I'm trying to load papaja in R (version 3.6.0). I'm running Windows 10 on my computer. When I try to run devtools::install_github("crsh/papaja") I get the following error message:
package ‘markdown’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\My
Name\AppData\Local\Temp\RtmpKCmBDG\downloaded_packages
ERROR
cannot change to directory 'C:\Users\My'
The system cannot find the path specified.
Error in (function (command = NULL, args = character(), error_on_status =
TRUE, :
System command error
From some research, including this post and this post, I realise that this is a common issue, but none of the answers I can find help me work around this in papaja.
For info, I don't have this problem when installing other packages using install.packages().
I have managed to solve this problem after hours and hours of googling. The problem is not papaja; it is the presence of spaces in the path, which devtools does not deal with well.
To solve this, I first changed my library path:
.libPaths("C:/Program Files/R/R-3.6.1/library") # for R v.3.6.1
At first I couldn't get this to work - I kept getting the error 'lib = "C:/Program Files/R/R-3.6.1/library"' is not writable. Basically, this is because I did not have permission to write into this folder. To fix this, you simply close RStudio, go to the folder where the programme is saved and right click, then select 'Run as administrator'.
Related
I have installed h2o package(in R from RStudio console). Post h2o.init() I am trying to use the built in function upload_model()/upload_mojo() but I am getting following error.
h2o.upload_mojo()
Error in h2o.upload_mojo() : could not find function "h2o.upload_mojo"
h2o.upload_model()
Error in h2o.upload_model() : could not find function "h2o.upload_model"
I found work around to resolve this issue. Please find below the steps I followed:
Remove the package using: remove.packages("h2o")
Quit the current session and launch the new one.
Move out lock file for h2o from path where package was installed mostly under R with file name like - 00LOCK-h2o
Install new/latest version of package via RStudio console using install.packages()
It should now resolve this issue.
I am connecting remotely to a work server and need to be able to install R packages via RStudio. I have read through other questions/answers on this topic, but haven't been able to solve this for myself. I think the following input and output shows my issues the best: (edit: I do not have admin powers, but can call IT as last resort)
>.libPaths("C:/RWorkSpace") #setting new file path
>.libpaths() #testing
[1] "C:/RWorkSpace" "C:/Program Files/R/R-3.4.1/library"
>install.packages("bibliometrix", dependencies = TRUE, lib="C:/RWorkSpace")
The downloaded source packages are in
‘C:\Users\cortiz\AppData\Local\Temp\7\RtmpOsVuTB\downloaded_packages’
>library(bibliometrix)
Error in library(bibliometrix) : There is no package called 'bibliometrix'
>installed.packages()["bibliometrix","C:/RWorkSpace"]
Error in installed.packages()["bibliometrix","C:/RWorkSpace"] : subscript out of bounds
I just need to download the package and dependencies, and I expected them to be downloaded to the folder I specified ("C:/RWorkSpace").
very new to working with R in general so please bear with me. Any help greatly appreciated!
im using R and quite new at rmarkdown. i want to knit my rmarkdown into pdf formatted file and i already read that i need to install tinytex package.
i enter the code as instructed on https://yihui.org/tinytex/
install.packages('tinytex')
tinytex::install_tinytex()
and i got this error code
Starting to install TinyTeX to C:\Users*****\AppData\Roaming\TinyTeX. It will take a few minutes.
Automated TeX Live installation using profile: ../tinytex.profile
Loading https://mirror.unpad.ac.id/ctan/systems/texlive/tlnet/tlpkg/texlive.tlpdb
C:\Users*****\AppData\Local\Temp\RtmpW6xVT8\install-tl-20191206\install-tl: TLPDB::from_file could not initialize from: https://mirror.unpad.ac.id/ctan/systems/texlive/tlnet/tlpkg/texlive.tlpdb
C:\Users*****\AppData\Local\Temp\RtmpW6xVT8\install-tl-20191206\install-tl: Maybe the repository setting should be changed.
C:\Users*****\AppData\Local\Temp\RtmpW6xVT8\install-tl-20191206\install-tl: More info: https://tug.org/texlive/acquire.html
TinyTeX installed to C:\Users*****\AppData\Roaming\TinyTeX
Please quit and reopen your R session and IDE (if you are using one, such as RStudio or Emacs) and check if tinytex:::is_tinytex() is TRUE.
