package I'm trying to install is called gEcon. It can be found here. In particular, I am getting the following error message after "installing" the package:
Error: package or namespace load failed for ‘gEcon’:
package ‘gEcon’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version
I assume it's the way I'm installing it.
Thanks in advance.
You're going to need to install Xcode apparently, because you've got to install this from source per these directions:
Now, you've gotta update R to the latest stable release, or if you prefer you can find the exact minimum newest version needed for gEcon.
After upgrading R you can complete the installation from source.
Original answer to original question:
Two things:
To access the command line and use R CMD on an Apple computer, please use the terminal.app app. Please see this for more details.
An easier and probably better approach is to install your package from the author's Github (or BitBucket, etc) repository using devtools::install_github or just use devtools::install on the downloaded source project.
I am trying to publish my R package. I ran 'check' from R studio and got a clean OK (without Notes or Errors).
After submitting it, I got feedback from CRAN saying that I have NOTES about "no visible global function definition for ‘quantile’"
I re-checked my package on R studio and got a clean OK again. I didn't see this note on my end. Does anyone know why we get different checking results?
Maybe the best place to catch these things today (if your problem is not OS specific) is with win-builder as some people have said in the comments.
The devtools package has a really convenient function to send your package to win-builder, just run build_win() when inside your Rstudio project for the package. It will compile the package and then upload it to win-builder, which will run tests both on the R-release and R-devel and thensend you the link for the results on the email specified on the description file.
This behavior has been part of R-devel since late June this year (see here for details). As it says in the CRAN Repository Policy:
Please ensure that R CMD check --as-cran has been run on the tarball to be uploaded before submission. This should be done with the current version of R-devel (or if that is not possible and explained in the submission, current R-patched or the current release of R.)
So, you need to run R CMD check --as-cran on your package, using R-devel.
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 version of package XYZ that is hosted on R-forge? I tried to install it with install.packages, but this is what happened:
> install.packages("XYZ",repos="http://r-forge.r-project.org")
Warning message: package ‘XYZ’ is not available (for R version 2.15.0)
Looking on the R-forge website for XYZ, I see that the package failed to build.
Therefore, there is no link to download the source. Is there any other way
to get the source code? Once I get the source code, how can I turn that into a
package that I can load with library("XYZ")?
R-Forge may fail to build a package for a few different reasons. It could be that
the documentation has not been updated to reflect recent changes in the code. Or,
it could be that some of the dependencies were not available at build time.
You can checkout the source code using svn. First, search for the project on the
R-Forge website and go to the project home page -- for example http://r-forge.r-project.org/projects/returnanalytics/
Click the SCM link to get to a page like this http://r-forge.r-project.org/scm/?group_id=579
This page will tell you the command to use to checkout the project. In this case you get
This project's SVN repository can be checked out through anonymous access with the following command(s).
svn checkout svn://svn.r-forge.r-project.org/svnroot/returnanalytics/
If you are on Windows, you probably want to download and install TortoiseSVN
Once you have installed TortoiseSVN, you can right click in a Windows Explorer window and select
"SVN checkout". In the "URL of repository:" field, enter everything except the
"svn checkout " part of the command that you found on R-Forge. In this case, you'd
enter "svn://svn.r-forge.r-project.org/svnroot/returnanalytics/".
When you click OK, the project will be downloaded into the current directory.
If you are on a UNIX-alike system (or if you installed the command line client tools
when you installed TortoiseSVN for Windows, which is not the default), you can
type the command that R-forge gave you in your terminal (System terminal, not the R terminal)
svn checkout svn://svn.r-forge.r-project.org/svnroot/returnanalytics/
That will create a new directory under the current working directory that
contains all of the files in the package. In the top level of that directory
will be a subdirectory called "pkg". This particular project (returnanalytics)
contains more than one package.
ls returnanalytics/pkg
#FactorAnalytics MPO PApages PerformanceAnalytics PortfolioAnalytics
But some R-forge projects only have a single package. e.g.
svn checkout svn://svn.r-forge.r-project.org/svnroot/random/
#Checked out revision 14.
ls random/pkg
#DESCRIPTION inst man NAMESPACE R
Now that you have a local copy all of the code, if you would like to be able to
install the package, you have to build it first.
