I just finished some minor updates to an R package I've had on CRAN for a few years (haven't had to update in a while). My package passes Check on my local machine and on winbuilder, but it just bounced back from CRAN with the message
checking whether package 'riverdist' can be installed ... WARNING
Found the following significant warnings:
Warning: S4 exports specified in 'NAMESPACE' but not defined in package 'riverdist'
I use roxygen2 to build my package NAMESPACE and don't have any S4 exports that I'm aware of.
Perhaps this might be related to changes in R version 4.0.0?
If anyone's encountered this error, I'd love to hear how you were able to resolve it. Thanks!
Resolved. roxygen2's #exportClass adds to NAMESPACE exportClasses() which is intended for S4 classes. S3 classes do not need to be exported, only constructor and method functions should be exported, and this is done using #export. In my case deleting all #exportClass commands solved the problem as my package defines only S3 classes. So, indeed the WARNING message is correct in diagnosing S4 exports. Found answer with the help from a thread in R-package-devel mail list from yesterday.
In the case of my packages, the problem existed in only one package that the other 9 which were also triggering the warning depend on.
The WARNING is triggered only under r-devel (future R 4.1.0).
I received this message from rdevel
"This is a new check in R-devel. The NEWS say:
R CMD check etc now warn when a package exports non-existing S4 classes or methods, also in case of no "methods" presence
In your case, the NAMESPACE contains
exportClasses(classify)
exportClasses(gonad_mature)
exportClasses(morphMat)
but your package does not define these S4 classes.
You seem to instruct roxygen2 to create these invalid directives using
#exportClass tags manually instead of just #export. Simply remove these
wrong #exportClass tags from your source files and regenerate your
NAMESPACE.
Best regards,
Sebastian Meyer"
https://www.mail-archive.com/r-package-devel#r-project.org/msg05436.html
Related
I am trying to load a package in RStudio from GitHub but I get an error.
I have also updated all the packages in order to see if this was the problem but I still get the same error. I have a MAC pc (I don't know if this may cause some problems).
The link of the package that I would like to load is:
https://github.com/andrewraim/COMMultReg
and there is written that in order to load it I need to run
library(devtools)
install_github("andrewraim/COMMultReg")
But when I run the second line I get as error:
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘COMMultReg’ in namespaceExport(ns, exports):
undefined exports: d_cmb, d_cmb_sample, d_cmm, d_cmm_sample, gunterize, loglik_score_fim_cmm, normconst_cmb, normconst_cmm, r_cmb
Errore: loading failed
Esecuzione interrotta
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/COMMultReg’
Warning message:
In i.p(...) :
installation of package ‘/var/folders/n0/4lmr1lrj7qqfylmh6s8qx0nr0000gn/T//RtmpldrmHr/file72e1e4469d/COMMultReg_0.1.0.tar.gz’ had non-zero exit status
Can somebody help me telling me what to do?
Thanks!!
The package has no function named d_cmb, but it tries to export that function. That's what the error message says, and it's true.
I think the reason for this error is that the author used Roxygen2 to generate his NAMESPACE file where the exports are declared, but that file is out of sync with the contents of the package.
It's possible this happened because the author forgot to commit a new file containing the new code. In that case, the best solution is to contact the author, and point out the issue.
Alternatively, it may have happened because at one time there was a d_cmb function, but the author removed it, without updating the NAMESPACE file. This one you might be able to fix yourself.
To fix this, you'll need to run Roxygen2 yourself, which is a little more complicated than just installing what's on Github. Here are the steps:
Fork the package to your own Github account if you have one. (This step is optional, but it makes some later steps easier.)
Download the source for the package. In RStudio, the quickest way to do this is to create a new project using Version Control, Git, and give the URL
of your forked copy, or the original URL if you skipped that.
Run Roxygen2 on the package. In RStudio, you do this by choosing "Document" in the "More" menu of the Build tab.
Try to build it. If you're lucky, it will now build properly. If not, fix the next problem.
