After updating R to 4.0.3 and RStudio to the newest version, I have issues with the cointegration of RStudio and RTools described in these questions (before R was 3.6 and RTools 35 and everything worked fine):
https://community.rstudio.com/t/problems-with-r-4-0-0-windows-error-package-or-namespace-load-failed-for-stats-in-indl-x-as-logical-local-as-logical-now/62958/6
https://community.rstudio.com/t/rtools-not-found-after-r-4-0-0-installation/63356/3
I found that I should set some environmental variables for my user. However, I do not understand how to do it, despite the fact that the new path to RTolls should have path C:\rtools40\usr\bin (with older Rtools version it is C:\RTools\bin. Could you help with that?
Additionally,I did these steps, but then got error when downloading package
> Sys.setenv(PATH = paste("C:/rtools40/usr/bin", Sys.getenv("PATH"), sep=";"))
> install_github("brettjbush/R-Websockets")
Downloading GitHub repo brettjbush/R-Websockets#HEAD
√ checking for file 'C:\Users\NAME\AppData\Local\Temp\RtmpSMB4KM\remotes2bcc582622c6\brettjbush-R-Websockets-fc7ee9c/DESCRIPTION' (598ms)
- preparing 'websockets':
√ checking DESCRIPTION meta-information ...
- cleaning src
Warning in system2(command, args, stdout = NULL, stderr = NULL, ...) :
'CreateProcess' failed to run 'C:\rtools40\usr\bin\make.exe -f "C:/PROGRA~1/R/R-40~1.3/share/make/clean.mk" -f Makevars.win clean'
Then I tried following and got different error
> Sys.setenv(PATH = paste("C:/rtools40/usr/bin", Sys.getenv("PATH"), sep=";"))
> Sys.setenv(BINPREF = "C:/rtools40/mingw_$(WIN)/bin/")
> install_github("brettjbush/R-Websockets")
Downloading GitHub repo brettjbush/R-Websockets#HEAD
brettjbush-R-Websockets-fc7ee9c/man/websocket_close.Rd: truncated gzip input
tar.exe: Error exit delayed from previous errors.
Error: Failed to install 'websockets' from GitHub:
Does not appear to be an R package (no DESCRIPTION)
In addition: Warning messages:
1: In utils::untar(tarfile, ...) :
‘tar.exe -xf "C:\Users\NAME\AppData\Local\Temp\RtmpSMB4KM\file2bccd21558.tar.gz" -C "C:/Users/NAME/AppData/Local/Temp/RtmpSMB4KM/remotes2bcc2b6a75d4"’ returned error code 1
2: In system(cmd, intern = TRUE) :
running command 'tar.exe -tf "C:\Users\NAME\AppData\Local\Temp\RtmpSMB4KM\file2bccd21558.tar.gz"' had status 1
Related
In my rocker/rstudio-derived docker container, I'm engulfed in a quagmire surrounding the yearly TexLive update and the R package tinytex.
I have gone through a plethora of iterations of tinytex::install_tinytex(), tinytex::uninstall_tinytex(), tinytex::reinstall(), etc.
I have installed the most current version via remotes::install_github("yiuhi/tinytex").
I have experimented with different (up to date) mirrors of CTAN.
When using a up to date mirror and having installed/reinstalled tinytex properly, I keep getting this behavior:
> tinytex::tinytex_root()
[1] "/home/rstudio/.TinyTeX"
> tinytex::pdflatex("<MYFILE>.tex")
tlmgr: package repository http://vesta.informatik.rwth-aachen.de/ftp/pub/mirror/ctan/systems/texlive/tlnet (verified)
[1/1, ??:??/??:??] install: koma-script [13745k]
running mktexlsr ...
done running mktexlsr.
tlmgr: package log updated: /home/rstudio/.TinyTeX/texmf-var/web2c/tlmgr.log
... 6 more successful package installs ...
tlmgr: package repository http://vesta.informatik.rwth-aachen.de/ftp/pub/mirror/ctan/systems/texlive/tlnet (verified)
[1/1, ??:??/??:??] install: babel-english [3k]
running mktexlsr ...
done running mktexlsr.
tlmgr: package log updated: /home/rstudio/.TinyTeX/texmf-var/web2c/tlmgr.log
! LaTeX Error: This NFSS system isn't set up properly.
! sh: 1: pdflatex: not found
Error: LaTeX failed to compile <MYFILE>.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See <MYFILE>.log for more info.