A WORD OF CAUTION: Since R-Forge failed to build the package, there is a good chance
that there are problems with the package. Therefore, if you just build it, you may find
that some things do not work as expected. In particular, it is likely that there
is missing or incomplete documentation.
If you are on a UNIX-alike system, the package can be built and installed relatively easily. For a multi-package project like returnanalytics, if you want to install, e.g. the
PortfolioAnalytics package, you can do it like this
R --vanilla CMD INSTALL --build returnanalytics/pkg/PortfolioAnalytics
"PortfolioAnalytics" is the name of the directory that contains the package that
you want to build/install. For a single-package project, you can build and install like
this
R --vanilla CMD INSTALL --build random/pkg
If you would like to build/install a package on Windows, see this question and follow the two links that #JoshuaUlrich provided
More information can be found in R Installation and Administration, the R-Forge User Manual, and the SVN manual.
If (and only if) you have the appropriate toolchain for your OS, then this may succeed:
# First download source file to your working directory
# As an example use browser to download pkg:partykit from:
# http://download.r-forge.r-project.org/src/contrib/partykit_1.1-2.tar.gz
# Move to working directory
# Or in the case of returnanalytics (which is a bundle of packages):
# http://r-forge.r-project.org/R/?group_id=579 and download the tar.gz (source)
# Then in R:
install.packages( "partykit_1.1-2.tar.gz", repo=NULL, type="source")
# for the first of the ReturnAnalytics packages:
install.packages( "Dowd_0.11.tar.gz", repo=NULL, type="source")
These direction should be "cross-platform". I'm not sure the directions in the accepted answer are applicable to Macs (OSX). (I later confirmed that they do "work" on a Mac but found the process more involved that what I suggested above. They do result in a directory that do contain the packages in a form that should succeed with R --vanilla CMD INSTALL --build pathToEachPackageSeparately)
It is also possible that the current version of the package you are trying to install requires a newer version of R, for example, you may see error like:
"ERROR: this R is version 2.15.0, package 'PerformanceAnalytics' requires R >= 3.0.0"
then you can try to update your R
or, if you are facing the same situation with me, which is trying to use pqR (currently using R version 2.15), you can find the out-of-date achieved package here:
http://cran.at.r-project.org/src/contrib/Archive/PerformanceAnalytics/
You can get here from R-Forge packages page -> "Stable Release: Get PerformanceAnalytics 1.4.3541 from CRAN" -> Old sources: PerformanceAnalytics archive
for example, you will find package PerformanceAnalytics version 1.1.0 just requires R >= 2.14
Good luck
Alternatively, you can install the particular package from GitHub, if it has a repo at GitHub.
I ran install.packages('ggfortify'), and got
Warning message: “package ‘ggfortify’ is not available (for R version
3.3.2)”
ggfortify was the GitHub repo for the same package.
The devtools library allows you to install a package from GitHub directly with install_github('username/repo').
library(devtools)
install_github('sinhrks/ggfortify')
Some time ago, you used to be able to install the rcom package in R to use COM scripting (eg, access to external programs.) Unfortunately, it seems to be discontinued:
Package ‘rcom’ was removed from the CRAN repository.
Formerly available versions can be obtained from the archive.
This depends on statconnDCOM, which nowadays restricts use, contrary
to the CRAN policy for a package with a FOSS licence. See
http://rcom.univie.ac.at/ and http://www.statconn.com/.
Following the archive and statconn links and installing one of the older versions in R version 3 gives the error:
“Error: package ‘rcom’ was built before R 3.0.0: please re-install
it”.
I am not very familiar with R, but there seems no way around this message - after all, it occurs when installing, so re-installing doesn't seem to be the answer. It appears as though rcom is simply not available for recent (3.0+) versions of R. I have also scanned the package list, although searching for "COM" there returns over a hundred results and it is possible I missed the right one when clicking through them.
How can I use the rcom package, or use COM from within R some other way?
(Note: I am asking this question on behalf of a colleague. I have no experience with R myself at all. Both of us, when searching for answers, could not find anything. I am sure that others are also using COM in the latest version of R, though!)
