I have a problem with the R package "gridExtra". Everything is ok, when I go into R and load it, but when I execute a python script, which among others also loads this package, everything stops. I don't understand it, since I checked the library and the right library is selected.
It's a little complicated, because the script is from someone else. It can be accessed from here: https://github.com/guigolab/ggsashimi/blob/master/sashimi-plot.py. The package is loaded at row 430. Loading the previous packages was no problem, after installing them into the custom library. During the python script, a custom R script is generated and executed. Within this R script, the package is loaded usign the function library(gridExtra).
The error message is:
Error in library(gridExtra) : there is no package called ‘gridExtra’
Execution halted
I checked, if the generated R script really accesses the right library and it does, so there is no problem with the library selection.
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.
I am trying to use this source from github.
devtools::source_url('https://raw.githubusercontent.com/brooksandrew/Rsenal/master/R/bin.R')
I could use this and work with it till few hours back. but now it gives me the following error
Error in loadNamespace(name) : there is no package called ‘Rsenal’
The code is still there in the provided url. I did re run the following two commands but still not working.
install.packages("devtools")
library("devtools")
What should I do to fix this issue?
I believe your issue is arising because you are sourcing functions that live inside a package, that is meant to be distributed as a package.
Instead of using devtools::source_url(), try this:
devtools::install_github('brooksandrew/Rsenal')
library("Rsenal")
Once the package is properly installed, all of the primary functions (such as binCat()) should be available for use.
I believe you ran into this error because some functions within the package probably depend on others that are not found within the two files you manually sourced. So when those lines are executed, R looks for the Rsenal package file and does not find them.
Further troubleshooting would require a reproducible example.
If I use devtools::use_vignette("my-vignette") in my package, running devtools::build_vignette() works fine.
However, once I add a call to anything from my package, it stops working, with error could not find function "myfunc". If I add a library(mypackage) call, I get the error there is no package called 'mypackage'.
(I should note that my package checks, builds & installs perfectly cleanly [with no vignettes], and running devtools::load_all() also works fine for interactive sessions.)
I know that if I build & install my package, I can then get the vignettes built. This seems like a really inefficient and dangerous way to develop; essentially forcing me to re-build and re-install the entire package on every commit, to test that the vignette isn't breaking.
Is there another way to get the vignette to recognize the package-in-progress?
If you are using RStudio IDE (which is very helpful for package developpement), you can render your Rmd document created by devtools::use_vignette, by clicking on the Knit button. It will create a preview version of your vignette.
By the way, RStudio IDE provides you with helpful shortkeys and buttons to execute your Rmd document chunk by chunk to test if it's working.
If you are not using RStudio IDE, you could render your document without building the package by using the function rmarkdown::render.
However, in order to be working, your vignette requires your package to be loaded. So, as you said, you'll have to call library(mypackage) and so your package have to be installed.
You can install your package without the vignette in the command line with devtools::install(build_vignette = FALSE). In the RStudio IDE, the button Build & Reload is enougth to intall your package.`
Another solution for non user of Rstudio IDE is to use devtools::load_all(path to your package) in your vignette in order to simulate the installation of your package in the vignette environment. Then you can build your vignette with devtools::build vignette whithout needing to install your package before.
I should underline that vignette is build automatically when your build your package. So, when development are finish, replace in the vignette devtools::load_all by library because your package is loaded before building the vignette when you build a package.
If you look up Hadley Wickham's packages in github, you will see he includes a library(xyz) at the top of his vignette, e.g. https://github.com/tidyverse/dplyr/blob/master/vignettes/dplyr.Rmd
Then his recommended way to build vignettes works:
You can build all vignettes from the console with
*devtools::build_vignettes()*, but this is rarely useful. Instead
use devtools::build() to create a package bundle with the vignettes
included.
I believe this is what you will need to submit a package to CRAN.
It is a slow development cycle, though, so for active coding, you can insert a line with devtools::load_all() to use the knit in RStudio.
I know there is already an answer but this is how I solved the same issue when using a hand written vignette.
I'm not sure if this will work for build_vignette() but when I was having trouble knitting my vignette because of this same error, what I had to do was:
<path/to/your/Rpackage>/NAMESPACE I had to add export(myFuncName) for each function I want to use in the vignette along with useDynLib(myPackageName) once.
I had to specify a VignetteBuilder option in the <path/to/your/Rpackage>/DESCRIPTION file for me it is VignetteBuilder: knitr.
I develop my R package in RStudio. I use load_all() from devtools (either typing in the console or from the Build menu), which seems to work fine. If I then work on an R function in my package and source it, when I try and run the function I need to load the libraries it depends on, despite these other packages being imported (through the DESCRIPTION file).
So for example, I will get the message:
could not find function "trellis.par.get"
and I need to load the lattice package etc.
Is this expected behaviour? I would have thought devtools would have imported these other package dependencies, or am I misunderstanding something here?
Thanks
David