I'm writing a package containing several functions to make running and evaluating models more streamlined.
I have a function that I'm going to make the first function within my package detailed with roxygen2 comments, which I can include into this write-up as an edit if necessary, but my issue is more with Package Creation.
I've created a separate .R file for the function and it lives within the R folder in within my package folder. I've run R CMD build pkgname and R CMD INSTALL pkgname successfully.
At the document() stage I run it (from console or whether in my terminal using R -e 'library(devtools);document()', deleting the existing NAMESPACE file first) and I get the following error: Try removing ‘/Library/Frameworks/R.framework/Versions/ 3.5/Resources/library/00LOCK-pkgname.
I've already seen the [issue posted here][1] and haven't had success after deleting the 00LOCK-pkgname folder, for two reasons: when I run document(), even when it throws the above error, it doesn't stop running, it just keeps looping (that happens whether I run this in R or use the Terminal). Additionally, no matter how many times I delete the folder, it keeps re-appearing even though I've stopped running the function.
Any insight into why that error is being thrown and the document() function continually runs in a loop?
Best answer I've found is in this blog post: Hilary Parker R-Package Blog Post
The steps I follow to document and install are as follows:
Within the project that contains my package, open a new R Script and run setwd('..')
Run devtools::document()
Run devtools::install()
This works for me when initially installing my package and also updating it.
Related
I have some code in my R profile that I've found interferes with package installation. For example, I like to automatically load devtools when I'm working on packages, so I have this
if (file.exists("DESCRIPTION")) {
try({suppressMessages(library(devtools))})
}
However, I've found that this interferes with package installation, I get errors like ERROR: lazy loading failed for package ‘rlang’. If I comment out the loading of devtools in the R profile, the package installs without error.
Is there any way to check if .Rprofile is being executed during package installation so that I could put that condition in the if and stop devtools from loading at inappropriate times?
I’d generally recommend against putting such code into your ~/.Rprofile! — The ~/.Rprofile should contain only general configuration that is always valid. For further customisation, use a project-local ~/.Rprofile instead.
However, I would make one exception to the above guideline, because one useful distinction you can make is to only execute certain code in interactive sessions:
if (interactive()) {
if (file.exists("DESCRIPTION")) {
try({suppressMessages(library(devtools))})
}
}
.Rprofile files are sourced on R startup. They won't be called later by other functions so you can't use the checking logic during install.packages().
For this reason loading packages using RProfile is not always advisable as it can make your code non-reproducible. However, as a helper package, devtools is probably a good exception (ignoring your particular problem here).
If you use base R only you can tell R not to load Rprofile during startup by using the --vanilla or --no-init-file arguments.
If you are using RStudio one workaround would be to use project level Rprofile files. Rstudio starts a new R session for each project, and loads the user Rprofile from the project root. If it then can't find that it will attempt to load the user RProfile.
Create a new project and within the the project options tick the option to disable the Rprofile loading.
Whenever you want to install a package switch to this project.
One caveat is to make sure you are running this as the only project session open, having multiple RStudio sessions open when installing new packages can lead to problems without putting the Rprofile in the mix.
Rstudio article on startup files https://support.rstudio.com/hc/en-us/articles/360047157094-Managing-R-with-Rprofile-Renviron-Rprofile-site-Renviron-site-rsession-conf-and-repos-conf
Base R documentation on R initialization https://stat.ethz.ch/R-manual/R-devel/library/base/html/Startup.html
A diagram of the R startup flow and some commentary on use of renviron and rprofile
https://rstats.wtf/r-startup.html
I was trying to modify the BiasedUrn package to be able to generate more random numbers. The current limit is 32 random numbers.
I followed the steps provided by [1].
I had a hard time dealing with the error below. I finally added one more option as R CMD build BiasedUrn --no-manual to temporarily get rid of the error.
Now I successfully built and installed the modified package. However, whenever I run a function from this new package in R Studio, the program quits abruptly.
P.S. The only change that I make is in the Makevars file (from -DMAXCOLORS=32 to -DMAXCOLORS=10000).
Any idea how I can fix this issue?
Executive Summary
I need assistance to fix the errors as I attempt to create a manual for a new R package. I have created an R package on my computer that I would like to distribute. At the moment, the package is available as a repository on GitHub (http://www.github.com/greenspb/poker), but I want to contribute it to the Comprehensive R Archive Network. I wrote the code years ago, but never shared it out of fear. This is my first repository on GitHub and my first submission to CRAN. I have researched how to get my package on CRAN by reading a blog post at http://kbroman.org/pkg_primer/pages/cran.html . I am stuck on step 1:
"Run R CMD check --as-cran and eliminate all problems. If there are any errors or warnings, your package will not be accepted at CRAN. And even a “Note” will likely disqualify you. So figure out what all of those errors, warnings, and notes mean and then revise your package so that they are no longer issued."