I looked at the rcom source code a few months ago. It seems I can get it to build and install OK on R3.0.1. Below is the procedure if it helps.
Get a checkout of the latest source code of rcom. I have rcom_2.2-5.tar.gz locally. I can google something at the following address, but I have no idea of the provenance, so up to you to check it is legit. http://cran.open-source-solution.org/web/packages/rcom/index.html
in R do install.packages('rscproxy')
install Rtools as per the instructions on the R web site (http://cran.r-project.org/bin/windows/Rtools),
open a Windows command prompt i.e. run "CMD"
go to the folder containing the 'rcom' folder, and at the command prompt:
set R="c:\Program Files\R\R-3.0.1\bin\i386\R.exe"
%R% CMD check --no-manual rcom
check it passes without too many complaints. Your call as to the --no-manual option (if you have MiKTeX installed you may remove it)
%R% CMD INSTALL rcom
should result in
installing to c:/Rlib/rcom/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
rcom requires a current version of statconnDCOM installed.
To install statconnDCOM type
installstatconnDCOM()
This will download and install the current version of statconnDCOM
You will need a working Internet connection
because installation needs to download a file.
* DONE (rcom)
in R:
library(rcom)
installstatconnDCOM()
I tried a comRegisterRegistry() ; comRegisterServer()
; x<-comGetObject("Excel.Application") but I get a NULL for x. I am not a user of rcom so while it all seems to compile fine; it may just not work anymore.
If you happen to need to access .NET code, a viable option (and yes I have a vested interest in mentioning it) may be the rClr package.
Hope this helps; I'd be interested to hear how you go.
This really should be a comment, but I don't have enough rep points yet to leave one.
I found that the above steps did not work for me, but the answer posted by Lisa Ann on this question, RExcel in R 3.0.x, did solve my problem installing rcom. Since you need rcom to run RExcel, the initial steps to install RExcel cover installing rcom on newer versions of R (such as 3.0.2).
Specifically, following the advice on statconn's wiki, http://homepage.univie.ac.at/erich.neuwirth/php/rcomwiki/doku.php?id=wiki:how_to_install
You also need to follow these instructions if you upgrade R, i.e. you install a new >release of R after you have installed RExcel.
Download the statconn DCOM server and execute the program you downloaded
Start R as administrator (on Windows 7 you need to right-click the R icon and click the >corresponding item)
In R, run the following commands (you must start R as administrator to do this)
install.packages(c("rscproxy","rcom"),repos="http://rcom.univie.ac.at/download",lib=.Library)
library(rcom)
comRegisterRegistry()
Now you have rcom installed, [instructions for installing RExcel follow...]
New versions of rcom and rscproxy (also for current versions of R) are available from a different repository. Just use http://rcom.univie.ac.at/download as the R repository to install from and you can download and install binary versions of statconn packages from there.
Hope this helps!
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 version of package XYZ that is hosted on R-forge? I tried to install it with install.packages, but this is what happened:
> install.packages("XYZ",repos="http://r-forge.r-project.org")
Warning message: package ‘XYZ’ is not available (for R version 2.15.0)
Looking on the R-forge website for XYZ, I see that the package failed to build.
Therefore, there is no link to download the source. Is there any other way
to get the source code? Once I get the source code, how can I turn that into a
package that I can load with library("XYZ")?
R-Forge may fail to build a package for a few different reasons. It could be that
the documentation has not been updated to reflect recent changes in the code. Or,
it could be that some of the dependencies were not available at build time.
You can checkout the source code using svn. First, search for the project on the
R-Forge website and go to the project home page -- for example http://r-forge.r-project.org/projects/returnanalytics/
Click the SCM link to get to a page like this http://r-forge.r-project.org/scm/?group_id=579
This page will tell you the command to use to checkout the project. In this case you get
This project's SVN repository can be checked out through anonymous access with the following command(s).
svn checkout svn://svn.r-forge.r-project.org/svnroot/returnanalytics/
If you are on Windows, you probably want to download and install TortoiseSVN
Once you have installed TortoiseSVN, you can right click in a Windows Explorer window and select
"SVN checkout". In the "URL of repository:" field, enter everything except the
"svn checkout " part of the command that you found on R-Forge. In this case, you'd
enter "svn://svn.r-forge.r-project.org/svnroot/returnanalytics/".
