[R] rmarkdown linux mint 17

[Sun Shine]

Hi Aurora

I wonder if the problem you are having concerns the GCC (GNU c) compiler 
rather than R itself? I know it doesn't help you, but using the exact 
same rig as yourself, rmarkdown installed successful after pulling down 
the dependencies it needs.

As sudo, check: apt-cache search gcc as it should already be installed.

If not, or just to be sure, run the following:

sudo apt-get update
sudo apt-get upgrade
sudo apt-get install build-essential
gcc -V
make -V

and then restart R and try the installation of rmarkdown again.

Hope this helps.
Sun

On 10/04/15 12:22, AURORA GONZALEZ VIDAL wrote:
> Hello.
> I am trying to intstall the R package "rmarkdown" in my linux mint 17
> quiana computer but I'm having strange problems:
> install.packages("rmarkdown") returns errors when installing the
> dependencies such as mime, digest, bitops, yaml, knitr...etc. And
> installing one by one it happens the same.
>
> The errors are:
> * installing *source* package ‘mime’ ...
> ** package ‘mime’ successfully unpacked and MD5 sums checked
> ** libs
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3
> -pipe  -g  -c rawmatch.c -o rawmatch.o
> In file included from rawmatch.c:1:0:
> /usr/share/R/include/R.h:28:20: fatal error: stdlib.h: No existe el archivo
> o el directorio
>   #include <stdlib.h>
>                      ^
> compilation terminated.
> make: *** [rawmatch.o] Error 1
> ERROR: compilation failed for package ‘mime’
> * removing ‘/home/aurora/R/i686-pc-linux-gnu-library/3.0/mime’
> Warning in install.packages :
>    installation of package ‘mime’ had non-zero exit status
> * installing *source* package ‘digest’ ...
> ** package ‘digest’ successfully unpacked and MD5 sums checked
> ** libs
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3
> -pipe  -g  -c aes.c -o aes.o
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3
> -pipe  -g  -c crc32.c -o crc32.o
> In file included from crc32.c:23:0:
> zutil.h:21:22: fatal error: string.h: No existe el archivo o el directorio
>   #  include <string.h>
>                        ^
> compilation terminated.
> make: *** [crc32.o] Error 1
> ERROR: compilation failed for package ‘digest’
> * removing ‘/home/aurora/R/i686-pc-linux-gnu-library/3.0/digest’
> Warning in install.packages :
>    installation of package ‘digest’ had non-zero exit status
> * installing *source* package ‘bitops’ ...
> ** package ‘bitops’ successfully unpacked and MD5 sums checked
> ** libs
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3
> -pipe  -g  -c bit-ops.c -o bit-ops.o
> In file included from bit-ops.c:1:0:
> /usr/share/R/include/R.h:28:20: fatal error: stdlib.h: No existe el archivo
> o el directorio
>   #include <stdlib.h>
>                      ^
> compilation terminated.
> make: *** [bit-ops.o] Error 1
> ERROR: compilation failed for package ‘bitops’
> * removing ‘/home/aurora/R/i686-pc-linux-gnu-library/3.0/bitops’
> Warning in install.packages :
>    installation of package ‘bitops’ had non-zero exit status
> * installing *source* package ‘yaml’ ...
> ** package ‘yaml’ successfully unpacked and MD5 sums checked
> ** libs
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -DNDEBUG     -fpic
> -O3 -pipe  -g  -c api.c -o api.o
> In file included from yaml_private.h:6:0,
>                   from api.c:2:
> yaml.h:18:20: fatal error: stdlib.h: No existe el archivo o el directorio
>   #include <stdlib.h>
>                      ^
> compilation terminated.
> make: *** [api.o] Error 1
> ERROR: compilation failed for package ‘yaml’
> * removing ‘/home/aurora/R/i686-pc-linux-gnu-library/3.0/yaml’
> Warning in install.packages :
>    installation of package ‘yaml’ had non-zero exit status
> ERROR: dependency ‘mime’ is not available for package ‘markdown’
> * removing ‘/home/aurora/R/i686-pc-linux-gnu-library/3.0/markdown’
> Warning in install.packages :
>    installation of package ‘markdown’ had non-zero exit status
> ERROR: dependency ‘digest’ is not available for package ‘htmltools’
> * removing ‘/home/aurora/R/i686-pc-linux-gnu-library/3.0/htmltools’
> Warning in install.packages :
>    installation of package ‘htmltools’ had non-zero exit status
> ERROR: dependency ‘bitops’ is not available for package ‘caTools’
> * removing ‘/home/aurora/R/i686-pc-linux-gnu-library/3.0/caTools’
> Warning in install.packages :
>    installation of package ‘caTools’ had non-zero exit status
> ERROR: dependencies ‘digest’, ‘markdown’ are not available for
> package ‘knitr’
> * removing ‘/home/aurora/R/i686-pc-linux-gnu-library/3.0/knitr’
> Warning in install.packages :
>    installation of package ‘knitr’ had non-zero exit status
> ERROR: dependencies ‘knitr’, ‘yaml’, ‘htmltools’, ‘caTools’
> are not available for package ‘rmarkdown’
> * removing ‘/home/aurora/R/i686-pc-linux-gnu-library/3.0/rmarkdown’
> Warning in install.packages :
>    installation of package ‘rmarkdown’ had non-zero exit status
>
> This is my sessionInfo() in case that it could help:
> R version 3.0.2 (2013-09-25)
> Platform: i686-pc-linux-gnu (32-bit)
>
> locale:
>   [1] LC_CTYPE=es_ES.UTF-8       LC_NUMERIC=C
>   
>   [3] LC_TIME=es_ES.UTF-8        LC_COLLATE=es_ES.UTF-8
>   [5] LC_MONETARY=es_ES.UTF-8    LC_MESSAGES=es_ES.UTF-8
>   [7] LC_PAPER=es_ES.UTF-8
> LC_NAME=C
>   [9] LC_ADDRESS=C
> LC_TELEPHONE=C
> [11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods
> base
>
> loaded via a namespace (and not attached):
> [1] tools_3.0.2
>
> Thank you very much for any advice.
>
>
> ------
> Aurora González Vidal
>
> Sección Apoyo Estadístico.
> Servicio de Apoyo a la Investigación (SAI).
> Vicerrectorado de Investigación.
> Universidad de Murcia
> Edif. SACE . Campus de Espinardo.
> 30100 Murcia
>
> @. aurora.gonzalez2 at um.es
> T. 868 88 7315
> F. 868 88 7302
> www.um.es/sai
> www.um.es/ae
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.