Merge branch 'develop'

IARC-CSU · Oct 19, 2020 · dbd093d · dbd093d
2 parents c483b09 + 1431ded
commit dbd093d
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diff --git a/appinfo.properties b/appinfo.properties
@@ -1,10 +1,10 @@
 #Everything can be manually updated except buildnum and builddate.
-#Wed, 17 Jun 2020 17:01:22 +0200
-program.BUILDNUM=1710
+#Mon, 19 Oct 2020 16:22:02 +0200
+program.BUILDNUM=1713
 program.AUTHOR=Morten Johannes Ervik, CSU/IARC
-program.BUILDDATE=20200617170122
+program.BUILDDATE=20201019162202
 program.DESCRIPTION=CanReg5 is a multi user, multi platform, open source tool to input, store, check and analyse cancer registry data.
 program.COPYRIGHT=2008-2020
-program.VERSION=5.00.44d
+program.VERSION=5.00.44e
 program.COMPANY=International Agency for Research on Cancer
 program.PROGNAME=CanReg
diff --git a/buildnumber.properties b/buildnumber.properties
@@ -1,3 +1,3 @@
 #Build Number for ANT. Do not edit!
-#Wed Jun 17 17:01:22 CEST 2020
-build.number=1711
+#Mon Oct 19 16:22:02 CEST 2020
+build.number=1714
diff --git a/changelog.html b/changelog.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" />
   <meta name="generator" content="pandoc" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
-  <title>Changelog</title>
+  <title>CanReg5 Changelog</title>
   <style>
     code{white-space: pre-wrap;}
     span.smallcaps{font-variant: small-caps;}
@@ -17,7 +17,7 @@
     <script src="//cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv-printshiv.min.js"></script>
   <![endif]-->
   <style>
-
+    
   html {
     font-size: 100%;
     overflow-y: scroll;
@@ -356,9 +356,13 @@
 </head>
 <body>
 <header id="title-block-header">
-<h1 class="title">Changelog</h1>
+<h1 class="title">CanReg5 Changelog</h1>
 </header>
 <h1 id="canreg5-changelog">CanReg5 Changelog</h1>
+<h2 id="e">5.00.44e</h2>
+<ul>
+<li>Table builder is now compatible with latest version of R (4.0.3) libraries.</li>
+</ul>
 <h2 id="d">5.00.44d</h2>
 <ul>
 <li>Fixed a bug related to answering ‘no’ to ‘really close?’ for record with changes.</li>

diff --git a/changelog.rtf b/changelog.rtf
@@ -3,6 +3,8 @@
 \widowctrl\hyphauto
 
 {\pard \ql \f0 \sa180 \li0 \fi0 \b \fs36 CanReg5 Changelog\par}
+{\pard \ql \f0 \sa180 \li0 \fi0 \b \fs32 5.00.44e\par}
+{\pard \ql \f0 \sa0 \li360 \fi-360 \bullet \tx360\tab Table builder is now compatible with latest version of R (4.0.3) libraries.\sa180\par}
 {\pard \ql \f0 \sa180 \li0 \fi0 \b \fs32 5.00.44d\par}
 {\pard \ql \f0 \sa0 \li360 \fi-360 \bullet \tx360\tab Fixed a bug related to answering \u8216'no\u8217' to \u8216'really close?\u8217' for record with changes.\sa180\par}
 {\pard \ql \f0 \sa180 \li0 \fi0 \b \fs32 5.00.44c\par}

diff --git a/changelog.txt b/changelog.txt
@@ -1,5 +1,8 @@
 # CanReg5 Changelog
 
+## 5.00.44e
+- Table builder is now compatible with latest version of R (4.0.3) libraries. 
+
 ## 5.00.44d
 - Fixed a bug related to answering 'no' to 'really close?' for record with changes.
 

diff --git a/conf/tables/r/Rcan_ASR_bar_top.r b/conf/tables/r/Rcan_ASR_bar_top.r
@@ -17,7 +17,7 @@ tryCatch({
 
   #load dependency packages
 	canreg_load_packages(c("data.table", "ggplot2", "gridExtra", "scales", "Cairo","bmp", "jpeg", "shiny.i18n", "Rcan"))
-	i18n <- Translator(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
+	i18n <- Translator$new(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
 	i18n$set_translation_language(ls_args$lang)
 
   #merge incidence and population

diff --git a/conf/tables/r/Rcan_CI5_comp.r b/conf/tables/r/Rcan_CI5_comp.r
@@ -17,7 +17,7 @@ tryCatch({
 
   #load dependency packages
   canreg_load_packages(c("data.table", "ggplot2", "gridExtra", "scales", "Cairo","bmp", "jpeg",  "shiny.i18n", "Rcan"))
-	i18n <- Translator(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
+	i18n <- Translator$new(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
 
 	i18n$set_translation_language(ls_args$lang)
 

diff --git a/conf/tables/r/Rcan_EAPC_scatter.r b/conf/tables/r/Rcan_EAPC_scatter.r
@@ -17,7 +17,7 @@ tryCatch({
 
