When running the checks for my R-package (via devtools::check()) I face the warning ''qpdf' is needed for checks on size reduction of PDFs. I found this question were it was suggested (if I understood the answer correctly) to run Sys.which(Sys.getenv("R_QPDF", "qpdf")) and see whether qpdf is found or not. In my case this just returns
qpdf
""
so, I think I didn't install qpdf correctly. Unfortunately it seems to be quite complicated to install qpdf on Windows. My first side question is: does it really is so painful and complicated to install qpdf for Windows or is there an easy solution?
I've followed the instructions until it is said to add C:\MinGW-w64\bin and C:\MinGW-w64\lib\mingw to the PATH variable. But then I don't find further specific instructions to install qpdf, only about how to build qpdf with different other programs. The second side question is: is my assumption correct that after I've build qpdf it is installed? But the real question is: What is the best way to build qpdf? I tried the ./config-mingw32 and ./config-mingw64 commands from the section "Building with MinGW" in my C:\MinGW\msys\1.0\bin\bash.exe but got the error messages ./config-mingw32: No such file or directory and have no idea how to fix this issue.
I'm using Windows 10, R version 3.3.2 Patched (2017-01-07 r71934) -- "Sincere Pumpkin Patch" and RStudio 1.0.136.
You basically do not need to build the file on windows. Please follow three steps below:
Download qpdf for windows from https://sourceforge.net/projects/qpdf/?source=typ_redirect
Extract files in a temp folder
Copy the contents of the bin folder to %SystemRoot%\System32
job done!
Sys.which(Sys.getenv("R_QPDF", "qpdf"))
qpdf
"C:\\WINDOWS\\SYSTEM32\\qpdf.exe"
To flesh out an answer provided elsewhere:
If you are running the 32-bit version of R, it is important that you download the 32-bit version of qpdf, which is the version linked from the SourceForge homepage. If you are running a 64-bit installation of R, you will need to do a bit of digging to locate the 64-bit version of qpdf, which is buried a little more deeply (version 10.0.1 is listed here).
Rather than copying files to C:/Windows/System32, a potentially safer option is to extracted the zipped qpdf directory to C:\Program Files. If you do this, you'll need to add C:\Program Files\qpdf-version_number\bin to your system PATH under the environment variables.
To do this within R, run Sys.setenv('PATH' = paste0('C:\Program Files\qpdf-version_numer\bin;', Sys.getenv('PATH')))
To do this in Windows, open the start menu, type "edit the system environment variables" to open the System Properties, and at the bottom of the "Advanced" tab click "Environment variables". Find the "Path" entry under "System variables" and click "Edit". Then, re-start R so it picks up the modified PATH.
One further step may be required to convince Windows that pqdf is safe to run.
Navigate to C:\Program Files\qpdf-version_numer\bin and execute qpdf.exe (by double-clicking). Windows 10 throws up a security warning, as it's an unrecognized executable file. You'll need to use the more options link to find the button to run the program. This done, Windows will recognize the file as safe to run and allow other software, including R, to use it.
Related
First of all, I am working on a Mac. I am trying to install Blotter from GitHub. I found several descriptions of how to do that but my RStudio tells me that I am missing Building tools and gives me a link (https://www.cnet.com/how-to/install-command-line-developer-tools-in-os-x/) where it is described to do that. So far so good. I downloaded Xcode and the command line tools for Mac and installed those. Nothing changed even after restarting R. Then I found this https://cran.r-project.org/bin/macosx/tools/. I installed it and during that, it told me that I had to do the following
"This package will install clang 6.0.0 for OS X 10.11 (El Capitan) or higher with OpenMP support in /usr/local/clang6
In order to use this compiler you have to add /usr/local/clang6/bin to the PATH environment variable such as
export PATH=/usr/local/clang6/bin:$PATH"
So I changed the environmental variable path as follows http://blog.tonytsai.name/blog/2018-05-07-setting-path-variable-for-gs-command-in-rstudio/.
How I changed the PATH variable.
Again I restarted R but still, nothing changed. I still get the notice that the building tool is missing.
Somehow it seems to me that I installed everything correctly but R doesn't recognize the Programmes. Does anyone have an idea? I tried to search for settings to tell R that I installed the command line tool but couldn't really find anything helpful.
Ok, a bit of an update.
Best I can see it that Blotter is built and stored on R-Forge packages under a package called RStrategist
In R console type/cut & paste this.
install.packages('RStrategist',repos='http://R-Forge.r-project.org')
See R forR-Forge for more details. Once this has been installed run instead.
library(RStrategist)
Unfortunately, I am not willing to install this package and see if it works mainly because 1) don't need it nor know how to use it, 2) not sure how good packages are from R-forge, though it seems legit, but, this brings me back to point one.
So before i read the updated answer of Conrad Thiele i was trying around bit. Basically i deleted R, R Studio, Xcode and Command Line tools. Then i installed Xcode, Command Line tools, R and RStudio. Then i followed the notice on https://cran.r-project.org about the tools and installed both stated tools. As mentioned in the original question the Clang package tells you to change the Environmental Variable. And there was the mistake i believe. I originally simply pasted "PATH=/usr/local/clang6/bin:$PATH" into the the ".Renviron" file. With reading up online i noticed that "export PATH=/usr/local/clang6/bin:$PATH" is actually a Command for the Mac Terminal. After executing it, it sill didn't work but then i remembered that i still had the Path "PATH=/usr/local/clang6/bin:$PATH" in the the ".Renviron" file. Once i deleted that it worked. So i guess the key was that with changing the Environmental Variable correctly R found the connection with the right tool. Patients paid off.
