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 Gonz?lez Vidal
>
> Secci?n Apoyo Estad?stico.
> Servicio de Apoyo a la Investigaci?n (SAI).
> Vicerrectorado de Investigaci?n.
> 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]]
>
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