Issues Installing ggpubr; R Studio Version 4.1.3 - r

I am rather new to r, and I am struggling with pulling up ggpubr into the library.
My code starts like this. I already have 'tidyverse' successfully installed:
install.packages('ggpubr', lib = 'C:/CustomR')
This returns:
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
also installing the dependencies ‘pkgload’, ‘praise’, ‘waldo’, ‘testthat’, ‘numDeriv’, ‘SparseM’, ‘MatrixModels’, ‘sp’, ‘minqa’, ‘nloptr’, ‘RcppEigen’, ‘carData’, ‘abind’, ‘pbkrtest’, ‘quantreg’, ‘maptools’, ‘lme4’, ‘corrplot’, ‘car’, ‘ggrepel’, ‘ggsci’, ‘cowplot’, ‘ggsignif’, ‘gridExtra’, ‘polynom’, ‘rstatix’
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/pkgload_1.2.4.zip'
Content type 'application/zip' length 155868 bytes (152 KB)
downloaded 152 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/praise_1.0.0.zip'
Content type 'application/zip' length 19837 bytes (19 KB)
downloaded 19 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/waldo_0.4.0.zip'
Content type 'application/zip' length 102183 bytes (99 KB)
downloaded 99 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/testthat_3.1.3.zip'
Content type 'application/zip' length 2558147 bytes (2.4 MB)
downloaded 2.4 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/numDeriv_2016.8-1.1.zip'
Content type 'application/zip' length 116205 bytes (113 KB)
downloaded 113 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/SparseM_1.81.zip'
Content type 'application/zip' length 1066525 bytes (1.0 MB)
downloaded 1.0 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/MatrixModels_0.5-0.zip'
Content type 'application/zip' length 429091 bytes (419 KB)
downloaded 419 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/sp_1.4-6.zip'
Content type 'application/zip' length 2200540 bytes (2.1 MB)
downloaded 2.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/minqa_1.2.4.zip'
Content type 'application/zip' length 855878 bytes (835 KB)
downloaded 835 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/nloptr_2.0.0.zip'
Content type 'application/zip' length 1749120 bytes (1.7 MB)
downloaded 1.7 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/RcppEigen_0.3.3.9.1.zip'
Content type 'application/zip' length 2870044 bytes (2.7 MB)
downloaded 2.7 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/carData_3.0-5.zip'
Content type 'application/zip' length 1820557 bytes (1.7 MB)
downloaded 1.7 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/abind_1.4-5.zip'
Content type 'application/zip' length 63748 bytes (62 KB)
downloaded 62 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/pbkrtest_0.5.1.zip'
Content type 'application/zip' length 356907 bytes (348 KB)
downloaded 348 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/quantreg_5.88.zip'
Content type 'application/zip' length 1943351 bytes (1.9 MB)
downloaded 1.9 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/maptools_1.1-3.zip'
Content type 'application/zip' length 2220324 bytes (2.1 MB)
downloaded 2.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/lme4_1.1-28.zip'
Content type 'application/zip' length 5349300 bytes (5.1 MB)
downloaded 5.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/corrplot_0.92.zip'
Content type 'application/zip' length 3844791 bytes (3.7 MB)
downloaded 3.7 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/car_3.0-12.zip'
Content type 'application/zip' length 1413444 bytes (1.3 MB)
downloaded 1.3 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/ggrepel_0.9.1.zip'
Content type 'application/zip' length 1119220 bytes (1.1 MB)
downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/ggsci_2.9.zip'
Content type 'application/zip' length 2978469 bytes (2.8 MB)
downloaded 2.8 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/cowplot_1.1.1.zip'
Content type 'application/zip' length 1375525 bytes (1.3 MB)
downloaded 1.3 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/ggsignif_0.6.3.zip'
Content type 'application/zip' length 600832 bytes (586 KB)
downloaded 586 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/gridExtra_2.3.zip'
Content type 'application/zip' length 1109446 bytes (1.1 MB)
downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/polynom_1.4-0.zip'
Content type 'application/zip' length 312672 bytes (305 KB)
downloaded 305 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/rstatix_0.7.0.zip'
Content type 'application/zip' length 606899 bytes (592 KB)
downloaded 592 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/ggpubr_0.4.0.zip'
Content type 'application/zip' length 1906849 bytes (1.8 MB)
downloaded 1.8 MB
package ‘pkgload’ successfully unpacked and MD5 sums checked
package ‘praise’ successfully unpacked and MD5 sums checked
package ‘waldo’ successfully unpacked and MD5 sums checked
package ‘testthat’ successfully unpacked and MD5 sums checked
package ‘numDeriv’ successfully unpacked and MD5 sums checked
package ‘SparseM’ successfully unpacked and MD5 sums checked
package ‘MatrixModels’ successfully unpacked and MD5 sums checked
package ‘sp’ successfully unpacked and MD5 sums checked
package ‘minqa’ successfully unpacked and MD5 sums checked
package ‘nloptr’ successfully unpacked and MD5 sums checked
package ‘RcppEigen’ successfully unpacked and MD5 sums checked
package ‘carData’ successfully unpacked and MD5 sums checked
package ‘abind’ successfully unpacked and MD5 sums checked
package ‘pbkrtest’ successfully unpacked and MD5 sums checked
package ‘quantreg’ successfully unpacked and MD5 sums checked
package ‘maptools’ successfully unpacked and MD5 sums checked
package ‘lme4’ successfully unpacked and MD5 sums checked
package ‘corrplot’ successfully unpacked and MD5 sums checked
package ‘car’ successfully unpacked and MD5 sums checked
package ‘ggrepel’ successfully unpacked and MD5 sums checked
package ‘ggsci’ successfully unpacked and MD5 sums checked
package ‘cowplot’ successfully unpacked and MD5 sums checked
package ‘ggsignif’ successfully unpacked and MD5 sums checked
package ‘gridExtra’ successfully unpacked and MD5 sums checked
package ‘polynom’ successfully unpacked and MD5 sums checked
package ‘rstatix’ successfully unpacked and MD5 sums checked
package ‘ggpubr’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\alitt\AppData\Local\Temp\RtmpWGGjmm\downloaded_packages
It appears to me that based upon one of the last lines that package 'ggpubr' successfully unpacked.
