update dockerfile for the new examples

Dockerfile

@@ -2,7 +2,10 @@ FROM rocker/geospatial:latest
 
 SHELL ["/bin/bash", "-c"]
 
-RUN R -e 'install.packages(c("diveMove", "trip", "adehabitatLT", "plm", "cshapes", "plumber", "STEPCAM", "MCMCglmm", "MCMCpack", "gdistance", "compositions", "latticeExtra", "ggplot2", "dplyr", "rasterVis", "RColorBrewer", "mapproj", "gridExtra", "ggplot2", "plyr", "reshape2", "wesanderson", "grid", "plotrix", "shotGroups", "reshape", "RSAGA", "pROC", "vcd", "caret", "fields", "extRemes", "truncnorm", "palaeoSig", "rioja", "FME", "SoilR", "verification", "MASS"))'
+RUN R -e 'install.packages(c("diveMove", "trip", "adehabitatLT", "plm", "cshapes", "plumber", "STEPCAM", "MCMCglmm", "MCMCpack", "gdistance"))'
+RUN R -e 'install.packages(c("compositions", "latticeExtra", "ggplot2", "dplyr", "rasterVis", "RColorBrewer", "mapproj", "gridExtra", "ggplot2"))'
+RUN R -e 'install.packages(c("plyr", "reshape2", "wesanderson", "grid", "plotrix", "shotGroups", "reshape", "RSAGA", "pROC", "vcd", "caret", "fields", "extRemes", "truncnorm", "palaeoSig"))'
+RUN R -e 'install.packages(c("rioja", "FME", "SoilR", "verification", "MASS", "stringr", "plyr", "lubridate", "metafor", "forecast", "expsmooth", "mice", "mitools", "Zelig", "VIM"))'
 RUN R -e 'install.packages("INLA", repos=c(getOption("repos"), INLA="https://inla.r-inla-download.org/R/stable"), dep=TRUE)'
 # based on https://gist.github.com/remarkablemark/aacf14c29b3f01d6900d13137b21db3a
 RUN apt-get update \

controllers/bindings.js

@@ -67,9 +67,9 @@ bindings.manipulateFigure = function(binding, response) {
                 binding.purpose, binding.result.value, binding.id);
     let fileContent = fn.readRmarkdown(binding.id, binding.code.file);
         fn.modifyMainfile(fileContent, binding.result, binding.code.file, binding.id);
-        fileContent = fn.replaceVariable(fileContent, binding.code.parameter);
     let codeLines = fn.handleCodeLines(binding.code.codeLines);
     let extractedCode = fn.extractCode(fileContent, codeLines);
+        extractedCode = fn.replaceVariable(extractedCode, binding.code.parameter);
     let wrappedCode = fn.wrapCode(extractedCode, binding.id, binding.result.value, binding.code.parameter.val);
     fn.saveResult(wrappedCode, binding.id, binding.result.value.replace(/\s/g, '').toLowerCase());
     fn.createRunFile(binding.id, binding.result.value.replace(/\s/g, '').toLowerCase(), binding.port);

controllers/generalFunctions.js

@@ -100,17 +100,23 @@ fn.wrapCode = function(sourcecode, compendiumId, result, value) {
     debug('Start wrapping code');
     let get = "#' @get /" + result.replace(/\s/g, '').toLowerCase() + '\n' +
                 "#' @png \n" +
-                'function(newValue){ \n';
+                'function(newValue){ \n' +
+                'startAnalysis <- Sys.time() \n';
     if (!isNaN(value)) {
         get = get + 'newValue = as.numeric(newValue) \n';
+    } else if (value === 'false' || value === 'FALSE' || value === 'true' || value === 'TRUE') {
+        get = get + 'newValue = as.logical(newValue) \n';
     }
     let code = sourcecode.split('\n');
         //code[code.length-2] = 'print(' + code[code.length-2] + ')';
     let newCode = '';
         code.forEach(function(elem) {
             newCode += elem + '\n';
         });
-    let newContent = get + newCode + '}';
+    let newContent = get + newCode + 'endAnalysis <- Sys.time() \n' + 
+                                    'totaltime <- difftime(endAnalysis, startAnalysis, units="secs") \n' +
+                                    'message(paste("Total time is: ", totaltime)) \n' +  
+                                    '}';
     debug('End wrapping code');
     return newContent;
 };