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'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.
Even though I duly setwd() (within an R session running in an Emacs/ESS buffer) to the root of my R package and run devtools::load_all() there, when I call a function I find that I am running a version of the function that no longer exists in the present R package. Running rm(<function_name>), followed by source-ing the relevant file, do not help.
Might I perhaps be running a version of the package that I inadvertently installed?, I ask myself. I run lapply(.libPaths(), dir) to answer, but my package does not appear.
What is happening? Where/how is this caching happening?
Update
Running
rm(list=ls())
as described here solved the problem. Although it's not clear what the problem might have been in the first place. An explanation is very welcome.
R caches your global environment in a file .Rdata. Delete it and start a new session.
I'm building an R package and have run into a perplexing warning during R CMD check:
* checking for missing documentation entries ... WARNING
Undocumented data sets:
‘.Random.seed’
The package has one small data set, which is documented. I'm using R 3.1.1 and RStudio 0.98.1062 on OS X Yosemite, but I get the same error on Windows 7 (and from CRAN). The project also has a vignette that is built with knitr. devtools etc. are all up to date. The file '.Random.seed' doesn't exist in the "data" folder before building, and my reasoning is that it's getting transiently written to disk during the build process by...something. I tried adding '.Random.seed' to .Rbuildignore without success, presumably because it doesn't exist when the build process begins.
Has anyone encountered this before?
Ran into this problem as well. You have almost certainly solved it by now, but I'll post an answer just in case somebody else hits the same problem. At some point, you generated a random number or set the seed in the creation of the Rdata file (or at least that's what happened to me). Simply load the workspace from you data folder, and rm(.Random.seed). Save it. You're done. Easy as pie.
http://www.inside-r.org/r-doc/base/set.seed
I had a similar problem when I was uploading the my.csv dataset, if anyone faces a similar problem the answer is inhere.
I am using R 2.13.0 with windows 7, after giving my user full privileges to the R folder (as described here).
This allows me to install new packages just fine.
However, when using update.packages(), to update existing packages, I keep getting the following error (for example, when updating the MASS package):
package 'MASS' successfully unpacked and MD5 sums checked
Warning: unable to move temporary installation
'C:\Program
Files\R\R-2.13.0\library\file6cae3bcf\MASS'
to 'C:\Program
Files\R\R-2.13.0\library\MASS'
Any suggestions on how to fix this?
p.s: Running R as an administrator or shifting the library location out of Program Files is not a solution (it's a hack - but I am looking for a solution)
I found that the problem indeed is the antivirus "real time file system protection". I do the following to fix the problem:
trace(utils:::unpackPkgZip, edit=TRUE)
I edit line 140 (line 142 in R 3.4.4):
Sys.sleep(0.5)
to:
Sys.sleep(2)
I seems like the antivirus stalls the creation of the package tmp dir. After changing it to 2 seconds the error is gone.
EDIT: to do this programmatically execute
trace(utils:::unpackPkgZip, quote(Sys.sleep(2)), at = which(grepl("Sys.sleep", body(utils:::unpackPkgZip), fixed = TRUE)))
(credits #DavidArenburg)
Just to update everyone, I (think that I) found out the source of the problem: antivirus.
The "real time file system protection" was blocking R from copying the files between folders once they were downloaded.
Upon adding the R directory to the exception list (coupled with adding user permission and installing R on D:\R), and the problem went away. With all of this work, I might as well switch to Linux (I should, really...)
(I updated my post with the above information: http://www.r-statistics.com/2011/04/how-to-upgrade-r-on-windows-7/)
I hope it will help someone in the future,
Tal
If you cannot turn off your antivirus, due to corporate policy for example, here is a workaround that I found. Debugging the unzip package function and then stepping through it gives the antivirus enough time to do its job without interfering. Use this command:
debug(utils:::unpackPkgZip)
install.packages("packageName")
and then step through the code (by pressing enter many times) when R starts debugging during the installation.
I found this solution here.
If you can just download the binary straight from CRAN. On windows when downloaded it will be a zip file. Now manually unzip this into the ..library/ folder of your R (.libPaths()). It worked for me on some packages.
I had this problem installing both swirl and dplyr. I am working on Windows 64-bit.
Warning: unable to move temporary installation
What I did is I accessed my temporary files on the C: drive, and opened my file extractor program and I extracted the files from the temp file in the C: drive to my R program files in the C: drive, by manually copying them. THIS WORKED FOR BOTH dpylr and swirl. Stoked!
Cheers,
Peach
Can you not use the lib.loc parameter to only update packages in your personal library (in user)?
There should be no way to enable a normal, non-augmented user to change files in the program files folder, so the only thing you can do (if you don't want to augment the user) is to have R not updating packages there.
A workaround is to avoid installing R in the program files folder (which may be more or less of a hack than just shifting the library location out of it, depending on your point of view).
Finally, if lib.loc doesn't cut it, you can look at the source code for update.packages and create your own customized version that will always avoid the common library location in program files.
I just met the same question, and the solution I found out was that you should install packages using the original R software (plus, you should choose the right mirror site, some of them are blocked). At first I used Rstudio to install packages and I got the same problem as you met. Hope this is helpful.
I have run into this error several times. In my own case, it is because our admins want us to use remote virtual disks (on Windows 7) for our files and everything is locked up tight as a drum. The only way I can use R packages is in a lib directory on that remote virtual disk. This wouldn't be a problem except that the network isn't always smooth and fast. Thus, when I need a package, especially one with several other packages in tow (e.g., MBESS), I either have to go through the get.packages() process multiple times until it finally finishes or make it IT's headache to do quick like the bunny for me. I can't always wait for IT.
I just went to the library folder (Windows XP) and deleted all fileXXXX folders. Reran the install an it is worked.
I had the same problem. Since the issue seems to be the antivirus blocking the transf of a downloaded file, I tried a different download method in the install.packages and it worked.
For example:
install.packages("stringr", method = "curl")
You must go into the properties of the R folder and change the security parameters. You can enable the option to write and modify for all users.
The error : "unable to move temporary installation" is basically arising due to any of the antivirus running on your system.
Try unzipping the downloaded file from the Temp folder into the default library path (you can get it by running .libPaths() in R session).
I'm using a MRAN and I was having so many versioning issues. Trying to work with tidyverse and ggplot2 and by upgrading to the latest version from Microsoft it solved all of my R-Studio versioning issues.
Version info:
Microsoft R Open 3.5.1
The enhanced R distribution from Microsoft
Default CRAN mirror snapshot taken on 2018-08-01.
Download Microsoft R Open 3.5.1