In addition: Warning messages:
1: In system2(..., stdout = if (use_file_stdout()) f1 else FALSE, stderr = f2) :
error in running command
2: In system2("tlmgr", args, ...) : error in running command
> tinytex::tinytex_root()
[1] ""
After this, ~/.TinyTeX (which was present before) is literally GONE from the file system!?
Can anybody shed light on why 1) tinytex appears to install, 2) it appears to properly process my *.tex file and pulling in the appropriate packages from CTAN and than 3) proceeds in one of those package installations to delete it's entire own installation!?
The observed behavior was a bug in the tinytex R package and has since been resolved (https://github.com/yihui/tinytex/issues/197).
Until the CRAN-available version is >= 0.21.5, one may remedy the behavior by installing directly from the author's repository by:
install.packages("remotes")
remotes::install_github("yihui/tinytex")
follow my previous question, now I am able to manually download gganimate and unzip to my PC. When I try to load h package, there is an error:
shell("R CMD build gganimate")
checking for file 'gganimate/DESCRIPTION' ... OK
preparing 'gganimate':
checking DESCRIPTION meta-information ... OK
checking for LF line-endings in source and make files and shell scripts
checking for empty or unneeded directories
building 'gganimate_0.9.9.9999.tar.gz'
Warning in gzfile(tarfile, "wb", compression = compression_level) :
cannot open compressed file 'C:/Program Files/R/R-3.5.1/library/gganimate_0.9.9.9999.tar.gz',
probable reason 'Permission denied'
Error in gzfile(tarfile, "wb", compression = compression_level) :
cannot open the connection
Execution halted
Warning message:
In shell("R CMD build gganimate") :
'R CMD build gganimate' execution failed with error code 1
Tried to turn off antivus, but it won't help:
trace(utils:::unpackPkgZip, quote(Sys.sleep(2)), at = which(grepl("Sys.sleep",
body(utils:::unpackPkgZip), fixed = TRUE)))
I am having trouble getting DeepWater up and running in R via H2O. I have downloaded the most recent .jar file ( I think) but I get the following error this install command:
install.packages("C:\\Users\\..\\Documents\\R\\win-
library\\3.4\\h2o_3.10.3.99999.tar.gz", repos = NULL, type = "source",
lib="C:\\Users\\..\\Documents\\R\\win-library\\3.4")
* installing *source* package 'h2o' ...
** R Error in .install_package_code_files(".", instdir) : files in 'C:/Users/.../AppData/Local/Temp/RtmpuyZ5fc/R.INSTALL3783508571d/h2o/R' missing from 'Collate' field: xgboost.R ERROR: unable to collate and parse R files for package 'h2o'
* removing 'C:/Users/.../Documents/R/win-library/3.4/h2o'
* restoring previous 'C:/Users/.../Documents/R/win-library/3.4/h2o' Warning in install.packages : running command '"C:/PROGRA~1/R/R-34~1.0/bin/x64/R" CMD INSTALL -l "C:\Users\...\Documents\R\win-library\3.4" "C:/Users/.../Documents/R/win-library/3.4/h2o_3.10.3.99999.tar.gz"' had status 1 Warning in install.packages : installation of package ‘C:/Users/.../Documents/R/win-library/3.4/h2o_3.10.3.99999.tar.gz’ had non-zero exit status Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) && : missing value where TRUE/FALSE needed
Yes we had some unused deps in one of our files in version 3.10.3.x, the one you're using.
It should be fixed in the newest version, which is 3.11.0.X and which you can get from here.
#Edit:
The above version was built for Linux, though - if you want to run it on windows you'll have to build it yourself according to the instructions here for deepwater and here for h2o. We don't have nightly builds for Windows just yet.
I've been writing a lot of code for my personal use and finally reached a point where I realised I should really be including this all in a package which I can load in instead of copy and pasting it in each time.
I followed the following tutorial for the creation of a basic package.
https://hilaryparker.com/2014/04/29/writing-an-r-package-from-scratch/
As far as I can tell everything went well with the actual creation element. Here are screenshots of the result:
The cats folder:
The /cats/R folder
The /cats/man folder
The problem comes when I want to run the line:
install("cats")
When I try to do that I get the following error:
Installing cats
"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL "/Documents/cats" --library="C:/Users/Aodhán/Documents/R/win-library/3.3" --install-tests
* installing *source* package 'cats' ...
