keep asking to install markdown and knitr????

cmiranda · September 8, 2022, 10:36am

Until yesterday, everything was ok. Today, after upgrading some packages, starts to ask to install markdown and knitr. I've installed the latest version of R-Studio but keeps showing the same message when I knit a file. Even after installing the required packages. I don't know what to do.
This is what I get:

** Installing R Packages: 'rmarkdown', 'knitr'



[1/5] Installing bslib...

Installing package into 'C:/Users/user/Documents/R/win-library/3.6'
(as 'lib' is unspecified)
also installing the dependency 'htmltools'


  There are binary versions available but the source versions are later:
           binary source needs_compilation
htmltools 0.5.1.1  0.5.3              TRUE
bslib       0.2.4  0.4.0             FALSE

  Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/htmltools_0.5.1.1.zip'
Content type 'application/zip' length 242935 bytes (237 KB)
==================================================
downloaded 237 KB

package 'htmltools' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\user\AppData\Local\Temp\Rtmp6FKfJu\downloaded_packages
installing the source package 'bslib'

trying URL 'https://cran.rstudio.com/src/contrib/bslib_0.4.0.tar.gz'
Content type 'application/x-gzip' length 4835866 bytes (4.6 MB)
==================================================
downloaded 4.6 MB

* installing *source* package 'bslib' ...
** package 'bslib' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  namespace 'htmltools' 0.5.1.1 is being loaded, but >= 0.5.2 is required
Calls: <Anonymous> ... withCallingHandlers -> loadNamespace -> namespaceImport -> loadNamespace
Execution halted
ERROR: lazy loading failed for package 'bslib'
* removing 'C:/Users/user/Documents/R/win-library/3.6/bslib'


[2/5] Installing xfun...


The downloaded source packages are in
	'C:\Users\user\AppData\Local\Temp\Rtmp6FKfJu\downloaded_packages'
Installing package into 'C:/Users/user/Documents/R/win-library/3.6'
(as 'lib' is unspecified)

  There is a binary version available but the source version is later:
     binary source needs_compilation
xfun   0.22   0.32              TRUE

  Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/xfun_0.22.zip'
Content type 'application/zip' length 323923 bytes (316 KB)
==================================================
downloaded 316 KB

package 'xfun' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\user\AppData\Local\Temp\Rtmp6FKfJu\downloaded_packages


[3/5] Installing knitr...

Installing package into 'C:/Users/user/Documents/R/win-library/3.6'
(as 'lib' is unspecified)
also installing the dependency 'xfun'


  There are binary versions available but the source versions are later:
      binary source needs_compilation
xfun    0.22   0.32              TRUE
knitr   1.33   1.40             FALSE

  Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/xfun_0.22.zip'
Content type 'application/zip' length 323923 bytes (316 KB)
==================================================
downloaded 316 KB

package 'xfun' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\user\AppData\Local\Temp\Rtmp6FKfJu\downloaded_packages
installing the source package 'knitr'

trying URL 'https://cran.rstudio.com/src/contrib/knitr_1.40.tar.gz'
Content type 'application/x-gzip' length 903328 bytes (882 KB)
==================================================
downloaded 882 KB

* installing *source* package 'knitr' ...
** package 'knitr' successfully unpacked and MD5 sums checked
** using staged installation
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  namespace 'xfun' 0.22 is being loaded, but >= 0.29 is required
Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace
Execution halted
ERROR: lazy loading failed for package 'knitr'
* removing 'C:/Users/user/Documents/R/win-library/3.6/knitr'


[4/5] Installing tinytex...


The downloaded source packages are in
	'C:\Users\user\AppData\Local\Temp\Rtmp6FKfJu\downloaded_packages'
Installing package into 'C:/Users/user/Documents/R/win-library/3.6'
(as 'lib' is unspecified)
also installing the dependency 'xfun'


  There are binary versions available but the source versions are later:
        binary source needs_compilation
xfun      0.22   0.32              TRUE
tinytex   0.31   0.41             FALSE

  Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/xfun_0.22.zip'
Content type 'application/zip' length 323923 bytes (316 KB)
==================================================
downloaded 316 KB

package 'xfun' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\user\AppData\Local\Temp\Rtmp6FKfJu\downloaded_packages
installing the source package 'tinytex'

trying URL 'https://cran.rstudio.com/src/contrib/tinytex_0.41.tar.gz'
Content type 'application/x-gzip' length 32910 bytes (32 KB)
==================================================
downloaded 32 KB

* installing *source* package 'tinytex' ...
** package 'tinytex' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  namespace 'xfun' 0.22 is being loaded, but >= 0.29 is required
Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace
Execution halted
ERROR: lazy loading failed for package 'tinytex'
* removing 'C:/Users/user/Documents/R/win-library/3.6/tinytex'


[5/5] Installing rmarkdown...


