Reputation: 1867

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'
Content type 'application/zip' length 41981 bytes (40 KB)
==================================================
downloaded 40 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/digest_0.6.9.zip'
Content type 'application/zip' length 169286 bytes (165 KB)
==================================================
downloaded 165 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/formatR_1.3.zip'
Content type 'application/zip' length 52656 bytes (51 KB)
==================================================
downloaded 51 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/highr_0.5.1.zip'
Content type 'application/zip' length 35637 bytes (34 KB)
==================================================
downloaded 34 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/markdown_0.7.7.zip'
Content type 'application/zip' length 167151 bytes (163 KB)==================================================
downloaded 163 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/stringr_1.0.0.zip'
Content type 'application/zip' length 83315 bytes (81 KB)
==================================================
downloaded 81 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/yaml_2.1.13.zip'
Content type 'application/zip' length 175748 bytes (171 KB)
==================================================
downloaded 171 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/htmltools_0.3.5.zip'
Content type 'application/zip' length 571964 bytes (558 KB)==================================================
downloaded 558 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/caTools_1.17.1.zip'
Content type 'application/zip' length 287027 bytes (280 KB)==================================================
downloaded 280 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/bitops_1.0-6.zip'
Content type 'application/zip' length 36372 bytes (35 KB)
==================================================
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'
Content type 'application/x-gzip' length 12545 bytes (12 KB)
==================================================
downloaded 12 KB

trying URL 'https://cran.rstudio.com/src/contrib/stringi_1.0-1.tar.gz'
Content type 'application/x-gzip' length 3643002 bytes (3.5 MB)==================================================
downloaded 3.5 MB

trying URL 'https://cran.rstudio.com/src/contrib/magrittr_1.5.tar.gz'
Content type 'application/x-gzip' length 200504 bytes (195 KB)==================================================
downloaded 195 KB

trying URL 'https://cran.rstudio.com/src/contrib/Rcpp_0.12.4.tar.gz'
Content type 'application/x-gzip' length 2402065 bytes (2.3 MB)==================================================
downloaded 2.3 MB

trying URL 'https://cran.rstudio.com/src/contrib/bitops_1.0-6.tar.gz'
Content type 'application/x-gzip' length 8734 bytes
==================================================
downloaded 8734 bytes

trying URL 'https://cran.rstudio.com/src/contrib/evaluate_0.9.tar.gz'
Content type 'application/x-gzip' length 19165 bytes (18 KB)
==================================================
downloaded 18 KB

trying URL 'https://cran.rstudio.com/src/contrib/digest_0.6.9.tar.gz'
Content type 'application/x-gzip' length 116746 bytes (114 KB)
==================================================
downloaded 114 KB

trying URL 'https://cran.rstudio.com/src/contrib/formatR_1.3.tar.gz'
Content type 'application/x-gzip' length 28139 bytes (27 KB)==================================================
downloaded 27 KB

trying URL 'https://cran.rstudio.com/src/contrib/highr_0.5.1.tar.gz'
Content type 'application/x-gzip' length 16744 bytes (16 KB)
==================================================
downloaded 16 KB

trying URL 'https://cran.rstudio.com/src/contrib/markdown_0.7.7.tar.gz'
Content type 'application/x-gzip' length 79427 bytes (77 KB)==================================================
downloaded 77 KB

trying URL 'https://cran.rstudio.com/src/contrib/stringr_1.0.0.tar.gz'
Content type 'application/x-gzip' length 34880 bytes (34 KB)
==================================================
downloaded 34 KB

trying URL 'https://cran.rstudio.com/src/contrib/yaml_2.1.13.tar.gz'
Content type 'application/x-gzip' length 81045 bytes (79 KB)
==================================================
downloaded 79 KB

trying URL 'https://cran.rstudio.com/src/contrib/htmltools_0.3.5.tar.gz'
Content type 'application/x-gzip' length 44048 bytes (43 KB)
==================================================
downloaded 43 KB

trying URL 'https://cran.rstudio.com/src/contrib/caTools_1.17.1.tar.gz'
Content type 'application/x-gzip' length 63358 bytes (61 KB)
==================================================
downloaded 61 KB

trying URL 'https://cran.rstudio.com/src/contrib/knitr_1.12.3.tar.gz'
Content type 'application/x-gzip' length 830827 bytes (811 KB)==================================================
downloaded 811 KB

trying URL 'https://cran.rstudio.com/src/contrib/rmarkdown_0.9.6.tar.gz'
Content type 'application/x-gzip' length 2013956 bytes (1.9 MB)==================================================
downloaded 1.9 MB

'\\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")
>

Upvotes: 5

Answers (3)

Markus Bauer

Reputation: 165

I copied my knitr folder and its dependencies from

C:\Users\MB\Documents\R\win-library

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

Upvotes: 0

Luks

Reputation: 143

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.

Upvotes: 1

Richie Cotton

Reputation: 121187

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.

Upvotes: 2

knitr installation in R, error

Answers (3)

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