So, I ran this:
library(ggpubr)
And this error message returned:
Error in library(ggpubr) : there is no package called ‘ggpubr’
I'm at a loss, and I appreciate any assistance!

I discovered that the library path is pointing to my OneDrive. Since that is not writable for RStudio, I added the custom path in the original install.packages() code. I went to my custom folder, copied all of the subdirectories and pasted them into the OneDrive folder. A little backwards, but it works, and I can move forward. Many thanks!

Related

Errors with running a GUI in R

I'm attempting to run a code in R that creates a GUI- this was developed by a coworker who is no longer working with us and I was given the task to attempt to get it working again. I don't have a programming background (just familiar with R) and am at a loss with how to address the errors I'm getting to install a package for the GUI. Here is the code:
> install("Radamas")
√ checking for file 'Q:\aquatic\AqDataTemp\Vanvj\R-ADAMAS\R\JaneVScripts\Radamas/DESCRIPTION' ...
- preparing 'Radamas': (22s)
√ checking DESCRIPTION meta-information
- checking for LF line-endings in source and make files and shell scripts (555ms)
- checking for empty or unneeded directories
- building 'Radamas_0.0.0.9000.tar.gz'
Running "C:/Users/VANVES~1/DOCUME~1/R/R-40~1.0/bin/x64/Rcmd.exe" INSTALL \
"C:\Users\VANVES~1\AppData\Local\Temp\10\Rtmps151dc/Radamas_0.0.0.9000.tar.gz" --install-tests
* installing to library 'C:/Users/vanvj/Documents/R/R-4.0.0/library'
* installing *source* package 'Radamas' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/RGtk2_2.20.36.zip'
Content type 'application/zip' length 16529627 bytes (15.8 MB)
==================================================
downloaded 15.8 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/RODBC_1.3-17.zip'
Content type 'application/zip' length 878540 bytes (857 KB)
==================================================
downloaded 857 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/DBI_1.1.0.zip'
Content type 'application/zip' length 656596 bytes (641 KB)
==================================================
downloaded 641 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/sqldf_0.4-11.zip'
Content type 'application/zip' length 78361 bytes (76 KB)
==================================================
downloaded 76 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/FSA_0.8.30.zip'
Content type 'application/zip' length 1223853 bytes (1.2 MB)
==================================================
downloaded 1.2 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/magrittr_1.5.zip'
Content type 'application/zip' length 157428 bytes (153 KB)
==================================================
downloaded 153 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/dplyr_1.0.0.zip'
Content type 'application/zip' length 1294122 bytes (1.2 MB)
==================================================
downloaded 1.2 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/plotrix_3.7-8.zip'
Content type 'application/zip' length 1134284 bytes (1.1 MB)
==================================================
downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/ggplot2_3.3.1.zip'
Content type 'application/zip' length 4018097 bytes (3.8 MB)
==================================================
downloaded 3.8 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/gridExtra_2ERROR: lazy loading failed for package 'Radamas'
.3.zip'
Content type 'application/zip' length 1109251 bytes (1.1 MB)
==================================================
downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/lubridate_1.7.9.zip'
Content type 'application/zip' length 1749669 bytes (1.7 MB)
==================================================
downloaded 1.7 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/devtools_2.3.0.zip'
Content type 'application/zip' length 350872 bytes (342 KB)
==================================================
downloaded 342 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/roxygen2_7.1.0.zip'
Content type 'application/zip' length 1372118 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/RColorBrewer_1.1-2.zip'
Content type 'application/zip' length 55583 bytes (54 KB)
==================================================
downloaded 54 KB
package 'RGtk2' successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package 'RGtk2'
Warning in file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\vanvj\Documents\R\R-4.0.0\library\00LOCK\RGtk2\gtk\x64\bin\libatk-1.0-0.dll to C:\Users\vanvj\Documents\R\R-4.0.0\library\RGtk2\gtk\x64\bin\libatk-1.0-0.dll: Permission denied
Warning in file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\vanvj\Documents\R\R-4.0.0\library\00LOCK\RGtk2\libs\x64\RGtk2.dll to C:\Users\vanvj\Documents\R\R-4.0.0\library\RGtk2\libs\x64\RGtk2.dll: Permission denied
Warning: restored 'RGtk2'
package 'RODBC' successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package 'RODBC'
Warning in file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\vanvj\Documents\R\R-4.0.0\library\00LOCK\RODBC\libs\x64\RODBC.dll to C:\Users\vanvj\Documents\R\R-4.0.0\library\RODBC\libs\x64\RODBC.dll: Permission denied
Warning: restored 'RODBC'
package 'DBI' successfully unpacked and MD5 sums checked
package 'sqldf' successfully unpacked and MD5 sums checked
package 'FSA' successfully unpacked and MD5 sums checked
package 'magrittr' successfully unpacked and MD5 sums checked
package 'dplyr' successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package 'dplyr'
Warning in file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\vanvj\Documents\R\R-4.0.0\library\00LOCK\dplyr\libs\x64\dplyr.dll to C:\Users\vanvj\Documents\R\R-4.0.0\library\dplyr\libs\x64\dplyr.dll: Permission denied
Warning: restored 'dplyr'
package 'plotrix' successfully unpacked and MD5 sums checked
package 'ggplot2' successfully unpacked and MD5 sums checked
package 'gridExtra' successfully unpacked and MD5 sums checked
package 'lubridate' successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package 'lubridate'
Warning in file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\Users\vanvj\Documents\R\R-4.0.0\library\00LOCK\lubridate\libs\x64\lubridate.dll to C:\Users\vanvj\Documents\R\R-4.0.0\library\lubridate\libs\x64\lubridate.dll: Permission denied
Warning: restored 'lubridate'
package 'devtools' successfully unpacked and MD5 sums checked
package 'roxygen2' successfully unpacked and MD5 sums checked
package 'RColorBrewer' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\vanvj\AppData\Local\Temp\10\Rtmpm2yhXI\downloaded_packages
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/RColorBrewer_1.1-2.zip'
Content type 'application/zip' length 55583 bytes (54 KB)
==================================================
downloaded 54 KB
|
package 'RColorBrewer' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\vanvj\AppData\Local\Temp\10\Rtmpm2yhXI\downloaded_packages
Error : Can't find 'C:\Users\VANVES~1\AppData\Local\Temp\10\RtmpSseu9k\R.INSTALL1a085e0947fd\Radamas\ABioQuery'.
