Attempting to use the mread function to open a cpp file through R. However, when I run the script I get the following:
setwd("C:/Users/Gustavo/Documents/R/page-2018-mrgsolve-master/model")
getwd()
#> [1] "C:/Users/Gustavo/Documents/R/page-2018-mrgsolve-master/model"
library(mrgsolve)
mod <- mread("simple", "model")
#> Error: project directory 'model' must exist and be readable.
Obviously I am setting the directory to "model" itself. So why isn't R able to read it? Any help would be appreciated as I am still learning R and want to learn the mrgsolve package as well.
Additional info: R version 3.4.4. Rtools version 3.4.0. Rstudio version 1.1.463.
An adaptation to the email I sent my colleagues that were assisting me with a similar issue:
To review, I was unable to open any files through RStudio because RStudio returned error messages indicating either that the file itself or the work directory did not exist. I've done multiple installations of different versions of R, RStudio, and Rtools in an attempt to resolve the issue. I also moved the locations of files and programs of interest and changed the work directory to see if that made a difference. Unfortunately, when RStudio is first initiated on a computer, it establishes a "hidden directory" folder that retains the settings of the program when it was first initiated. However, by deleting this folder, RStudio was wiped and I was able to regain control of where files would be stored and read as desired (more on this in the following link: https://support.rstudio.com/hc/en-us/articles/200534577-Resetting-RStudio-Desktop-s-State). A combination of this and forcing Rtools to the front of the 'path' also allowed me to resolve 'status 127' errors that I was receiving as well.
Unfortunately, this is the result of a more personal issue between the initial settings that RStudio took to my computer and my attempt to manipulate where RStudio should read files which I guess were discordant of one another? Regardless, it seems that I would need to be more cognizant of how RStudio establishes a folder which retains its initial settings.
A bit frustrated right now. I have an R project that I built several weeks ago that I have not touched in those weeks. Come back to R Studio to do some debugging, and it will not rebuild the package. When I run the Check command from within the RStudio UI, the error I get is:
Error: Check failed: 'P:\MosaicPA\R Packages/Mosaic.VoronoiV2.Rcheck' doesn't exist
Execution halted
Exited with status 1.
When I try the Install and Restart option, I get this error:
==> Rcmd.exe INSTALL --no-multiarch --with-keep.source Mosaic.VoronoiV2
Warning: invalid package 'Mosaic.VoronoiV2'
Error: ERROR: no packages specified
Exited with status 1.
I have not seen these messages before, and cannot figure out what I am doing wrong, since nothing has changed.
I am not new to programming, but I am new-ish to the R environment. Cannot figure out what has changed, and I dont know what the .Rcheck file is, and I dont know why R doesnt create it. None of my other projects have a .Rcheck file or directory, and I dont know if this is supposed to be a file or directory. I have tried creating the project from scratch. Same issue.
Using R 3.4.1 and the latest R Studio version.
Well, Windows permissions strikes again...personally, I find Windows to be a HUGE POS because of stuff like this. Problem resolved after I reinstalled R under my domain account...I was suspicious of this, but couldn't find a way to confirm. Just reinstalled R and it worked. What I really wish is that when it IS a permissions problem, that Windows would report it as such, so the software can tell the end user this, vs sending us down some rabbit hole, chasing some non-existent problem, which happens too much as it is. Thanks, Redmond! But...I understand...after all, MS is too busy working on the next emoji standard...which is a priority, so who has time to make the OS better. End of rant.
I've found a number of questions related to this warning when installing or updating packages in R/RStudio, but none seem to completely match my situation:
Corporate Windows 7 system, so no access to admin privileges
No way to make changes to McAfee Anti-Virus exceptions lists
R is fully installed in the user space C:\Users\[myname]\R
RStudio fully installed in userspace C\Users\[myname]\RStudio
no permission issues in either of the directories... I have full access control over them
Problem only started after installing R 3.4, but RStudio has randomly failing at start or hanging for a few months now
R_LIBS_USER added as user environment variable, pointing to right directory
.libPaths() show correct directories, both system and user
R version 3.4.2, RStudio version 1.0.153
Uninstalled both R and Rstudio and did a clean re-install of both
Tried trace(utils:::unpackPkgZip,edit = T) and edited Line 140 Sys.sleep(0.5) to Sys.sleep(2), which sometimes works temporarily but the edit won't stay put... resets to Sys.sleep(0.5) on every session restart
Happens in both RStudio and RGui
Any package larger than a few Kb gives the message:
package ‘packagename’ successfully unpacked and MD5 sums checked
Warning in install.packages :
unable to move temporary installation ‘C:\Users\[myname]\R\win-library\3.4\file2b884fc37c13\packagename’ to ‘C:\Users\[myname]\R\win-library\3.4\packagename’
The packages are failing to install or update. So, my questions are:
is there a way to avoid the problem altogether that doesn't require admin privileges or changes to the antivirus policies?