Warning message:
In file.remove("TinyTeX/install-tl.log") :
cannot remove file 'TinyTeX/install-tl.log', reason 'No such file or directory'
i restart my r and rstudio, run tinytex::is_tinytex(), returned FALSE.
i guess the repository cannot be accessed anymore so i tried to change the repo but still it doesnt change.
can anyone help me with solution? thanks
UPDATE :
i tried to run this as Yihui Xie told me :
tinytex::install_tinytex(repository = 'http://dante.ctan.org/tex-archive/')
and
tinytex::install_tinytex(repository = 'http://mirrors.ibiblio.org/CTAN/')
and return this
trying URL
'http://dante.ctan.org/tex-archive/systems/texlive/tlnet/install-tl.zip'
length 22539829 bytes (21.5 MB) downloaded 21.5 MB trying URL
'https://yihui.name/gh/tinytex/tools/pkgs-custom.txt' Content length
81 bytes downloaded 351 bytes trying URL
'https://yihui.name/gh/tinytex/tools/tinytex.profile' Content length
81 bytes downloaded 295 bytes Starting to install TinyTeX to
C:\Users\Kandu\AppData\Roaming/TinyTeX. It will take a few minutes.
Automated TeX Live installation using profile: ../tinytex.profile
Loading
https://mirror.unpad.ac.id/ctan/systems/texlive/tlnet/tlpkg/texlive.tlpdb
C:\Users\Kandu\AppData\Local\Temp\Rtmp8OFCvK\install-tl-20191209\install-tl:
TLPDB::from_file could not initialize from:
https://mirror.unpad.ac.id/ctan/systems/texlive/tlnet/tlpkg/texlive.tlpdb
C:\Users\Kandu\AppData\Local\Temp\Rtmp8OFCvK\install-tl-20191209\install-tl:
Maybe the repository setting should be changed.
C:\Users\Kandu\AppData\Local\Temp\Rtmp8OFCvK\install-tl-20191209\install-tl:
More info: https://tug.org/texlive/acquire.html TinyTeX installed to
C:\Users\Kandu\AppData\Roaming/TinyTeX Please quit and reopen your R
session and IDE (if you are using one, such as RStudio or Emacs) and
check if tinytex:::is_tinytex() is TRUE. Warning messages:
1: In
file.remove("TinyTeX/install-tl.log") : cannot remove file
'TinyTeX/install-tl.log', reason 'No such file or directory'
2: In
in_dir(target, { : The repository
http://dante.ctan.org/tex-archive/systems/texlive/tlnet does not seem
to be accessible. Reverting to the default CTAN mirror.
idk why but it keep trying to download from https://mirror.unpad.ac.id.
any explanation?
At the moment, the mirror https://mirror.unpad.ac.id does not seem to have a valid SSL certificate, so the site is not accessible. You can find other accessible mirrors at https://ctan.org/mirrors/mirmon. To specify the mirror, use the repository argument. Below are two possible examples:
tinytex::install_tinytex(repository = 'http://mirrors.ibiblio.org/pub/mirrors/CTAN/')
tinytex::install_tinytex(repository = 'http://dante.ctan.org/tex-archive/')
installed.packages() command in R lists your installed packages. Mine was working for almost a year and then this command randomly started throwing an error. As this is a built-in command, I am not even sure how to "reinstall" it or address this. Any ideas how to fix the error and get the command working again?
> installed.packages()
Error in gzfile(file, mode) : cannot open the connection
In addition: Warning message:
In gzfile(file, mode) :
cannot open compressed file `'C:\Users\Mitch\AppData\Local\Temp\Rtmp6Dawpa/libloc_190_4464fd2b.rds', probable reason 'No such file or directory'`
One suggestion on here involved this in combination:
.libPaths()
installed.packages(lib.loc = 'my path')
The results of this produced yet another error as shown here. Looks like an issue with the installed file still but how to address is the question:
> installed.packages(lib.loc = 'C:/ProgramFilesCoders/R/R-3.3.2/library')
Error in gzfile(file, mode) : cannot open the connection
In addition: Warning message:
In gzfile(file, mode) :
cannot open compressed file 'C:\Users\Mitch\AppData\Local\Temp\Rtmp6Dawpa/libloc_190_4464fd2b.rds', probable reason 'No such file or directory'
>
That is odd.
What version of R are you running, standard R or Microsoft R? And did you recently update?
If you did recently update, perhaps your packages did not get copied over, hence the 'No such file or directory' statement.
If you haven't updated, I would install a newer version and see if it fixes the issue.
If your uncertain, you can always use the updateR function to check if you have the latest version and choose to install it or not.
library(installr)
updateR()
Good luck,
I think the issue lies in terms of the where the function is looking for the package information. installed.packages() needs an argument lib.loc.
From official documentation
lib.loc character vector describing the location of R library trees to search through
Looks like the function for some reason is looking in AppData\Local\Temp which is the download location and not the installed location.