Error: unable to load R code in package 'Radamas'
Execution halted
Error in (function (command = NULL, args = character(), error_on_status = TRUE, :
System command 'Rcmd.exe' failed, exit status: 1, stdout & stderr were printed
Type .Last.error.trace to see where the error occured
> .Last.error.trace
Stack trace:
1. devtools:::install("Radamas")
2. pkgbuild::with_build_tools(required = FALSE, callr::rcmd("INSTALL", ...
3. withr::with_path(rtools_path(), code)
4. base:::force(code)
5. callr::rcmd("INSTALL", c(install_path, opts), echo = !quiet, ...
6. callr:::run_r(options)
7. base:::with(options, with_envvar(env, do.call(processx::run, ...
8. base:::with.default(options, with_envvar(env, do.call(processx::run, ...
9. base:::eval(substitute(expr), data, enclos = parent.frame())
10. base:::eval(substitute(expr), data, enclos = parent.frame())
11. callr:::with_envvar(env, do.call(processx::run, c(list(bin, args = real_cmdargs, ...
12. base:::force(code)
13. base:::do.call(processx::run, c(list(bin, args = real_cmdargs, ...
14. (function (command = NULL, args = character(), error_on_status = TRUE, ...
15. throw(new_process_error(res, call = sys.call(), echo = echo, ...
x System command 'Rcmd.exe' failed, exit status: 1, stdout & stderr were printed
Could anyone at least point me in the direction of how to address this error? I admittedly don't even know what the errors are telling me, even after days of google searches. Thank you!
Well, the binary package is reported to be in
C:\Users\ vanvj \AppData\Local\Temp\10\Rtmpm2yhXI\downloaded_packages
and then the error message says it was looking in
Can't find 'C:\Users\ VANVES~1 \AppData\Local\Temp\10\RtmpSseu9k\R.INSTALL1a085e0947fd\Radamas\ABioQuery'.
That suggests that the originator of the package may have hard-coded his username into something in the build code. I'm not 100$ sure, but I'd start by looking in your appdata\local\temp\10... directories and see what you find.

error installing devtools in R 3.5.2 (probably related to rcmdcheck)

I'm not able to install packages from github using the install_github function in devtools. I have read many other questions on the topic but didn't find a solution. Here is my case:
I have just installed R 3.5.2 and R Studio 1.1.463. I have Rtools 3.5.0.4.
When I open Rstudio and try to install devtools with install.packages("devtools") I get the following log:
> install.packages("devtools")
Installing package into ‘C:/Users/davidri/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
also installing the dependencies ‘ps’, ‘magrittr’, ‘backports’, ‘Rcpp’, ‘ini’, ‘processx’, ‘R6’, ‘assertthat’, ‘crayon’, ‘curl’, ‘mime’, ‘openssl’, ‘desc’, ‘prettyunits’, ‘rprojroot’, ‘rlang’, ‘xopen’, ‘clipr’, ‘clisymbols’, ‘fs’, ‘gh’, ‘glue’, ‘whisker’, ‘callr’, ‘cli’, ‘digest’, ‘git2r’, ‘httr’, ‘jsonlite’, ‘memoise’, ‘pkgbuild’, ‘pkgload’, ‘rcmdcheck’, ‘remotes’, ‘rstudioapi’, ‘sessioninfo’, ‘usethis’, ‘withr’
There is a binary version available but the source version is later:
binary source needs_compilation
rcmdcheck 1.3.1 1.3.2 FALSE
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/ps_1.3.0.zip'
Content type 'application/zip' length 305676 bytes (298 KB)
downloaded 298 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/magrittr_1.5.zip'
Content type 'application/zip' length 155587 bytes (151 KB)
downloaded 151 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/backports_1.1.3.zip'
Content type 'application/zip' length 65997 bytes (64 KB)
downloaded 64 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/Rcpp_1.0.0.zip'
Content type 'application/zip' length 4479299 bytes (4.3 MB)
downloaded 4.3 MB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/ini_0.3.1.zip'
Content type 'application/zip' length 15467 bytes (15 KB)
downloaded 15 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/processx_3.2.1.zip'
Content type 'application/zip' length 306262 bytes (299 KB)
downloaded 299 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/R6_2.3.0.zip'
Content type 'application/zip' length 57273 bytes (55 KB)
downloaded 55 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/assertthat_0.2.0.zip'
Content type 'application/zip' length 53713 bytes (52 KB)
downloaded 52 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/crayon_1.3.4.zip'
Content type 'application/zip' length 749419 bytes (731 KB)
downloaded 731 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/curl_3.2.zip'
Content type 'application/zip' length 2986344 bytes (2.8 MB)
downloaded 2.8 MB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/mime_0.6.zip'
Content type 'application/zip' length 47811 bytes (46 KB)
downloaded 46 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/openssl_1.1.zip'
Content type 'application/zip' length 3937329 bytes (3.8 MB)
downloaded 3.8 MB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/desc_1.2.0.zip'
Content type 'application/zip' length 283292 bytes (276 KB)
downloaded 276 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/prettyunits_1.0.2.zip'
Content type 'application/zip' length 33096 bytes (32 KB)
downloaded 32 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/rprojroot_1.3-2.zip'
Content type 'application/zip' length 84007 bytes (82 KB)
downloaded 82 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/rlang_0.3.0.1.zip'
Content type 'application/zip' length 1031444 bytes (1007 KB)
downloaded 1007 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/xopen_1.0.0.zip'
Content type 'application/zip' length 24454 bytes (23 KB)
downloaded 23 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/clipr_0.4.1.zip'
Content type 'application/zip' length 37368 bytes (36 KB)
downloaded 36 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/clisymbols_1.2.0.zip'