is there a way to get the edit to unpackPkgZip to save permanently?
At this point, I'm stumped. I suspect it has something to do with the antivirus temporarily locking the file/directory after download, but I can't do anything about it from that end. The Sys.sleep(2) seems to do the trick, but I can't keep doing that before every package install or update and can't seem to get the edit to stay put.
This was the only thing that worked for me on this issue (the uninstalling antivirus software didn't get me anywhere, unfortunately), so hopeful it works for you.
On Windows systems, sometimes installation of libraries may be running too fast, creating the error "unable to move temporary installation". Then the package is not found in the user library, because it hasn't been moved over...
To fix, try: trace(utils:::unpackPkgZip, edit=TRUE)
Then go to Line 140 in the code and change Sys.sleep(0.5) to Sys.sleep(2.5)
This is a nice longer term solution that does not require manual package moving, uninstalling software, replacing admin responsibilities, or individually routing packages to certain locations.
My original reply is below, but I've subsequently found a better solution.
Execute the following line:
Trace(utils:::unpackPkgZip, edit=TRUE)
Note that there three colons in there, not two.
Then edit line 142, from Sys.sleep(0.5) to: Sys.sleep(2.0), and click to save the edit (the line number may vary slightly). Unfortunately this does not hold across R sessions, but it only takes 10 seconds to do this, and then you can install packages for the current session to your heart's content.
Original answer:
I ran into the same problem at work. I was able to use Sheldon's suggested approach, but as noted that can get tedious quickly. As an alternative, I found I could go to the location of the downloaded zip file(s) in my temp directory (as reported by install.packages), unzip the file or files (there will be multiple zip files if there are dependent packages), and then move or copy all the unzipped directories straight into my R\win-library\3.4 directory. This isn't a whole lot of fun either, but I find it to be less painful than stepping through the debugger, per Sheldon's method, especially when multiple dependencies are involved and also have to be installed.
If you cannot turn off your antivirus here is a workaround that I found that doesn't involve editing the unpackPkgZip file. 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 want to make this change more permanent you can add the debug code into your Rprofile file, see here, but you'll still need to use step through the unzip function each time a package is installed.
Got the same error - seems to be a company gp / access security problem.
It might also be worthwhile checking whether the folder it fails to write to has a Read Only structure (Right Click - Properties). This folder's address can be found by running: .libPaths()[1] in R.
An ad hoc solution to this problem is to unzip and store the downloaded (but not moved) packages using a piece of R code below. You will get an error stating where the binary packages are located (something like: C:/Users/....AppData/...)
Now you can simply unzip the files from here to your .libPaths() location
zipF <- list.files("C:/Users/<YOURNAMEHERE>/AppData/Local/Temp/Rtmp4Apz6Z/downloaded_packages", full.names = TRUE)
outDir <- .libPaths()[1]
for(i in 1: length(zipF)) {
unzip(zipF[i],exdir=outDir)
}
A more general solution will still be extremely worthwhile, as this is unfortunately a common problem when updating R on Windows.
We've had the same problem at my workplace, and one of my coworkers discovered a great workaround. Unfortunately it's a temporary thing you'll need to do each time you install packages, rather than a permanent fix. We're running corporate Windows 8 (no admin privileges) with McAfee, and I've tested this in R 3.4.0-3.4.3.
Temporarily turning off McAfee's "On-Access Scan" feature (in Threat Prevention) solved this for us -- R packages now all install on the first try the way they're intended to. Here's detailed steps to turn that off:
Right-click the McAfee icon in the notification area at the right of
your taskbar, and select McAfee Endpoint Security.