Without looking at your R_Home and .libPaths() is difficult to nail down where the problem is, however running .libPaths() should give you one or more paths as shown in the below example. None of these should be temp locations.
>.libPaths()
[1] "C:/Users/UserName/Documents/R/win-library/3.4"
[2] "C:/Program Files/R/R-3.4.0/library"
If not, you can set the path within the .libPaths("your path") or pass the path of the library as part of installed.packages(lib.loc = 'your path') and try again.
Sometimes the most simple obvious solution is what works:
I closed my RStudio environment saving it to .RData
I re-opened RStudio and tried the command again
it worked
For the future, some good ideas got posted on here before I thought to try the above. Here are the suggestions that others included in case the above does not work if this problem is encountered by anyone in the future:
Use .libPaths() to find out proper path where this is installed, and then re-run the command with the path included in it like so: installed.packages(lib.loc = 'your path')
Try debugging it with: debug(installed.packages); Expectation is that we will likely find something wrong with .readPkgDesc(lib, fields) while stepping through debug. This was not tried yet so you may encounter things not written up here when you do try it.
Try Updating R in case it is out of date with these commands: library(installr) and updateR().
For some reason I am suddenly not able to install packages in R (I have subsequently updated to the latest version of R and am running Windows 7). For example, if I type:
install.packages('beeswarm')
Installing package into ‘D:/Rlibs’ (as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session --- trying URL 'http://www.stats.bris.ac.uk/R/bin/windows/contrib/3.0/beeswarm_0.1.5.zip'
Content type 'text/html' length unknown opened URL downloaded 1859
bytes
Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
"Type")) : cannot open the connection In addition: Warning
messages: 1: In unzip(zipname, exdir = dest) : error 1 in extracting
from zip file 2: In read.dcf(file.path(pkgname, "DESCRIPTION"),
c("Package", "Type")) : cannot open compressed file
'beeswarm/DESCRIPTION', probable reason 'No such file or directory'
I have read that in Windows 7 there can be important restrictions on rights to writing to certain folders etc. so I've gone to some lengths to install R and library folders in non-default areas of my computer, and to allow myself rights to certain folders, but to no avail. Possibly also of importance is when I type:
.libPaths()
# [1] "D:/Rlibs"
# [2] "C:/Users/L.Halsey/Documents/R/win-library/3.0"
# [3] "C:/Users/L.Halsey/Documents/Documents/R-3.0.1/library"
I have created several folders in an attempt to create one that I could successfully install libraries into and set them up to be recognised by R using 'environment variables' from the start button. I don't know how to delete any of them though - not sure if this is relevant to my overall problem of not now being able to install/update packages for some reason.
The error being reported is inability to open a connection. In Windows that is often a firewall problem and is in the Windows R FAQ. The usual first attempt should be to run internet2.dll. From a console session you can use:
setInternet2(TRUE)
(You are correct in thinking this is not due to your library setup. The error says nothing about permissions.) I don't think just typing .libPaths should return that character vector since on my machine I would need to type .libPaths() to see something like that. If you wanted to reduce the number of places for libraries you can use the .libPaths function for setting the values. This would pick the second and third of the existing paths
.libPaths( .libPaths()[2:3] )
The inner call retrieves the path vector and the outer call sets it to a reduced vector.
Running RStudio as administrator fixed it for me!
I will probably duplicate a lot of other answers on the stackoverflow, but I got exactly the same error as OP, namely:
Warning messages: 1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file 2: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : cannot open compressed file 'zoo/DESCRIPTION', probable reason 'No such file or directory'
Turned out, while I as a user had permissions to write in a certain directory, R did not. In order to be sure you don't have something similar, do following:
get a usb drive, let's name it E
download package source as a .zip file and store it onto usb-drive in some directory, let's name it E:/source
Create directory for libraries on the usb drive, let's name it E:/libs
Install packages calling R command install.package from the R console and setting all relevant directories to point to your usb drive:
(here I use package zoo as an example)
install.packages("E:/source/zoo_1.7-12.zip",
destdir = 'E:/source', # no "/" after the path
lib = 'E:/libs',
repos = NULL)
Load the package from the directory, where you installed it:
library('zoo', lib.loc = 'E:/libs')
After you are sure, it works this way on your usb drive, you can start resolving directories permissions, and try out by changing the paths in the code above.
update:
In some windows environments even your usb-stick might be protected from read-write by the R. Make sure you check the permissions using the machine you are working from.
The following worked for me (based on the answer above)
install.packages("clustvarsel", lib = "C:/Users/dnentchev/My Programs/R-3.2.2/library")
I had the same problem. I turned the windows firewall off, and Run RStudio as administrator. so, that error fixed.