Content type 'application/zip' length 20882 bytes (20 KB)
downloaded 20 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/fs_1.2.6.zip'
Content type 'application/zip' length 954023 bytes (931 KB)
downloaded 931 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/gh_1.0.1.zip'
Content type 'application/zip' length 49081 bytes (47 KB)
downloaded 47 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/glue_1.3.0.zip'
Content type 'application/zip' length 108422 bytes (105 KB)
downloaded 105 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/whisker_0.3-2.zip'
Content type 'application/zip' length 80986 bytes (79 KB)
downloaded 79 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/callr_3.1.1.zip'
Content type 'application/zip' length 245254 bytes (239 KB)
downloaded 239 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/cli_1.0.1.zip'
Content type 'application/zip' length 589903 bytes (576 KB)
downloaded 576 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/digest_0.6.18.zip'
Content type 'application/zip' length 194555 bytes (189 KB)
downloaded 189 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/git2r_0.23.0.zip'
Content type 'application/zip' length 2874053 bytes (2.7 MB)
downloaded 2.7 MB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/httr_1.4.0.zip'
Content type 'application/zip' length 496847 bytes (485 KB)
downloaded 485 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/jsonlite_1.6.zip'
Content type 'application/zip' length 1160524 bytes (1.1 MB)
downloaded 1.1 MB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/memoise_1.1.0.zip'
Content type 'application/zip' length 36540 bytes (35 KB)
downloaded 35 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/pkgbuild_1.0.2.zip'
Content type 'application/zip' length 128427 bytes (125 KB)
downloaded 125 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/pkgload_1.0.2.zip'
Content type 'application/zip' length 154873 bytes (151 KB)
downloaded 151 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/remotes_2.0.2.zip'
Content type 'application/zip' length 272964 bytes (266 KB)
downloaded 266 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/rstudioapi_0.8.zip'
Content type 'application/zip' length 178918 bytes (174 KB)
downloaded 174 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/sessioninfo_1.1.1.zip'
Content type 'application/zip' length 46417 bytes (45 KB)
downloaded 45 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/usethis_1.4.0.zip'
Content type 'application/zip' length 520837 bytes (508 KB)
downloaded 508 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/withr_2.1.2.zip'
Content type 'application/zip' length 151064 bytes (147 KB)
downloaded 147 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/devtools_2.0.1.zip'
Content type 'application/zip' length 383825 bytes (374 KB)
downloaded 374 KB
package ‘ps’ successfully unpacked and MD5 sums checked
package ‘magrittr’ successfully unpacked and MD5 sums checked
package ‘backports’ successfully unpacked and MD5 sums checked
package ‘Rcpp’ successfully unpacked and MD5 sums checked
package ‘ini’ successfully unpacked and MD5 sums checked
package ‘processx’ successfully unpacked and MD5 sums checked
package ‘R6’ successfully unpacked and MD5 sums checked
package ‘assertthat’ successfully unpacked and MD5 sums checked
package ‘crayon’ successfully unpacked and MD5 sums checked
package ‘curl’ successfully unpacked and MD5 sums checked
package ‘mime’ successfully unpacked and MD5 sums checked
package ‘openssl’ successfully unpacked and MD5 sums checked
package ‘desc’ successfully unpacked and MD5 sums checked
package ‘prettyunits’ successfully unpacked and MD5 sums checked
package ‘rprojroot’ successfully unpacked and MD5 sums checked
package ‘rlang’ successfully unpacked and MD5 sums checked
package ‘xopen’ successfully unpacked and MD5 sums checked
package ‘clipr’ successfully unpacked and MD5 sums checked
package ‘clisymbols’ successfully unpacked and MD5 sums checked
package ‘fs’ successfully unpacked and MD5 sums checked
package ‘gh’ successfully unpacked and MD5 sums checked
package ‘glue’ successfully unpacked and MD5 sums checked
package ‘whisker’ successfully unpacked and MD5 sums checked
package ‘callr’ successfully unpacked and MD5 sums checked
package ‘cli’ successfully unpacked and MD5 sums checked
package ‘digest’ successfully unpacked and MD5 sums checked
package ‘git2r’ successfully unpacked and MD5 sums checked
package ‘httr’ successfully unpacked and MD5 sums checked
package ‘jsonlite’ successfully unpacked and MD5 sums checked
package ‘memoise’ successfully unpacked and MD5 sums checked
package ‘pkgbuild’ successfully unpacked and MD5 sums checked
package ‘pkgload’ successfully unpacked and MD5 sums checked
package ‘remotes’ successfully unpacked and MD5 sums checked
package ‘rstudioapi’ successfully unpacked and MD5 sums checked
package ‘sessioninfo’ successfully unpacked and MD5 sums checked
package ‘usethis’ successfully unpacked and MD5 sums checked
package ‘withr’ successfully unpacked and MD5 sums checked
package ‘devtools’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\davidri\AppData\Local\Temp\RtmpGoihSi\downloaded_packages
installing the source package ‘rcmdcheck’
trying URL 'http://ftp.cixug.es/CRAN/src/contrib/rcmdcheck_1.3.2.tar.gz'
Content type 'application/x-gzip' length 1408582 bytes (1.3 MB)
downloaded 1.3 MB
In R CMD INSTALL
Warning in install.packages :
installation of package ‘rcmdcheck’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\davidri\AppData\Local\Temp\RtmpGoihSi\downloaded_packages’
QUESTION: can I assume devtools is properly installed based on this log?