Warning in file(file, if (append) "a" else "w") :
cannot open file 'C:/Users/Aodhán/Documents/R/win-library/3.3/cats/DESCRIPTION': No such file or directory
Error in file(file, if (append) "a" else "w") :
cannot open the connection
ERROR: installing package DESCRIPTION failed for package 'cats'
* removing 'C:/Users/Aodhán/Documents/R/win-library/3.3/cats'
Error: Command failed (1)
This error happens for my own package, but it also happens if I run the command:
devtools::install_github("klutometis/roxygen")
Any advice would be appreciated.
EDIT: Could it be that my username contains the character á in it?
EDIT 2:The DESCRIPTION file is:
Package: cats
Title: What the Package Does (one line, title case)
Version: 0.0.0.9000
Authors#R: person("First", "Last", email = "first.last#example.com",
role = c("aut", "cre"))
Maintainer: Aodhán O'Leary
Author: Aodhán O'Leary [aut, cre]
Description: What the package does (one paragraph).
Depends: R (>= 3.3.1)
License: What license is it under?
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Sys.getenv("R_HOME") returns "C:/PROGRA~1/R/R-33~1.1"
Sys.getenv("R_LIBS_USER") returns "C:\Users\Aodhán\Documents/R/win-library/3.3"
Sys.getenv("R_HOME") returns "C:\Users\Aodhán\Documents"
devtools::build("cats") creates "cats_0.0.0.9000.tar.gz"
install.packages("../cats_version.tar.gz") returns the same error as above
Note: This is on a Win10 machine, using R 3.3.1, which I apologise for not mentioning up top. I was quite tired when writing the post yesterday.
Edit 3: Here's the result of using the following commands: R CMD build cats followed by R CMD check cats
00check:
using log directory 'C:/Users/Aodhán/Documents/cats.Rcheck'
using R version 3.3.1 (2016-06-21)
using platform: x86_64-w64-mingw32 (64-bit)
using session charset: ISO8859-1
checking for file 'cats/DESCRIPTION' ... OK
this is package 'cats' version '0.0.0.9000'
package encoding: UTF-8
checking package namespace information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking if there is a namespace ... OK
checking for .dll and .exe files ... OK
checking for hidden files and directories ... NOTE Found the following hidden files and directories: .gitignore These were most
likely included in error. See section 'Package structure' in the
'Writing R Extensions' manual.
checking for portable file names ... OK
checking whether package 'cats' can be installed ... ERROR Installation failed. See
'C:/Users/Aodhán/Documents/cats.Rcheck/00install.out' for details.
DONE
Status: 1 ERROR, 1 NOTE
00install.out
installing source package 'cats' ...
Warning in file(file, if (append) "a" else "w") :
cannot open file 'C:/Users/Aodhan/Documents/cats.Rcheck/cats/DESCRIPTION':
No such file or directory
Error in file(file, if (append) "a" else "w") :
cannot open the connection
ERROR: installing package DESCRIPTION failed for package 'cats'
removing 'C:/Users/Aodhán/Documents/cats.Rcheck/cats'
The problem was the special character in my name, á. When I put it in the C:\ directory and ran R CMD build cats and R CMD check cats it passed that error (though there was an error later on with the pdf - I'll see if I can resolve that myself).
I'll try and post this as a bug. Moderately annoying. Should have thought of that test earlier.
I've run into this problem recently (R version 3.5.2) on two different computers. I don't have the full, exact error message right now, but it contained the following two snippets:
Error in writeLines(paste0(c(out[is_not_empty]), eor), file, useBytes = useBytes) :
(converted from warning) invalid char string in output conversion
and
ERROR: installing package DESCRIPTION failed for package
The problem, I believe, was the existence of special characters in my .Rprofile file. I'd been meaning to get rid of that file anyway (for the sake of reproducibility), and doing so fixed the problem.
To do this in R, the code below will (1) copy your .Rprofile and save it as .Rprofile-old (in case you want to use/restore it later on) and then (2) delete your .Rprofile.
## copy backup of .Rprofile
file.copy("~/.Rprofile", "~/.Rprofile-old")
## delete .Rprofile
unlink("~/.Rprofile")
Once you've run the above code, restart R and the problem will [hopefully] be fixed!
Installing source package..