Click on Threat Prevention. This opens up a screen where you should see categories such as "Access Protection", "Exploit Prevention", and "On-Access Scan".
Un-check "Enable On-Access Scan", and then click Apply. (NB: it's
easy to forget to click Apply, but it's essential)
Once you've installed your packages, it's best to repeat the process to turn On-Access Scan back on.
I fixed my instance of this problem (Windows 7) by removing the 'Read-Only' attribute of the folder R was trying to move stuff to.
I went to the Run command from the Start menu in Windows (7) and typed
attrib -r +s drive:\\
Note that just right clicking the folder and trying to change properties didn't take, as per this link from Microsoft: https://support.microsoft.com/en-us/help/326549/you-cannot-view-or-change-the-read-only-or-the-system-attributes-of-fo
Hope that helps someone.
I hope this change doesn't screw me in other ways.
This was the error message that was spit out for me:
package ‘mlogit’ successfully unpacked and MD5 sums checked
Warning in install.packages :
unable to move temporary installation ‘C:\Users\E\Documents\R\win-
library\3.4\file9ec6cfb5e40\mlogit’ to ‘C:\Users\E\Documents\R\win-
library\3.4\mlogit’
The downloaded binary packages are in
C:\Users\E\AppData\Local\Temp\RtmpS0uNDm\downloaded_packages
What I did was went to where the package was downloaded (C:\Users\E\AppData\Local\Temp\RtmpS0uNDm\downloaded_packages) and then copied that zipped file to the desktop then used Winzip to unzip to my file directory where all the packages for R are stored (C:\Users\E\Documents\R\win-library\3.4). It now will load in R.
library("mlogit")
Loading required package: Formula
Loading required package: maxLik
Loading required package: miscTools
....
It worked well for me as it was the only package that was not downloading for some reason. Might not be helpful if you have to do this for every package.
I also found one solution if above solutions wouldn't work in corporate antivirus.
First change the path of package installation use this command and execute in R:
install.packages('caTools','D:\\ML\\Tools\\Installed\\RPackages')
Now it will show a console's error that unable to move and the package is placed on to some location. just remember this location, we need this zip file for further operations.
Now use this command:
install.packages("D:/ML/Tools/Installed/RPackages/caTools_1.17.1.zip", repos = NULL, type = "win.binary", lib="D:/ML/Tools/Installed/R-3.4.3/library")
I struggled with the same issue. For me (on Windows 10), the issue was using MalwareBytes (Premium trial). I uninstalled it and went back to using Windows Defender, and the issue was resolved. Perhaps if more time, I can find out how to create an exception and/or file checking delay for MalwareBytes (i.e., which is a pretty good program), but the user-guide (https://www.malwarebytes.com/pdf/guides/Malwarebytes-User-Guide.pdf) is unclear on this.
Extending the Sys.sleep value to 3.5 on line 142 in the unpackPkgZip function works manually via
trace(utils:::unpackPkgZip, edit=TRUE)
However, it can also be done programmatically by running the following before install.packages:
localUnpackPkgZip <- utils:::unpackPkgZip
body(localUnpackPkgZip)[[14]][[4]][[4]][[4]][[3]][[3]][[2]][[2]] <- substitute(3.5)
assignInNamespace("unpackPkgZip", localUnpackPkgZip, "utils")
This must be run every time you have a new session. You can run it multiple times in the same session without issue.
If you run the below statement right before the install.packages expression then it should install the package:
trace("unpackPkgZip", where=asNamespace("utils"), quote(Sys.sleep(2.5)), at=14L, print=FALSE)
Knitr / Rmarkdown Execution halted
When I run Knitr and Rmarkdown, even with the knitr example scripts, I get the below error message.
Error in system(paste(shQuote(pandoc_path), "--version"), intern = TRUE) :
'"C:/Program Files/RStudio/bin/pandoc/pandoc"' not found
Calls: <Anonymous> ... get_pandoc_version -> with_pandoc_safe_environment -> force -> system Execution halted
I have installed and loaded knitr and rmarkdown from the libraries and alternatively using dev tools to get the most recent versions from github.