Then I try to use devtools to install packages from github, but it doesn't work. That's why I think devtools is not properly installed. Example:
devtools::install_github("vinayudyawer/ATT")
Downloading GitHub repo vinayudyawer/ATT#master
Installing 36 packages: ade4, adehabitatHR, adehabitatLT, adehabitatMA, BH, bindr, bindrcpp, CircStats, colorspace, deldir, dplyr, fansi, filehash, ggplot2, gtable, labeling, lazyeval, lubridate, maptools, munsell, pillar, pkgconfig, plogr, plyr, purrr, raster, RColorBrewer, reshape2, scales, sp, stringi, stringr, tibble, tidyselect, utf8, viridisLite
Installing packages into ‘C:/Users/davidri/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/ade4_1.7-13.zip'
Content type 'application/zip' length 5204011 bytes (5.0 MB)
downloaded 5.0 MB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/adehabitatHR_0.4.15.zip'
Content type 'application/zip' length 1387759 bytes (1.3 MB)
downloaded 1.3 MB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/adehabitatLT_0.3.23.zip'
Content type 'application/zip' length 2344449 bytes (2.2 MB)
downloaded 2.2 MB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/adehabitatMA_0.3.12.zip'
Content type 'application/zip' length 843921 bytes (824 KB)
downloaded 824 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/BH_1.66.0-1.zip'
Content type 'application/zip' length 17880019 bytes (17.1 MB)
downloaded 17.1 MB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/bindr_0.1.1.zip'
Content type 'application/zip' length 17686 bytes (17 KB)
downloaded 17 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/bindrcpp_0.2.2.zip'
Content type 'application/zip' length 623724 bytes (609 KB)
downloaded 609 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/CircStats_0.2-6.zip'
Content type 'application/zip' length 172817 bytes (168 KB)
downloaded 168 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/colorspace_1.3-2.zip'
Content type 'application/zip' length 527859 bytes (515 KB)
downloaded 515 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/deldir_0.1-15.zip'
Content type 'application/zip' length 237915 bytes (232 KB)
downloaded 232 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/dplyr_0.7.8.zip'
Content type 'application/zip' length 3069483 bytes (2.9 MB)
downloaded 2.9 MB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/fansi_0.4.0.zip'
Content type 'application/zip' length 220201 bytes (215 KB)
downloaded 215 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/filehash_2.4-1.zip'
Content type 'application/zip' length 310000 bytes (302 KB)
downloaded 302 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/ggplot2_3.1.0.zip'
Content type 'application/zip' length 3621915 bytes (3.5 MB)
downloaded 3.5 MB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/gtable_0.2.0.zip'
Content type 'application/zip' length 85156 bytes (83 KB)
downloaded 83 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/labeling_0.3.zip'
Content type 'application/zip' length 61841 bytes (60 KB)
downloaded 60 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/lazyeval_0.2.1.zip'
Content type 'application/zip' length 166601 bytes (162 KB)
downloaded 162 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/lubridate_1.7.4.zip'
Content type 'application/zip' length 1569004 bytes (1.5 MB)
downloaded 1.5 MB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/maptools_0.9-4.zip'
Content type 'application/zip' length 2143336 bytes (2.0 MB)
downloaded 2.0 MB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/munsell_0.5.0.zip'
Content type 'application/zip' length 243588 bytes (237 KB)
downloaded 237 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/pillar_1.3.1.zip'
Content type 'application/zip' length 154980 bytes (151 KB)
downloaded 151 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/pkgconfig_2.0.2.zip'
Content type 'application/zip' length 22208 bytes (21 KB)
downloaded 21 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/plogr_0.2.0.zip'
Content type 'application/zip' length 18735 bytes (18 KB)
downloaded 18 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/plyr_1.8.4.zip'
Content type 'application/zip' length 1297496 bytes (1.2 MB)
downloaded 1.2 MB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/purrr_0.2.5.zip'
Content type 'application/zip' length 295158 bytes (288 KB)
downloaded 288 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/raster_2.8-4.zip'
Content type 'application/zip' length 3768262 bytes (3.6 MB)
downloaded 3.6 MB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/RColorBrewer_1.1-2.zip'
Content type 'application/zip' length 55444 bytes (54 KB)
downloaded 54 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/reshape2_1.4.3.zip'
Content type 'application/zip' length 625902 bytes (611 KB)
downloaded 611 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/scales_1.0.0.zip'
Content type 'application/zip' length 1064924 bytes (1.0 MB)
downloaded 1.0 MB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/sp_1.3-1.zip'
Content type 'application/zip' length 1869135 bytes (1.8 MB)
downloaded 1.8 MB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/stringi_1.2.4.zip'
Content type 'application/zip' length 15268347 bytes (14.6 MB)
downloaded 14.6 MB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/stringr_1.3.1.zip'
Content type 'application/zip' length 194509 bytes (189 KB)
downloaded 189 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/tibble_1.4.2.zip'
Content type 'application/zip' length 243931 bytes (238 KB)
downloaded 238 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/tidyselect_0.2.5.zip'
Content type 'application/zip' length 624866 bytes (610 KB)
downloaded 610 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/utf8_1.1.4.zip'
Content type 'application/zip' length 214701 bytes (209 KB)
downloaded 209 KB
trying URL 'http://ftp.cixug.es/CRAN/bin/windows/contrib/3.5/viridisLite_0.3.0.zip'
Content type 'application/zip' length 60491 bytes (59 KB)
downloaded 59 KB
package ‘ade4’ successfully unpacked and MD5 sums checked
package ‘adehabitatHR’ successfully unpacked and MD5 sums checked
package ‘adehabitatLT’ successfully unpacked and MD5 sums checked
package ‘adehabitatMA’ successfully unpacked and MD5 sums checked
package ‘BH’ successfully unpacked and MD5 sums checked
package ‘bindr’ successfully unpacked and MD5 sums checked
package ‘bindrcpp’ successfully unpacked and MD5 sums checked
package ‘CircStats’ successfully unpacked and MD5 sums checked
package ‘colorspace’ successfully unpacked and MD5 sums checked
package ‘deldir’ successfully unpacked and MD5 sums checked
package ‘dplyr’ successfully unpacked and MD5 sums checked
package ‘fansi’ successfully unpacked and MD5 sums checked
package ‘filehash’ successfully unpacked and MD5 sums checked
package ‘ggplot2’ successfully unpacked and MD5 sums checked
package ‘gtable’ successfully unpacked and MD5 sums checked
package ‘labeling’ successfully unpacked and MD5 sums checked
package ‘lazyeval’ successfully unpacked and MD5 sums checked
package ‘lubridate’ successfully unpacked and MD5 sums checked
package ‘maptools’ successfully unpacked and MD5 sums checked
package ‘munsell’ successfully unpacked and MD5 sums checked
package ‘pillar’ successfully unpacked and MD5 sums checked
package ‘pkgconfig’ successfully unpacked and MD5 sums checked
package ‘plogr’ successfully unpacked and MD5 sums checked
package ‘plyr’ successfully unpacked and MD5 sums checked
package ‘purrr’ successfully unpacked and MD5 sums checked
package ‘raster’ successfully unpacked and MD5 sums checked
package ‘RColorBrewer’ successfully unpacked and MD5 sums checked
package ‘reshape2’ successfully unpacked and MD5 sums checked
package ‘scales’ successfully unpacked and MD5 sums checked
package ‘sp’ successfully unpacked and MD5 sums checked
package ‘stringi’ successfully unpacked and MD5 sums checked
package ‘stringr’ successfully unpacked and MD5 sums checked
package ‘tibble’ successfully unpacked and MD5 sums checked
package ‘tidyselect’ successfully unpacked and MD5 sums checked
package ‘utf8’ successfully unpacked and MD5 sums checked
package ‘viridisLite’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\davidri\AppData\Local\Temp\RtmpGoihSi\downloaded_packages
Error in processx::run(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdout), :
System command error
Same when trying to install other packages from github such as...
