
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> #! /usr/local/bin/Rscript --vanilla
> 
> ##z_make.r
> ##2014-03-31 dmontaner@cipf.es
> ##Runs spin using knitr
> 
> ## NOTE: the scripts are executed one after the other one.
> ##       The environment is not cleaned up.
> ##       The q() command at the end of the scripts ends the process.
> 
> ## NOTE: spin does not stop with errors 
> ## example: ~/Downloads/tutoR$ R CMD BATCH z_make.r
> 
> date ()
[1] "Fri Sep 24 16:46:52 2021"
> Sys.info ()[c("nodename", "user")]
        nodename             user 
"fgarcia-laptop"        "fgarcia" 
> commandArgs ()
[1] "/usr/lib/R/bin/exec/R" "-f"                    "z_make.r"             
[4] "--restore"             "--save"                "--no-readline"        
> rm (list = ls ())
> R.version.string ##"R version 3.0.2 (2013-09-25)"
[1] "R version 3.6.3 (2020-02-29)"
> library (rmarkdown); packageDescription ("rmarkdown", fields = "Version") #"1.8"
[1] "2.1"
> library (knitr); packageDescription ("knitr", fields = "Version") #"1.8"
[1] "1.28"
> ##help (package = knitr)
> 
> opts_chunk$set (comment = "#>")   ## symbol preceding the R output
> 
> 
> ### FILES TO COMPILE:
> dir ()
 [1] "010_lectura_datos.html"                      
 [2] "010_lectura_datos.r"                         
 [3] "020_gestion_datos.html"                      
 [4] "020_gestion_datos.r"                         
 [5] "025_guardar_resultados.html"                 
 [6] "025_guardar_resultados.r"                    
 [7] "030_estadistica_descriptiva.html"            
 [8] "030_estadistica_descriptiva.r"               
 [9] "040_inferencia_medias.html"                  
[10] "040_inferencia_medias.r"                     
[11] "050_anova.html"                              
[12] "050_anova.r"                                 
[13] "060_analisis_datos_categoricos.html"         
[14] "060_analisis_datos_categoricos.r"            
[15] "080_anova_friedman.html"                     
[16] "080_anova_friedman.r"                        
[17] "090_modelos_lineales_limma.html"             
[18] "090_modelos_lineales_limma.r"                
[19] "100_bootstrap.html"                          
[20] "100_bootstrap.r"                             
[21] "150_graficos_estadisticos_1_presentacion.pdf"
[22] "150_graficos_estadisticos_1_presentacion.tex"
[23] "150_graficos_estadisticos_1.html"            
[24] "150_graficos_estadisticos_1.r"               
[25] "151_estadistica_descriptiva_presentacion.pdf"
[26] "151_estadistica_descriptiva_presentacion.tex"
[27] "160_correlacion_coexpresion_PENDING.r"       
[28] "165_clustering_and_pcaplot.r"                
[29] "166_clasificators_PENDING.r"                 
[30] "170_ roc_curves_and_logistic_regression.r"   
[31] "171_circos_plots.r"                          
[32] "cor_metabolitos.jpeg"                        
[33] "cor_metabolitos.pdf"                         
[34] "cor_metabolitos.png"                         
[35] "dosresultados.RData"                         
[36] "figure"                                      
[37] "grafico1.png"                                
[38] "images"                                      
[39] "img"                                         
[40] "index.html"                                  
[41] "javascripts"                                 
[42] "jugando_con_distribuciones.r"                
[43] "params.json"                                 
[44] "practica_MEE.html"                           
[45] "practica_MEE.r"                              
[46] "prueba"                                      
[47] "R_basico_1_vectores.html"                    
[48] "R_basico_1_vectores.r"                       
[49] "R_basico_2_matrices.html"                    
[50] "R_basico_2_matrices.r"                       
[51] "R_basico_3_listas.html"                      
[52] "R_basico_3_listas.r"                         
[53] "README.md"                                   
[54] "resultados.RData"                            
[55] "resultados.txt"                              
[56] "riesgos.txt"                                 
[57] "S01_3.html"                                  
[58] "S01_3.r"                                     
[59] "S03.r"                                       
[60] "stylesheets"                                 
[61] "tdatos_metabolitos.txt"                      
[62] "z_make.r"                                    
[63] "z_make.r.Rout"                               
> 
> #bases <- c ("R_basico_1_vectores", "R_basico_2_matrices", "R_basico_3_listas",    "010_lectura_datos", "020_gestion_datos","025_guardar_resultados","030_estadistica_descriptiva","040_inferencia_medias", "050_anova", "060_analisis_datos_categoricos","080_anova_friedman", "100_bootstrap", "150_graficos_estadisticos_1", "090_modelos_lineales_limma", "practica_MEE", "S01", "S03") 
> #bases <- c ("R_basico_1_vectores", "R_basico_2_matrices", "R_basico_3_listas",  "S01_2") 
> bases <- c ("S01_3") 
> 
> #NOTE:   Here I have  new files to  compile!!
> 
> for (base in bases) {
+     print (base)
+ 
+     rm (list = setdiff (ls (), c("base", "bases")))  
+     
+     unlink (paste0 (base, ".html"))
+     spin   (paste0 (base, ".r"), doc = "^##+'[ ]?")  ## double has plus quote instead of single has plus quote is used to indicate md/text chunks (as in roxygen doc. using emacs)
+     unlink (paste0 (base, ".md"))
+     unlink (paste0 (base, ".Rmd"))
+ }
[1] "S01_3"


processing file: S01_3.Rmd

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output file: S01_3.md

> 
> unlink ("misdatos.txt")
> 
> 
> ###EXIT
> warnings ()
> sessionInfo ()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=es_ES.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=es_ES.UTF-8    LC_MESSAGES=en_US.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     

other attached packages:
[1] knitr_1.28    rmarkdown_2.1

loaded via a namespace (and not attached):
 [1] compiler_3.6.3  magrittr_2.0.1  markdown_1.1    tools_3.6.3    
 [5] htmltools_0.4.0 Rcpp_1.0.4.6    stringi_1.4.6   highr_0.8      
 [9] stringr_1.4.0   xfun_0.13       digest_0.6.25   rlang_0.4.6    
[13] evaluate_0.14  
> q ("no")
> proc.time()
   user  system elapsed 
  1.322   0.060   1.445 