As it was working previously and I haven't changed any settings, I was wondering whether it might be due to the new R release and whether that has caused this?
I have tried uploading pandoc to the specific location it requested in the error but the online guidance was difficult to follow so didn't move into folder just it case it made it worst, as it was not required before I was confused as to why it was an error?
Not sure what else to try out, I have googled, stackflowed and explored knitr and pandoc webpages for any clues but with not success.
If anyone knows how to fix this as soon as possible I would be very grateful!!
I know this is a very old question, but I had the exact same issue, where knitting an Rmd file worked perfectly yesterday, and today, stopped working with the identical error message above. Even knitting the default Rmd starter document failed.
It's possible that a Windows patch was applied by our IS folks that may have broken something, as I had not changed my setup at all.
Doing a Sys.which('pandoc') suggested that it was looking in the wrong place (a user-specific location).
Updating RStudio did not help. Adding the following to my Rmd file also did not work:
Sys.setenv(RSTUDIO_PANDOC="PATH_TO_MY_PANDOC_BIN")
What eventually worked was a subset of the response by Ivo Fugers:
install.packages('installr')
install.pandoc()
(I wasn't paying close attention but think I allowed it to uninstall another version of pandoc.) After a system restart, knitting is working again.
Hope this helps folks in the future, as it seems to be a problem that still sporadically recurs.
I had a similar problem in a Statistical Computing class. A solution that worked for some of my classmates (including myself) is installing a few version of MikTex (takes about an hour). Otherwise, this is a solution that our teacher gave us:
So here is a possible strategy when you end up with a pandoc error, or when your Latex Equations do not show up in the 'markup':
Step 1
Re-install pandoc manually in your R console:
installing/loading the package:
if(!require(installr)) { install.packages("installr"); require(installr)} #load / install+load installr
Installing pandoc
install.pandoc()
Step 2
Download the the self-extracting protext.exe file from http://www.tug.org/protext/ . Install MikTex from this .exe file using the default settings...
2a. Make sure you allow Protext to install packages on the fly without asking permission.
Step 3
Look at https://tex.stackexchange.com/questions/81739/the-memory-dump-file-could-not-be-found , not the solution. Change the persmissions of all users in
C:\Users\YourUsername\AppData\Local\Temp
and
C:\Program Files\MikTex 2.9\
to full control.
How to do this? Go to C:\Users\YourUsername\AppData\Local , and right click on the folder Temp. Go to properties --> Security... and make sure all users listed there (even the trusted install) will have full control acces.
I faced the exact same problem yesterday and shocked because everything was working until day before yesterday. I was finishing my project in R markdown and it started throwing error.
Without having much help, I just have upgraded my RStudio to its latest version (0.98.1091). It took less than 10 minutes and everything started working as it was. I believe this sudden chocking was due to Windows patch update, but not 100% sure.
change your file name "C:/Program Files/RStudio/bin/pandoc/pandoc" into
"C:/ProgramFiles/RStudio/bin/pandoc/pandoc" or something else.
It doesn't allow space in the file address (like Program Files).
I am trying to install custom packages in my Rprofile.site file. I want to install packages in the site file because I have to install these packages on several users' computers. However, I am getting the following the error whenever I launch R.
Error in readRDS(file) : unknown input format
I have the following code added to the end of my Rprofile.site file.
if(length(grep("customPackage", installed.packages()))==0) {
install.packages("customPackage", repos=NULL, type="source")
}
The error keeps repeating itself as well until I stop the R session. If I remove that code from the site file and just install the package directly in an R session though it works fine.
The only reason I want to do it in the site file is because I will keep adding more custom packages that need to be installed on each user's machine and I would rather just call it from the site file than have each user install each custom package once.
I tried searching for the error and got a variety of answers which spoke about deleting the .Rhistory file (which I tried, but didn't work), or installing the latest version of R (I am on R-2.15.0 which is the latest version so that won't help either). I was wondering if there was any other solution to fixing this problem.
I had the same error. Simply closing RStudio, then reopening it and trying again is what worked for me. Note that restarting the R session via the RStudio menu or via rs.restartR() didn't work - only closing and reopening RStudio worked. Not sure why.