This is very important: send your changes back to the original author. If you forked the package, this is easy; if not, figure out a way to do it.
this is the maintainer of the COMMultReg package. I didn't know about this thread until now, but it sounds like you were able to get started from the answer by user2554330.
The functions d_cmb, d_cmb_sample, etc are supposed to be exported. I think the problem may have been that, at the time of the question, I did not have src/RcppExports.cpp and R/RcppExports.R checked into Github. This seems to be necessary to use install_github on a package with exported Rcpp functions. Those were checked in around 8 months ago. (Coincidentally not long after this question was posted?)
Please let me know if you still having trouble with the install. Otherwise, enjoy the package!
When I use a package in R I install it and use it with loading it. Now what if I add a package which uses another package? Is this package automatically downloaded and loaded too? Or is it in general forbidden for a R package to use another package? I don't think that.
Suppose I want to publish a R package. Within my code, can I use functions from other packages and install and load these packages? Or how does this work when I need functions from other packages? Do I have to implement a message that this and that package is needed and that the user has to install and load it prior to it and I need to implement error catching functions in case the package cannot be found on the pc system?
When I want to publish a R package, can I use/call Java code within my package/code?
For a package which was already published - so let's take just as an example the fGarch package - I would like to see the complete code. How can I see this? I know that R is open source and I think it is more or less possible to just enter a function empty and get the code displayed, but sometimes this does not work and especially my question is: Is there a way I can look into the whole code of the package?
For a package which was already published, is it possible to see and look into all files which were submitted? So like a repository as git where all files are submitted - the code itself and further files which are needed like description files or whatever - and I can see these files and look into them?
Furthermore regarding this post here and hiding functions: Is there code in a R package which I cannot see as an end user? This refers also to my previous question, how can I or which way can I see the whole code in a R package?
I guess you have a few different questions here. Let's take them in the order you asked them:
What if I add a package which uses another package? Is this package automatically downloaded and loaded too? Or is it in general forbidden for a R package to use another package?
It is certainly not forbidden for an R package to use another R package. In fact, the majority of R packages rely on other packages.
The source code for each R package must include a text-based DESCRIPTION file in the root directory. In this file you will find (among other things) a "Depends" field, and an "Imports" field. Together, these two fields list all the other packages required to use this package. If a user doesn't already have these other packages installed in their local library, R will install them automatically when it installs the requested package.
If your package lists a dependency in "Depends", then the dependency package is attached whenever your package is attached. Thus if you looked at the source code for a package called "foo" and you see that its DESCRIPTION file contains the line
Depends: bar,
you know that when you call library(foo) in your R console, you have effectively done library(bar); library(foo)
This isn't always ideal. The package foo might only need a couple of functions from package bar, and bar might contain some other functions whose names could clash with other commonly used functions. Therefore, in general, if you are writing a package and you only want to use a few functions from another package, it would be better to use "Imports" rather than "Depends" to limit the number of unnecessary symbols being added to your user's search path.
Suppose I want to publish a R package. Within my code, can I use functions from other packages and install and load these packages
Yes, you can use functions from other packages. The simplest way to do this is to include the name of the package in the Depends field of your DESCRIPTION file.
However, when using just a few functions from another package inside your own package, best practice is to use the "Imports" field in the DESCRIPTION file, and use a namespace qualifier for the imported function in your actual R code. For example, if you wanted to use ggplot from the ggplot2 package, then inside your function you would call it ggplot2::ggplot rather than just ggplot.
If you publish your package for others to use, the dependencies will be installed automatically along with your package if the user calls install.packages with the default settings. For example, when I did:
install.packages("fGarch")
I got the associated message:
#> also installing the dependencies ‘timeSeries’, ‘fBasics’, ‘fastICA’
Do I have to implement a message that this and that package is needed and that the user has to install and load it prior to it and I need to implement error catching functions in case the package cannot be found on the pc system?
No, not in general. R will take care of this as long as you have listed the correct packages in your DESCRIPTION file.