When you click OK, the project will be downloaded into the current directory.
If you are on a UNIX-alike system (or if you installed the command line client tools
when you installed TortoiseSVN for Windows, which is not the default), you can
type the command that R-forge gave you in your terminal (System terminal, not the R terminal)
svn checkout svn://svn.r-forge.r-project.org/svnroot/returnanalytics/
That will create a new directory under the current working directory that
contains all of the files in the package. In the top level of that directory
will be a subdirectory called "pkg". This particular project (returnanalytics)
contains more than one package.
ls returnanalytics/pkg
#FactorAnalytics MPO PApages PerformanceAnalytics PortfolioAnalytics
But some R-forge projects only have a single package. e.g.
svn checkout svn://svn.r-forge.r-project.org/svnroot/random/
#Checked out revision 14.
ls random/pkg
#DESCRIPTION inst man NAMESPACE R
Now that you have a local copy all of the code, if you would like to be able to
install the package, you have to build it first.
A WORD OF CAUTION: Since R-Forge failed to build the package, there is a good chance
that there are problems with the package. Therefore, if you just build it, you may find
that some things do not work as expected. In particular, it is likely that there
is missing or incomplete documentation.
If you are on a UNIX-alike system, the package can be built and installed relatively easily. For a multi-package project like returnanalytics, if you want to install, e.g. the
PortfolioAnalytics package, you can do it like this
R --vanilla CMD INSTALL --build returnanalytics/pkg/PortfolioAnalytics
"PortfolioAnalytics" is the name of the directory that contains the package that
you want to build/install. For a single-package project, you can build and install like
this
R --vanilla CMD INSTALL --build random/pkg
If you would like to build/install a package on Windows, see this question and follow the two links that #JoshuaUlrich provided
More information can be found in R Installation and Administration, the R-Forge User Manual, and the SVN manual.
If (and only if) you have the appropriate toolchain for your OS, then this may succeed:
# First download source file to your working directory
# As an example use browser to download pkg:partykit from:
# http://download.r-forge.r-project.org/src/contrib/partykit_1.1-2.tar.gz
# Move to working directory
# Or in the case of returnanalytics (which is a bundle of packages):
# http://r-forge.r-project.org/R/?group_id=579 and download the tar.gz (source)
# Then in R:
install.packages( "partykit_1.1-2.tar.gz", repo=NULL, type="source")
# for the first of the ReturnAnalytics packages:
install.packages( "Dowd_0.11.tar.gz", repo=NULL, type="source")
These direction should be "cross-platform". I'm not sure the directions in the accepted answer are applicable to Macs (OSX). (I later confirmed that they do "work" on a Mac but found the process more involved that what I suggested above. They do result in a directory that do contain the packages in a form that should succeed with R --vanilla CMD INSTALL --build pathToEachPackageSeparately)
It is also possible that the current version of the package you are trying to install requires a newer version of R, for example, you may see error like:
"ERROR: this R is version 2.15.0, package 'PerformanceAnalytics' requires R >= 3.0.0"
then you can try to update your R
or, if you are facing the same situation with me, which is trying to use pqR (currently using R version 2.15), you can find the out-of-date achieved package here:
http://cran.at.r-project.org/src/contrib/Archive/PerformanceAnalytics/
You can get here from R-Forge packages page -> "Stable Release: Get PerformanceAnalytics 1.4.3541 from CRAN" -> Old sources: PerformanceAnalytics archive
for example, you will find package PerformanceAnalytics version 1.1.0 just requires R >= 2.14
Good luck
Alternatively, you can install the particular package from GitHub, if it has a repo at GitHub.
I ran install.packages('ggfortify'), and got
Warning message: “package ‘ggfortify’ is not available (for R version
3.3.2)”
ggfortify was the GitHub repo for the same package.
The devtools library allows you to install a package from GitHub directly with install_github('username/repo').
library(devtools)
install_github('sinhrks/ggfortify')