> devtools:install_github("twitter/AnomalyDetection")
QUESTION: Is the problem related to the installation of devtools as I think? Any suggestion on how to solve it?
In case it helps:
> .libPaths()
[1] "C:/Users/davidri/Documents/R/win-library/3.5" "C:/Program Files/R/R-3.5.2/library"
> Sys.info()
sysname release version nodename machine
"Windows" "7 x64" "build 7601, Service Pack 1" "DAVIDPC" "x86-64"
login user effective_user
"davidri" "davidri" "davidri"
Many thanks
devtools isn't installed as its dependency rcmdcheck did not install
Try re-installing that
Thanks, it seems I cannot properly install crmdcheck either...
> install.packages("rcmdcheck")
Installing package into ‘C:/Users/davidri/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
There is a binary version available but the source version is later:
binary source needs_compilation
rcmdcheck 1.3.1 1.3.2 FALSE
installing the source package ‘rcmdcheck’
trying URL 'http://ftp.cixug.es/CRAN/src/contrib/rcmdcheck_1.3.2.tar.gz'
Content type 'application/x-gzip' length 1408582 bytes (1.3 MB)
downloaded 1.3 MB
In R CMD INSTALL
Warning in install.packages :
installation of package ‘rcmdcheck’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\davidri\AppData\Local\Temp\RtmpE9Zll0\downloaded_packages’

R error in package "glmnet": error backage foreach

I have R version 3.4.3. I'm working on a school project with glmnet.
I've tried to install the package and I didn't get any error code, but when I ask for with library(glmnet) I get these errors.
I have tried to remove it, installing it back, install foreach alone: the same problem!!
install.packages("glmnet", dependencies=TRUE)
Installing package into �C:/Users/freel_000/Documents/R/win-library/3.4�
(as �lib� is unspecified)
also installing the dependency �foreach�
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/foreach_1.4.4.zip'
Content type 'application/zip' length 388581 bytes (379 KB)
downloaded 379 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/glmnet_2.0-13.zip'
Content type 'application/zip' length 1769167 bytes (1.7 MB)
downloaded 1.7 MB
package ‘foreach’ successfully unpacked and MD5 sums checked
package ‘glmnet’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\freel_000\AppData\Local\Temp\Rtmpy4iKye\downloaded_packages`

Dplyr not installing

Took a quick google search and couldn't find any issues like this.
I'm trying to install dplyr but it freezes part way through.
install.packages("dplyr")
Installing package into ‘W:/Documents/R/win-library/3.3’
(as ‘lib’ is unspecified)
also installing the dependencies ‘assertthat’, ‘R6’, ‘Rcpp’, ‘magrittr’,
‘lazyeval’, ‘DBI’, ‘BH’
trying URL
'https://cran.mtu.edu/bin/windows/contrib/3.3/assertthat_0.1.zip'
Content type 'application/zip' length 44746 bytes (43 KB)
downloaded 43 KB
trying URL 'https://cran.mtu.edu/bin/windows/contrib/3.3/R6_2.1.2.zip'
Content type 'application/zip' length 271158 bytes (264 KB)
downloaded 264 KB
trying URL 'https://cran.mtu.edu/bin/windows/contrib/3.3/Rcpp_0.12.5.zip'
Content type 'application/zip' length 3225584 bytes (3.1 MB)
downloaded 3.1 MB
trying URL 'https://cran.mtu.edu/bin/windows/contrib/3.3/magrittr_1.5.zip'
Content type 'application/zip' length 149394 bytes (145 KB)
downloaded 145 KB
trying URL 'https://cran.mtu.edu/bin/windows/contrib/3.3/lazyeval_0.2.0.zip'
Content type 'application/zip' length 137792 bytes (134 KB)
downloaded 134 KB
trying URL 'https://cran.mtu.edu/bin/windows/contrib/3.3/DBI_0.4-1.zip'
Content type 'application/zip' length 207812 bytes (202 KB)
downloaded 202 KB
trying URL 'https://cran.mtu.edu/bin/windows/contrib/3.3/BH_1.60.0-2.zip'
Content type 'application/zip' length 15529281 bytes (14.8 MB)
downloaded 14.8 MB
trying URL 'https://cran.mtu.edu/bin/windows/contrib/3.3/dplyr_0.4.3.zip'
Content type 'application/zip' length 2393257 bytes (2.3 MB)
downloaded 2.3 MB
package ‘assertthat’ successfully unpacked and MD5 sums checked
package ‘R6’ successfully unpacked and MD5 sums checked
package ‘Rcpp’ successfully unpacked and MD5 sums checked
package ‘magrittr’ successfully unpacked and MD5 sums checked
package ‘lazyeval’ successfully unpacked and MD5 sums checked
package ‘DBI’ successfully unpacked and MD5 sums checked
After that it just stops and doesn't move on to BH or dplyr. It's been about 10 minutes and still says its running but nothing happening. I deleted them out of the library and tried installing again, as well as another time from a different source. No luck. Any idea what's happening?
Apparently a little bit of patience is the trick. Give it a good 10 minutes or so and walk away.
If you look at the relative sizes, BH is 5 times larger than the next largest file, and Rccp, its over 25 times as large as the rest of the ones that come before it. So it makes sense that it takes a bit longer.
As someone above said patience is the key. It is true. I waited for some 2-3 min In your case it might take more or less but it worked after that so please wait until it's done hope you will find it helpful

knitr installation in R, error

I am fighting Another day with knitr installation and I can not come with new solutions. Last I deleted knitr and tried to install again. Below is a whole console from the process, what is wrong???? I got error message (see below) that is appearing everytime I start R studio and install new packages.