When I want to publish a R package, can I use/call Java code within my package/code?
R does not have a native Java API, but you can use your own Java code via the rJava package, which you can list as a dependency for your package. However, there are some users who have difficulty getting Java to run, for example business and academic users who may use R but do not have Java installed and do not have admin rights to install it, so this is something to bear in mind when writing a package.
For a package which was already published - so let's take just as an example the fGarch package - I would like to see the complete code. How can I see this?
Every package available for download from CRAN has its source code available. In the case of fGarch, its CRAN page contains a link to the gzipped tarball of the source code. You can download this and use untar in R to review all the source code. Alternatively, many packages will have an easily-found repository on Github or other source-control sites where you can examine the source code via a browser. For example, you can browse the fGarch source on Github here.
For a package which was already published, is it possible to see and look into all files which were submitted? So like a repository as git where all files are submitted - the code itself and further files which are needed like description files or whatever - and I can see these files and look into them?
Yes, you can look at all the sources files for all the packages uploaded to CRAN on Github at the unofficial Github CRAN mirror here
Is there code in a R package which I cannot see as an end user? This refers also to my previous question, how can I or which way can I see the whole code in a R package?
As above, you can get the source code for any package via CRAN or Github. As you said, you can look at the source code for exported functions just by typing the name of that function into R. For unexported functions, you can do the same with a triple colon. For example, ggplot2:::adjust_breaks allows you to see the function body of the unexported function adjust_breaks from ggplot2. There are some complexities when an object-oriented system like S4, ggproto or R6 is used, or when the source code includes compiled C or C++ code, but I haven't come across a situation yet in which I was not able to find the relevant source code after a minute or two with an R console and a good search engine.
Rcpp beginner's question:
I want to improve my execution efficiency in R. So I write some code in cpp and use Rcpp to help me compile them.
Question is that I use some other R packages in my .cpp files and I want those packages to be installed and imported automatically when a user installs my package.
e.g. If I use the R package 'gtools' in my files, I don't want the error:
* installing to library 'C:/Program Files/R/R-3.4.1/library'
* installing *source* package 'pkgname' ...
make: Nothing to be done for `all`.
** libs
installing to C:/Program Files/R/R-3.4.1/library/pkgname/libs/i386
** R
** preparing package for lazy loading
Error in library(gtools) : there is no package called 'gtools'
Error : unable to load R code in package 'pkgname'
ERROR: lazy loading failed for package 'pkgname'
* removing 'C:/Program Files/R/R-3.4.1/library/pkgname'
Exited with status 1.
I tried to add depended package name to the DESCRIPTION file. i.e.
Imports: Rcpp (>= 0.12.12),gtools
LinkingTo: Rcpp, gtools
But it gives me following error:
ERROR: dependency 'gtools' is not available for package 'pkgname'
I don't find any similar questions and please tell me if there are.
First, you should probably make sure gtools is installed on your system. I say this because of the following error:
Error in library(gtools) : there is no package called 'gtools'
With this being said, the main issue you are running into is uncertainty between the LinkingTo: and Imports: fields in the DESCRIPTION file. This is covered in Section 1.1.3: Package Dependencies of Writing R Extensions.
Specifically, we have:
The ‘Imports’ field lists packages whose namespaces are imported from (as specified in the NAMESPACE file) but which do not need to be attached. Namespaces accessed by the ‘::’ and ‘:::’ operators must be listed here, or in ‘Suggests’ or ‘Enhances’ (see below). Ideally this field will include all the standard packages that are used, and it is important to include S4-using packages (as their class definitions can change and the DESCRIPTION file is used to decide which packages to re-install when this happens). Packages declared in the ‘Depends’ field should not also be in the ‘Imports’ field. Version requirements can be specified and are checked when the namespace is loaded (since R >= 3.0.0).