The report generated by "Run R CMD check --as-cran poker" for my "poker" package ( available as a repository on GitHub ) contains errors. My concern is failure to make the LaTeX manual.
Resolved Issues
I used roxygen2 comment tags in the .R file in the project's R folder. roxygen2::document() successfully translated \cr in a comment tag into a new line in the LaTeX file, however it unsuccessfully translated every empty \tab in a comment tag into {} [empty curly parentheses] in the LaTeX file. This happened in dozens and dozens of instances. The \tabular environment was used in an attempt to preserve formatting. I was able to clean up LaTeX errors whenever "There was no line here to end" by searching for {} and replacing appropriate instances with \\{}.
Unresolved Issues
I have no idea how to solve the LaTeX error "Rd2.tex: File Ended while scanning definition of \LT#xxiii", although I believe \LT stands for long table. I am only able to make pdf manuals of several individual functions using R CMD Rd2pdf on the .rd documentation files.
My code is documented using roxygenize tags. When I execute the Run R CMD check --as-cran command, R encounters errors and warnings and fails to make the pdf for the entire package. I need assistance to fix the errors in the report. I want to get my package on CRAN.
See Also
Question on r-package-devel#r-project.org mailing list.
Removing comments on the local variables was the answer to fixing the errors ( replying to #Dason). Thank you.
I used packrat (v 0.4.8.-1) to to create a snapshot and bundle of the R package dependencies that go along with the corresponding R code. I want to provide the R code and packrat bundle to others to make the work I am doing (including the R environment) fully reproducible.
I tested unbundling using a different computer from the one I used to write R code and create the bundle. I opened an R code file in R studio, and called library(packrat) to load packrat (also v 0.4.8-1). I then called packrat::unbundle(bundle = "directory", where = "directory"), which unbundled successfully. But subsequently calling packrat::restore() gave me the error "This project has not yet been packified. Run 'packrat::init()' to init packrat". It seems like init() should not be necessary because I am not trying to create a new snapshot, but rather utilize the one in the bundle. The packrat page (https://rstudio.github.io/packrat/) and CRAN provide very little documentation about unbundling to help troubleshoot this, or that I could point users of my code to for instructions (who likely will be familiar with R, but may not have used packrat).
So, can someone please provide clear step-by-step instructions for how users of a bundled snapshot should unbundle, and then use that saved snapshot to run a R code file?
After some experimenting, I found an approach that seems to have worked so far.
I have provided users with three files:
-tar.gz (packrat bundle file)
-unbundle.R (R code file that includes a library statement to load
the packrat library, and the unbundle command for the tar.gz file)
-unbundle_readme.txt
The readme file includes instructions similar to those below, and so far users have been able to run R code using the package dependencies. The readme file tells users about requirements (R, R studio, packrat, R package development prerequisites (Rtools for Windows, XCode for Mac)), and includes output of sessionInfo() to document R package versions that the R code should use after instructions are followed. In the example below 'code_folder' refers to a folder within the tar.gz file that contains R. code and associated input files.
Example unbundle instructions:
Step 1
Save, but do not expand/unzip, the tar file to a directory.
Problems with accessing the saved package dependencies
are more likely when a program other than R or R studio
is used to unbundle the tar file.
If the tar file has already been expanded, re-save the
tar file to a new directory, which should not be a the same
directory as the expanded tar file, or a subdirectory of
the expanded tar file.
Step 2
Save unbundle.R in the same directory as the tar file
Step 3
Open unbundle.R using R studio
Step 4
Execute unbundle.R
(This will create a subfolder ‘code_folder’.
Please note that this step may take 5-15 minutes to run.)
Step 5
Close R studio
Step 6
Navigate to the subfolder ‘cold_folder’
Step 7
Open a R script using R studio
(The package library should correspond to that listed below.
This will indicate R studio is accessing the saved package
dependencies.)
Step 8
Execute the R code, which will utilize the project package library.
After the package library has been loaded using the above
steps, it is not necessary to re-load the package library for each
script. R studio will continue to access the package dependencies
for each script you open within the R studio session. If you
subsequently close R-studio, and then open scripts from within
the unbundle directory, R studio should still access the
dependencies without requiring re-loading of the saved package
snapshot.
I'm working on my first package (GitHub). Pretty basic. Two functions.
R CMD INSTALL --no-multiarch --with-keep.source qualtricsR
library(qualtricsR)
Works fine as far as I can tell. Running check in RStudio results in a final message of R CMD check succeeded.
However, when I try to run my functions (e.g., template <- importTemplate("inst/doc/template.xlsx")), I get an error that R cannot find my function. ?importTemplate shows my help page.
#jablacalle and #mdsumner put me on the right track.
Adding export(importTemplate) and export(writeQtxt) to NAMESPACE did the trick. running devtools::document() automated this process once I added #' #export before the function in my .R file.