R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
[Workspace loaded from ~/2016/KNUTSTORP/.RData]
> install.packages("knitr")
Installing package into ‘\\xxxxx.xxxxx/users/Eke/mali/Documents/R/win-library/3.1’
(as ‘lib’ is unspecified)
also installing the dependencies ‘mime’, ‘stringi’, ‘magrittr’, ‘evaluate’, ‘digest’, ‘formatR’, ‘highr’, ‘markdown’, ‘stringr’, ‘yaml’
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/mime_0.4.zip'
Content type 'application/zip' length 37255 bytes (36 Kb)
opened URL
downloaded 36 Kb
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/stringi_1.0-1.zip'
Content type 'application/zip' length 14266706 bytes (13.6 Mb)
opened URL
downloaded 13.6 Mb
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/magrittr_1.5.zip'
Content type 'application/zip' length 152098 bytes (148 Kb)
opened URL
downloaded 148 Kb
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/evaluate_0.9.zip'
Content type 'application/zip' length 42030 bytes (41 Kb)
opened URL
downloaded 41 Kb
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/digest_0.6.9.zip'
Content type 'application/zip' length 171597 bytes (167 Kb)
opened URL
downloaded 167 Kb
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/formatR_1.3.zip'
Content type 'application/zip' length 52426 bytes (51 Kb)
opened URL
downloaded 51 Kb
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/highr_0.5.1.zip'
Content type 'application/zip' length 35546 bytes (34 Kb)
opened URL
downloaded 34 Kb
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/markdown_0.7.7.zip'
Content type 'application/zip' length 165447 bytes (161 Kb)
opened URL
downloaded 161 Kb
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/stringr_1.0.0.zip'
Content type 'application/zip' length 83256 bytes (81 Kb)
opened URL
downloaded 81 Kb
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/yaml_2.1.13.zip'
Content type 'application/zip' length 180080 bytes (175 Kb)
opened URL
downloaded 175 Kb
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/knitr_1.12.3.zip'
Content type 'application/zip' length 811552 bytes (792 Kb)
opened URL
downloaded 792 Kb
package ‘mime’ successfully unpacked and MD5 sums checked
package ‘stringi’ successfully unpacked and MD5 sums checked
package ‘magrittr’ successfully unpacked and MD5 sums checked
package ‘evaluate’ successfully unpacked and MD5 sums checked
package ‘digest’ successfully unpacked and MD5 sums checked
package ‘formatR’ successfully unpacked and MD5 sums checked
package ‘highr’ successfully unpacked and MD5 sums checked
package ‘markdown’ successfully unpacked and MD5 sums checked
package ‘stringr’ successfully unpacked and MD5 sums checked
package ‘yaml’ successfully unpacked and MD5 sums checked
package ‘knitr’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\mali\AppData\Local\Temp\RtmpwHvHGn\downloaded_packages
Error: invalid version specification ‘NA’
In addition: Warning message:
In utils:::packageDescription(packageName, fields = "Version") :
no package 'knitr' was found
The output of the version
> version
platform i386-w64-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 3
minor 1.2
year 2014
month 10
day 31
svn rev 66913
language R
version.string R version 3.1.2 (2014-10-31)
nickname Pumpkin Helmet
As it was recommended I opened new session. But the Error is still the same. I tested several other packages and they work fine (i.e. nlme, lme4)
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
Error: invalid version specification ‘NA’
In addition: Warning message:
In utils:::packageDescription(packageName, fields = "Version") :
no package 'knitr' was found
[Workspace loaded from ~/R/TESTER/.RData]
What is even more strange is that knitr is somehow installed
Error: invalid version specification ‘NA’
In addition: Warning message:
In utils:::packageDescription(packageName, fields = "Version") :
no package 'knitr' was found
[Workspace loaded from ~/R/TESTER/.RData]
> library(knitr)
It does not give an error when loaded by library commend
When I install knitr in Rstudio than I got such comments
Installing packages into '\\xxx.xx/users/Eke/mali/Documents/R/win-library/3.3'
(as 'lib' is unspecified)
also installing the dependencies 'mime', 'stringi', 'magrittr', 'Rcpp'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/mime_0.4.zip'
Content type 'application/zip' length 37402 bytes (36 KB)
==================================================
downloaded 36 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/stringi_1.0-1.zip'
Content type 'application/zip' length 14302873 bytes (13.6 MB)
==================================================
downloaded 13.6 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/magrittr_1.5.zip'
Content type 'application/zip' length 149726 bytes (146 KB)
==================================================
downloaded 146 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/Rcpp_0.12.4.zip'
Content type 'application/zip' length 3249212 bytes (3.1 MB)==================================================
downloaded 3.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/evaluate_0.9.zip'
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trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/digest_0.6.9.zip'
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trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/formatR_1.3.zip'
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trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/highr_0.5.1.zip'
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trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/markdown_0.7.7.zip'
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trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/stringr_1.0.0.zip'
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trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/yaml_2.1.13.zip'
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trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/htmltools_0.3.5.zip'
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trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/caTools_1.17.1.zip'
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downloaded 280 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/bitops_1.0-6.zip'
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downloaded 35 KB
package 'mime' successfully unpacked and MD5 sums checked
package 'stringi' successfully unpacked and MD5 sums checked
package 'magrittr' successfully unpacked and MD5 sums checked
package 'Rcpp' successfully unpacked and MD5 sums checked
package 'evaluate' successfully unpacked and MD5 sums checked
package 'digest' successfully unpacked and MD5 sums checked
package 'formatR' successfully unpacked and MD5 sums checked
package 'highr' successfully unpacked and MD5 sums checked
package 'markdown' successfully unpacked and MD5 sums checked
package 'stringr' successfully unpacked and MD5 sums checked
package 'yaml' successfully unpacked and MD5 sums checked
package 'htmltools' successfully unpacked and MD5 sums checked
package 'caTools' successfully unpacked and MD5 sums checked
package 'bitops' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\mali\AppData\Local\Temp\RtmpeK2q5y\downloaded_packages
Installing packages into '\\xxxxx.xxxx/users/Eke/mali/Documents/R/win-library/3.3'
(as 'lib' is unspecified)
also installing the dependencies 'mime', 'stringi', 'magrittr', 'Rcpp', 'bitops', 'evaluate', 'digest', 'formatR', 'highr', 'markdown', 'stringr', 'yaml', 'htmltools', 'caTools'
trying URL 'https://cran.rstudio.com/src/contrib/mime_0.4.tar.gz'
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trying URL 'https://cran.rstudio.com/src/contrib/stringi_1.0-1.tar.gz'
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trying URL 'https://cran.rstudio.com/src/contrib/magrittr_1.5.tar.gz'
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trying URL 'https://cran.rstudio.com/src/contrib/Rcpp_0.12.4.tar.gz'
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trying URL 'https://cran.rstudio.com/src/contrib/bitops_1.0-6.tar.gz'
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trying URL 'https://cran.rstudio.com/src/contrib/evaluate_0.9.tar.gz'
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trying URL 'https://cran.rstudio.com/src/contrib/digest_0.6.9.tar.gz'
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trying URL 'https://cran.rstudio.com/src/contrib/formatR_1.3.tar.gz'
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'\\xxxx.xxx\users\Eke\mali\Documents\R\TESTER'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
* installing *source* package 'mime' ...