It is important to specify repo and type
Convert package into package_name.tar.gz
Get into project environment by double clicking the .Rproj file in
your project and click on build -> Build Source Package to build tar.gz file
install.packages("full_path/package_name.tar.gz", repo = NULL, type =
"source")
I'm trying to install development version of ggbiplotfrom Github. During installation I'm getting the following error message:
library(devtools)
install_github("ggbiplot", "vqv")
Installing github repo(s) ggbiplot/master from vqv
Installing ggbiplot.zip from https://github.com/vqv/ggbiplot/zipball
Installing ggbiplot
* checking for file 'C:\Users\Muhammad Yaseen\AppData\Local\Temp\Rtmpsx4n5u\vqv-ggbiplot-2623d7c/DESCRIPTION' ... OK
* preparing 'ggbiplot':
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a 'data/datalist' file should be added
* building 'ggbiplot_0.5.tar.gz'
cygwin warning:
MS-DOS style path detected: C:/Users/MUHAMM~1/AppData/Local/Temp/Rtmpsx4n5u/ggbiplot_0.5.tar.gz
Preferred POSIX equivalent is: /cygdrive/c/Users/MUHAMM~1/AppData/Local/Temp/Rtmpsx4n5u/ggbiplot_0.5.tar.gz
CYGWIN environment variable option "nodosfilewarning" turns off this warning.
Consult the user's guide for more details about POSIX paths:
http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
Warning: invalid package 'Yaseen/R/win-library/2.14'
Error: ERROR: cannot cd to directory 'C:/Users/Muhammad'
Error: Command failed (1)
In addition: Warning message:
running command '"C:/PROGRA~1/R/R-214~1.2/bin/i386/R" CMD INSTALL C:\Users\MUHAMM~1\AppData\Local\Temp\Rtmpsx4n5u/ggbiplot_0.5.tar.gz --library=C:/Users/Muhammad Yaseen/R/win-library/2.14' had status 1
Any idea to figure out this problem. Thanks in advance for your help and time.
Edit
After downloading from Github, also tried
install.packages("vqv-ggbiplot-2623d7c.tar.gz", repos=NULL, type="source")
which produced this error message
Installing package(s) into ‘C:/Users/Muhammad Yaseen/R/win-library/2.14’
(as ‘lib’ is unspecified)
Error in untar2(tarfile, files, list, exdir) : unsupported entry type 'g'
Warning messages:
1: running command 'C:/PROGRA~1/R/R-214~1.2/bin/i386/R CMD INSTALL -l "C:/Users/Muhammad Yaseen/R/win-library/2.14" "vqv-ggbiplot-2623d7c.tar.gz"' had status 1
2: In install.packages("vqv-ggbiplot-2623d7c.tar.gz", repos = NULL, :
installation of package ‘vqv-ggbiplot-2623d7c.tar.gz’ had non-zero exit status
It's because your Rlib path has a space in it: C:/Users/Muhammad Yasseen/R/win-library/2.14.
See how in the first error log the warning message was
running command '"C:/PROGRA~1/R/R-214~1.2/bin/i386/R" CMD INSTALL
C:\Users\MUHAMM~1\AppData\Local\Temp\Rtmpsx4n5u/ggbiplot_0.5.tar.gz
--library=C:/Users/Muhammad Yaseen/R/win-library/2.14'
had status 1
In particular, the --library=C:/Users/Muhammad Yaseen/R/win-library/2.14.
This should be --library="C:/Users/Muhammad Yaseen/R/win-library/2.14" to deal with the space.
Using install.packages takes care of the quotes for you - see how your second warning message (when you used install.packages) was
running command 'C:/PROGRA~1/R/R-214~1.2/bin/i386/R CMD INSTALL
-l "C:/Users/Muhammad Yaseen/R/win-library/2.14"
"vqv-ggbiplot-2623d7c.tar.gz"' had status 1
The -l "C:/Users/Muhammad Yasseen/R/win-library/2.14" has quote marks around it, so you don't get the same error.
I had a quick look at the install-github sources, and it constructs the R CMD INSTALL command via:
paste("CMD INSTALL ", built_path, " --library=", .libPaths()[1], sep="")
See how it doesn't surround .libPaths()[1] by double quotes in case of spaces? I'd guess that's your problem.
As to a fix - there seems to be an error using install.packages() on a tar file generated by git (as reported here). So, you can either:
change your R library location to somewhere without spaces
unzip the .tar.gz file (I don't know what software does this on Windows) and install from the extracted directories rather than the .tar.gz.
You can't unzip the .tar.gz because it cleans up that file quicker than you can grab it (I've watched it appear and get deleted again). Correct me if I'm wrong, but I also can't get devtools from github for teh same reason :S