Mateusz1981 Mateusz1981 - 20 days ago 6
R Question

Why do I get this error installing rmarkdown

I try to use

rmarkdown
and I've got many troubles so far. The first one is when the Rstudio as if it should install new versions of packages. It can not go over it. I tried to install one by one all the required packages but than I got this error

trying URL 'https://cran.rstudio.com/bin/windows/contrib/2.15/knitr_1.5.zip'
Content type 'application/zip' length 910172 bytes (888 Kb)
opened URL
downloaded 888 Kb

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 ‘knitr’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\mali\AppData\Local\Temp\Rtmpcz1Ywk\downloaded_packages
Error: invalid version specification ‘NA’
In addition: Warning message:
In utils:::packageDescription(packageName, fields = "Version") :
no package 'knitr' was found


I installed packages one by one and I can load them but it does not work as a whole i.r. file -> new -> rmarkdown

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=Swedish_Sweden.1252 LC_CTYPE=Swedish_Sweden.1252 LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C
[5] LC_TIME=Swedish_Sweden.1252

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] rmarkdown_0.9.6 knitr_1.12.3

loaded via a namespace (and not attached):
[1] digest_0.6.9 htmltools_0.3.5 Rcpp_0.12.4 tools_3.1.2


I spotted recently that I got this kind of message when starting Rstudio

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.

Error: invalid version specification ‘NA’
In addition: Warning message:
In utils:::packageDescription(packageName, fields = "Version") :
no package 'knitr' was found
>


I did as @DAV recommended. Tried to install other version. No success

> url <- "https://cran.r-project.org/src/contrib/Archive/knitr/knitr_1.0.tar.gz"
> install.packages(url, repos=NULL, type="source")
Installing package into ‘\\xxx/users/Eke/mali/Documents/R/win-library/3.1’
(as ‘lib’ is unspecified)
trying URL 'https://cran.r-project.org/src/contrib/Archive/knitr/knitr_1.0.tar.gz'
Content type 'application/x-gzip' length 451348 bytes (440 Kb)
opened URL
downloaded 440 Kb

* installing *source* package 'knitr' ...
** package 'knitr' successfully unpacked and MD5 sums checked
** R
** demo
** inst
** preparing package for lazy loading
Warning in file(con, "r") :
file("") only supports open = "w+" and open = "w+b": using the former
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Warning in library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE) :
there is no package called 'knitr'
Error: loading failed
Execution halted
ERROR: loading failed
* removing '\\xxxxxx/users/Eke/mali/Documents/R/win-library/3.1/knitr'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-31~1.2/bin/i386/R" CMD INSTALL -l "\\xxxxx\users\Eke\mali\Documents\R\win-library\3.1" "C:/Users/mali/AppData/Local/Temp/RtmpoN1qrM/downloaded_packages/knitr_1.0.tar.gz"' had status 1
Warning in install.packages :
installation of package ‘C:/Users/mali/AppData/Local/Temp/RtmpoN1qrM/downloaded_packages/knitr_1.0.tar.gz’ had non-zero exit status


It drives me crazy. I uninstalled "knitr" and tried to install again. ERROR

> install.packages("knitr", dependencies = F)
Installing package into ‘\\xxxx.se/users/Eke/mali/Documents/R/win-library/3.1’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/knitr_1.12.3.zip'
Content type 'application/zip' length 812186 bytes (793 Kb)
opened URL
downloaded 793 Kb

package ‘knitr’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\mali\AppData\Local\Temp\RtmpaChLQ5\downloaded_packages
Error: invalid version specification ‘NA’
In addition: Warning message:
In utils:::packageDescription(packageName, fields = "Version") :
no package 'knitr' was found


And it happened when I wanted to install
shiny


> install.packages("shiny", dependencies = F)
Installing package into ‘\\xxxxx.xxx/users/Eke/mali/Documents/R/win-library/3.1’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.1/shiny_0.13.2.zip'
Content type 'application/zip' length 2257481 bytes (2.2 Mb)
opened URL
downloaded 2.2 Mb

package ‘shiny’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\mali\AppData\Local\Temp\RtmpC0nOFC\downloaded_packages
Error: invalid version specification ‘NA’
In addition: Warning message:
In utils:::packageDescription(packageName, fields = "Version") :
no package 'knitr' was found

Answer

I was having the same issue you are describing here. The easiest solution I found was to tell RStudio the location of your library through the .libPaths() command and then manually selecting knitr and the other packages necessary to use the "rmarkdown" documents in RStudio through the Packages window in your screen. Hope it will work for you too.

getwd()

**"C:/Users/s146753/Dropbox/Chapter 2"

.libpaths()

**"\\home2.bio.ed.ac.uk/s146753/R/win-library/3.3" "C:/Program Files/R/R-3.3.2/library"

.libPaths("C:/Program Files/R/R-3.3.2/library")
.libPaths()

**"C:/Program Files/R/R-3.3.2/library"