The downloaded source packages are in
	'C:\Users\user\AppData\Local\Temp\Rtmp6FKfJu\downloaded_packages'
Installing package into 'C:/Users/user/Documents/R/win-library/3.6'
(as 'lib' is unspecified)
also installing the dependencies 'htmltools', 'bslib', 'knitr', 'tinytex', 'xfun'


  There are binary versions available but the source versions are later:
           binary source needs_compilation
htmltools 0.5.1.1  0.5.3              TRUE
bslib       0.2.4  0.4.0             FALSE
knitr        1.33   1.40             FALSE
tinytex      0.31   0.41             FALSE
xfun         0.22   0.32              TRUE
rmarkdown     2.8   2.16             FALSE

  Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/htmltools_0.5.1.1.zip'
Content type 'application/zip' length 242935 bytes (237 KB)
==================================================
downloaded 237 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/xfun_0.22.zip'
Content type 'application/zip' length 323923 bytes (316 KB)
==================================================
downloaded 316 KB

package 'htmltools' successfully unpacked and MD5 sums checked
package 'xfun' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\user\AppData\Local\Temp\Rtmp6FKfJu\downloaded_packages
installing the source packages 'bslib', 'knitr', 'tinytex', 'rmarkdown'

trying URL 'https://cran.rstudio.com/src/contrib/bslib_0.4.0.tar.gz'
Content type 'application/x-gzip' length 4835866 bytes (4.6 MB)
==================================================
downloaded 4.6 MB

trying URL 'https://cran.rstudio.com/src/contrib/knitr_1.40.tar.gz'
Content type 'application/x-gzip' length 903328 bytes (882 KB)
==================================================
downloaded 882 KB

trying URL 'https://cran.rstudio.com/src/contrib/tinytex_0.41.tar.gz'
Content type 'application/x-gzip' length 32910 bytes (32 KB)
==================================================
downloaded 32 KB

trying URL 'https://cran.rstudio.com/src/contrib/rmarkdown_2.16.tar.gz'
Content type 'application/x-gzip' length 3243854 bytes (3.1 MB)
==================================================
downloaded 3.1 MB

* installing *source* package 'bslib' ...
** package 'bslib' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  namespace 'htmltools' 0.5.1.1 is being loaded, but >= 0.5.2 is required
Calls: <Anonymous> ... withCallingHandlers -> loadNamespace -> namespaceImport -> loadNamespace
Execution halted
ERROR: lazy loading failed for package 'bslib'
* removing 'C:/Users/user/Documents/R/win-library/3.6/bslib'
* installing *source* package 'knitr' ...
** package 'knitr' successfully unpacked and MD5 sums checked
** using staged installation
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  namespace 'xfun' 0.22 is being loaded, but >= 0.29 is required
Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace
Execution halted
ERROR: lazy loading failed for package 'knitr'
* removing 'C:/Users/user/Documents/R/win-library/3.6/knitr'
* installing *source* package 'tinytex' ...
** package 'tinytex' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  namespace 'xfun' 0.22 is being loaded, but >= 0.29 is required
Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace
Execution halted
ERROR: lazy loading failed for package 'tinytex'
* removing 'C:/Users/user/Documents/R/win-library/3.6/tinytex'
ERROR: dependencies 'bslib', 'knitr', 'tinytex' are not available for package 'rmarkdown'
* removing 'C:/Users/user/Documents/R/win-library/3.6/rmarkdown'

The downloaded source packages are in
	'C:\Users\user\AppData\Local\Temp\Rtmp6FKfJu\downloaded_packages'


<U+2714> Packages successfully installed.
Warning messages:
1: In utils::install.packages("bslib", repos = "https://cran.rstudio.com/") :
  installation of package 'bslib' had non-zero exit status
2: In utils::install.packages("knitr", repos = "https://cran.rstudio.com/") :
  installation of package 'knitr' had non-zero exit status
3: In utils::install.packages("tinytex", repos = "https://cran.rstudio.com/") :
  installation of package 'tinytex' had non-zero exit status
4: In utils::install.packages("rmarkdown", repos = "https://cran.rstudio.com/") :
  installation of package 'bslib' had non-zero exit status
5: In utils::install.packages("rmarkdown", repos = "https://cran.rstudio.com/") :
  installation of package 'knitr' had non-zero exit status
6: In utils::install.packages("rmarkdown", repos = "https://cran.rstudio.com/") :
  installation of package 'tinytex' had non-zero exit status
7: In utils::install.packages("rmarkdown", repos = "https://cran.rstudio.com/") :
  installation of package 'rmarkdown' had non-zero exit status

andresrcs · September 8, 2022, 12:06pm

The problem is that you are using an old R version, there are no binaries of the latest package versions available for it and you do not have a compiler (RTools) installed in your system to install them from source.

I think the easiest solution for your problem would be to update R to the latest version 4.2.1, otherwise install and configure a suitable version of RTools in your system.

RStudio is an IDE (Integrated Development Environment) for the R programming language but it doesn't come with R bundled, they can have independent versions and your RStudio version has no effect on your R package library.

system · September 29, 2022, 12:06pm

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