** package 'mime' successfully unpacked and MD5 sums checked
** libs
*** arch - i386
Warning: running command 'make -f "C:/PROGRA~1/R/R-33~1.0/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-33~1.0/share/make/winshlib.mk" SHLIB="mime.dll" OBJECTS="rawmatch.o"' had status 127
ERROR: compilation failed for package 'mime'
* removing '\\xxxx-xxx/users/Eke/mali/Documents/R/win-library/3.3/mime'
* restoring previous '\\xxxx.xxxx/users/Eke/mali/Documents/R/win-library/3.3/mime'
'\\xxxxx.xxxx\users\Eke\mali\Documents\R\TESTER'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
* installing *source* package 'stringi' ...
** package 'stringi' successfully unpacked and MD5 sums checked
Warning: running command 'sh ./configure.win' had status 127
ERROR: configuration failed for package 'stringi'
* removing '\\xxxxxxx.xxxx/users/Eke/mali/Documents/R/win-library/3.3/stringi'
* restoring previous '\\xxxxx.xxxx/users/Eke/mali/Documents/R/win-library/3.3/stringi'
'\\xxxxx.xxxxxxx\users\Eke\mali\Documents\R\TESTER'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
* installing *source* package 'magrittr' ...
** package 'magrittr' successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
Warning in file(con, "w") :
cannot open file '\\xxxxx.xxxxxx/users/Eke/mali/Documents/R/win-library/3.3/magrittr/doc/index.html': No such file or directory
Error in file(con, "w") : cannot open the connection
ERROR: installing vignettes failed
* removing '\\xxxxx.xxxxx/users/Eke/mali/Documents/R/win-library/3.3/magrittr'
* restoring previous '\\xxxxx.xxxxxx/users/Eke/mali/Documents/R/win-library/3.3/magrittr'
'\\xxxxxx.xxxxxx\users\Eke\mali\Documents\R\TESTER'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
* installing *source* package 'Rcpp' ...
** package 'Rcpp' successfully unpacked and MD5 sums checked
I followed #Richie_Cotton proposal without succés
> .libPaths()
[1] "\\\\xxxxx.xxx/users/Eke/mali/Documents/R/win-library/3.3" "C:/Program Files/R/R-3.3.0/library"
> .libPaths("\\\\xxxxxx.xxx/users/Eke/mali/Documents/R/win-library/new")
> .libPaths()
[1] "\\\\xxxxxx.xxx/users/Eke/mali/Documents/R/win-library/new" "C:/Program Files/R/R-3.3.0/library"
> install.packages("knitr", dependencies = F)
Installing package into ‘\\xxxxxx.xxx/users/Eke/mali/Documents/R/win-library/new’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/knitr_1.12.3.zip'
Content type 'application/zip' length 812072 bytes (793 KB)
downloaded 793 KB
package ‘knitr’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\mali\AppData\Local\Temp\RtmpmwdUSv\downloaded_packages
Error: invalid version specification ‘NA’
In addition: Warning message:
In utils:::packageDescription(packageName, fields = "Version") :
no package 'knitr' was found
>
I user taceback but I do not know how to translate the result
5: stop(gettextf("invalid version specification %s", paste(sQuote(unique(x[!ok])),
collapse = ", ")), call. = FALSE, domain = NA)
4: .make_numeric_version(x, strict, .standard_regexps()$valid_package_version,
"package_version")
3: package_version(utils:::packageDescription(packageName, fields = "Version"))
2: .rs.getPackageVersion("knitr")
1: (function (markdownVersion, stitchVersion)
{
caps <- list()
caps$r_markdown_supported = .rs.scalar(FALSE)
caps$stitch_supported = .rs.scalar(FALSE)
if (.rs.isPackageInstalled("knitr")) {
knitrVersion <- .rs.getPackageVersion("knitr")
caps$r_markdown_supported = .rs.scalar(knitrVersion >=
markdownVersion)
caps$stitch_supported = .rs.scalar(knitrVersion >= stitchVersion)
}
return(caps)
})("1.2", "1.2")
>
It isn't clear from the question where things are going wrong, so you need a strategy to locate the problem. If possible, use the latest version of R for this.
When you install the packages use a fresh session. Additionally, install to a new library location so you can see exactly what is happening. You can always copy the contents of this library over to you existing library afterwards. To do this, create a new directory where you have write permissions (inside your home folder perhaps). Then when you call install.packages, use the lib.loc arguemnt to install to that location.
Rather than calling install.packages("knitr"), install each of the dependencies one by one, to see which one is causing the problem. That is, install.packages("mime"), then install.packages("stringi"), and so on. You can see the list of all the packages that you need in your question (or use packageDescription("knitr").
If you receive an error, use traceback() to see where the error occured, and include these details in your question in you need further help.
Facing the same problem, creating R_LIBS_USER in Windows environmental variables did the trick for me.
See Eric Krantz's comment here. The approach works for both Windows7 and 10.
I copied my knitr folder and its dependencies from
C:\Users\MB\Documents\R\win-library
to
C:\Program Files\R\R-4.1.3\library
Afterwards, I did not have any longer this error message :
Error: invalid version specification ‘NA’
In addition: Warning message:
In utils:::packageDescription(packageName, fields = "Version") :
no package 'knitr' was found

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