And the LinkingTo field:
A package that wishes to make use of header files in other packages needs to
declare them as a comma-separated list in the field ‘LinkingTo’ in the
DESCRIPTION file. For example
LinkingTo: link1, link2
The ‘LinkingTo’ field can have a version requirement which is checked at installation.
Specifying a package in ‘LinkingTo’ suffices if these are C++ headers containing source code or static linking is done at installation: the packages do not need to be (and usually should not be) listed in the ‘Depends’ or ‘Imports’ fields. This includes CRAN package BH and almost all users of RcppArmadillo and RcppEigen.
For another use of ‘LinkingTo’ see Linking to native routines in other packages.
So, the Imports: is meant to specify packages that contain R functions that you wish to import. In particular, the function from a given package or the entire package itself must be specified in the NAMESPACE file. For packages that use Rcpp, you can typically expect R functions to be available if the author has exported the routine from C++.
Now, regarding the LinkingTo:, this is a bit more specific. If an author wishes to make available a C++ API via header files they must explicitly declare the statements as is given in native methods of Writing R Extensions. Generally, packages that proceed in this manner are "header-only". These packages place the header definitions under inst/include, e.g.
|- pkgname
|- inst/
|- include/
|- pkgname.h
|- R/
|- man/
|- DESCRIPTION
|- NAMESPACE
However, another trend is to allow for "non-header" packages. This leads to a bit more complicated of topic as you have to understand shared objects and dynamic libraries. CRAN presents an overview of how to "Link" packages in Section 5.8: Linking to other packages of Writing R Extensions
If the author does not make available a C++ API, then there are four options:
Ask the author nicely to support calling the C++ API or submit a patch that enables access to the C++ API.
Call an R function from C++. (This negates any performance gain from writing your code in C++ though.)
Copy the implementation from the author's package while respecting their intellectual property.
Implement the desired functionality from scratch to avoid licensing issues.
Unfortunately, this is the case for gtools. As the author(s) do not provide a means to "link" to the C++ version of package's code.
I'm updating an R package and have two specific dependencies
httr (>= 0.6.1),
jsonlite (>= 0.9.14)
If these are not met the package will not function. I can see that if I put them both in Depends these version restrictions will be enforced by R. If I put them under Imports it appears they are not. There is no need for the packages to be put in Depends, I do not need them attached, and I know it is bad practice to do so.
Is it expected that Imports does not enforce version restrictions? Would it be kosher to leave the packages in Imports and have the .onLoad function check for out of date dependencies?
Writing R Extensions section 1.1.3 says
The ‘Imports’ field ... Version requirements
can be specified and are checked when the namespace is loaded (since R >= 3.0.0).
So it sounds like the lack of version checking is a bug and should be reported to the R-devel mailing list or bug tracker.
Hmm, I think the check is enforced when the namespace is loaded, e.g., import(httr) in the NAMESPACE file. If your code were to use httr::foo() without ever explicitly importing from httr, then there would be no check, or perhaps a check at run time. So again it seems like a bug, even if consistent with the documentation ('checked when the namespace is loaded').
I tried this:
z <- zscore(NMEBXTP_MeanDepth, na.rm=TRUE)
and got this:
Error: could not find function "zscore"
So I did this:
install.packages(c("R.basic"), contriburl="http://www.braju.com/R/repos/")
And got this:
Warning: unable to access index for repository http://www.braju.com/R/repos/
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
package ‘R.basic’ is not available
Besides being dysbinarylexic whats my problem?
Did you load the package for use before trying to use it? You need
library("R.basic")
or
require("R.basic")
to actually load the package functions into the running R session for you to be able to use them.
If you don't actually have it installed at all, then something looks amiss with the repository. If we look here we see that R.basic has been deprecated and is not on CRAN. Further, the page tells us that many of the R.basic are in the R.utils and aroma.light packages, both of which are on CRAN. Take a look at the CRAN pages for R.utils and aroma.light to see which one you need for the functionality you wanted to use.
If the problem installing from that repository continues, contact the maintainer of the repository to report the problem.