I recently upgraded to Architect version 0.9.7 on my Win 7 machine. However, after starting Architect, the RJ console wouldn't launch and I got the error message:
‘Launching the R Console was cancelled, because It seems starting the R engine failed.”
Please make sure that R package 'rj' (2.0 or compatible) is installed and
that the R library paths are set correctly for the R environment
configuration 'Embedded R Server'.
I installed the packages ‘rj’ and ‘rj.gd’ through the RTerm run console (which does happen to work) within Architect using the command suggested on www.walware.de:
install.packages(c("rj", "rj.gd"), repos="http://download.walware.de/rj-2.0")
Then, I restarted windows, and restarted Architect. Same error message. I zoomed in on the details of the error message and noticed the following line:
SEVERE: Path to rj package not found. Use R_LIBS or java property
'de.walware.rj.rpkg.path' to specify the location.
So I opened an RTerm run console to check whether any of my .libPaths() locations contains the directories ‘rj’ or ‘rj.gd’. Oddly enough, they do. My first .libPaths path contains both packages. So that doesn’t seem to be the reason.
How could this be fixed?
I received prompt and helpful feedback from Open Analytics (thanks!), who informed me that the problem is due to changes in Java 8. With Java 7, Architect works fine. The next release of Architect will incorporate the changes in Java 8.
In order to get it work with Java 7, enforce the use of a specific Java Runtime, by using the -vm argument in the architect.ini file as follows:
-vm
C:\Program Files\Java\jre7\bin\javaw.exe
(mind the line break, which is required)
This is particularly useful if you have several Java versions on your system where the default Java is not suitable for use with Architect. The architect.ini file is found directly at the top level of the installation folder of Architect. You can find out where this is by looking at the Properties of the Architect shortcut on your desktop.
N.B. the -vm argument should be put before the -vmargs argument otherwise it is simply ignored!
N.B. examples of -vm specification on GNU/Linux and Mac OS X:
http://wiki.eclipse.org/Eclipse.ini#-vm_value:_Linux_Example
http://wiki.eclipse.org/Eclipse.ini#-vm_value:_Mac_OS_X_Example
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
I'm trying to get R to recognize that I have installed Rtools.exe. I've tried installing it in several different locations. However, whenever I restart R and load devtools I get the same error:
> library(devtools)
WARNING: Rtools is required to build R packages, but is not currently installed.
Please download and install Rtools 3.0 from http://cran.r-project.org/bin/windows
/Rtools/ and then run find_rtools().
Naturally, whenever I try the function find_rtools() I get the same error message. I'm done trying to figure this out with help files, as the devtools help doesn't offer much. I've tried installing in several of the locations returned by get_path() but the problem persists.
FYI, currently my R is installed at D:/R.
Has anyone else had this problem, and more importantly, can anyone help me?
I'm sorry if this is a duplicate, and I've tried to include as many relevant details as possible so if you need any clarification please let me know.
Thanks,
Nick
Grab the batch file Rpathset.bat from batchfiles, edit the SET statements in it appropriately and then run R like this from the Windows console:
Rpathset
Rgui
I ran into this issue running a Windows 7 machine without admin rights. I leveraged G. Grothendieck's response, with a few additional steps.
Get Rpathset.bat from https://code.google.com/p/batchfiles/
Edit the Set statements in Rpathset.bat to your paths
Run CMD and change directories to where Rpathset.bat is stored
In the command prompt, run rpathset.bat > mypath.txt
Open mypath.txt with a text editor
Click Windows Start and search for environment
Click Edit environment variables for your account
Click path and then edit
Copy and paste the entire path from mypath.txt into the Windows path (everything after the path statement)
Restart RStudio and check that devtools::find_rtools() is TRUE
This file rtools.r contains the code for find_rtools(). It looks like it is trying to find ls and gcc in your system path (and then does some more checks based on the version) and if that fails it tries to look up SOFTWARE\R-core\Rtools in the the Windows registry.
As Thomas mentioned here, "Rtools is not a package." This is what I did to install Rtools. My RStudio is running R version 3.1.3. So I downloaded Rtools31.exe from https://cran.r-project.org/bin/windows/Rtools/. I executed the exe file, selected all the default options in the Setup Wizard and installed. (I had admin privilege on the computer I was using but I am not sure if that makes any difference.) To check that it was properly installed, you can enter find_rtools() in the R prompt which should return TRUE if Rtools installed properly.
For R 3.0, you probably just need to download Rtools30.exe and follow the same steps above.
I ran into this problem trying to install Rtools33 to use Hadley Wickham's lineprof package. I got that error multiple times. I'm running Windows 7 on a laptop.
I was able to fix the problem by running the Rtools installation file as the windows Admin (i.e. right-click the Rtools33.exe and choose "Run as administrator")
I also made sure to point the path to the R source directory, which I kept in C:\Rtools\ (which contains C:\Rtools\bin\ and C:\Rtools\gcc-4.6.3\).
This solved the problem for me and I am now able to install lineprof from GitHub and make use of it.
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