   #load dependency packages
   canreg_load_packages(c("data.table", "ggplot2", "gridExtra", "scales", "Cairo","bmp", "jpeg",  "shiny.i18n", "Rcan"))
- 	i18n <- Translator(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
+ 	i18n <- Translator$new(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
 	i18n$set_translation_language(ls_args$lang)
 
   #merge incidence and population

diff --git a/conf/tables/r/Rcan_EAPC_scatter_CI.r b/conf/tables/r/Rcan_EAPC_scatter_CI.r
@@ -17,7 +17,7 @@ tryCatch({
 
   #load dependency packages
   canreg_load_packages(c("data.table", "ggplot2", "gridExtra", "scales", "Cairo","bmp", "jpeg",  "shiny.i18n", "Rcan"))
- 	i18n <- Translator(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
+ 	i18n <- Translator$new(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
 	i18n$set_translation_language(ls_args$lang)
 
   #merge incidence and population

diff --git a/conf/tables/r/Rcan_age_specific_rate_site.r b/conf/tables/r/Rcan_age_specific_rate_site.r
@@ -17,7 +17,7 @@ tryCatch({
 
   #load dependency packages
 	canreg_load_packages(c("data.table", "ggplot2", "gridExtra", "scales", "Cairo","bmp", "jpeg", "shiny.i18n", "Rcan"))
-	i18n <- Translator(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
+	i18n <- Translator&new(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
 	i18n$set_translation_language(ls_args$lang)
 
   #merge incidence and population

diff --git a/conf/tables/r/Rcan_age_specific_rate_top.r b/conf/tables/r/Rcan_age_specific_rate_top.r
@@ -17,7 +17,7 @@ tryCatch({
 
   #load dependency packages
 	canreg_load_packages(c("data.table", "ggplot2", "gridExtra", "scales", "Cairo","bmp", "jpeg", "shiny.i18n", "Rcan"))
-	i18n <- Translator(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
+	i18n <- Translator$new(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
 	i18n$set_translation_language(ls_args$lang)
 
   #merge incidence and population

diff --git a/conf/tables/r/Rcan_bar_top_oneside.r b/conf/tables/r/Rcan_bar_top_oneside.r
@@ -17,7 +17,7 @@ tryCatch({
 
   #load dependency packages
   canreg_load_packages(c("data.table", "ggplot2", "gridExtra", "scales", "Cairo","bmp", "jpeg",  "shiny.i18n", "Rcan"))
- 	i18n <- Translator(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
+ 	i18n <- Translator$new(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
 	i18n$set_translation_language(ls_args$lang)
 
   #merge incidence and population

diff --git a/conf/tables/r/Rcan_cases_age_bar.r b/conf/tables/r/Rcan_cases_age_bar.r
@@ -17,7 +17,7 @@ tryCatch({
 
   #load dependency packages
 	canreg_load_packages(c("data.table", "ggplot2", "gridExtra", "scales", "Cairo","bmp", "jpeg", "shiny.i18n", "Rcan"))
-	i18n <- Translator(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
+	i18n <- Translator$new(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
 	i18n$set_translation_language(ls_args$lang)
 
   #merge incidence and population

diff --git a/conf/tables/r/Rcan_cases_age_pie.r b/conf/tables/r/Rcan_cases_age_pie.r
@@ -17,7 +17,7 @@ tryCatch({
 
   #load dependency packages
 	canreg_load_packages(c("data.table", "ggplot2", "gridExtra", "scales", "Cairo","bmp", "jpeg", "shiny.i18n", "Rcan"))
-	i18n <- Translator(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
+	i18n <- Translator$new(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
 	i18n$set_translation_language(ls_args$lang)
 
   #merge incidence and population

diff --git a/conf/tables/r/Rcan_cases_year_bar.r b/conf/tables/r/Rcan_cases_year_bar.r
@@ -17,7 +17,7 @@ tryCatch({
 
   #load dependency packages
 	canreg_load_packages(c("data.table", "ggplot2", "gridExtra", "scales", "Cairo","bmp", "jpeg", "shiny.i18n", "Rcan"))
-	i18n <- Translator(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
+	i18n <- Translator$new(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
 	i18n$set_translation_language(ls_args$lang)
 
   #merge incidence and population

diff --git a/conf/tables/r/Rcan_population_pyramid.r b/conf/tables/r/Rcan_population_pyramid.r
@@ -17,7 +17,7 @@ tryCatch({
 
   #load dependency packages
 	canreg_load_packages(c("data.table", "ggplot2", "gridExtra", "scales", "Cairo","bmp", "jpeg", "shiny.i18n", "Rcan"))
-	i18n <- Translator(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
+	i18n <- Translator$new(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
 	i18n$set_translation_language(ls_args$lang)
 
 

diff --git a/conf/tables/r/Rcan_report.r b/conf/tables/r/Rcan_report.r
@@ -17,7 +17,7 @@ tryCatch({
 
   #load dependency packages
   canreg_load_packages(c("data.table", "ggplot2", "gridExtra", "scales", "Cairo","officer","flextable", "zip", "bmp", "jpeg", "png","shiny.i18n", "Rcan"))
-	i18n <- Translator(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
+	i18n <- Translator$new(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
 	i18n$set_translation_language(ls_args$lang)
 
   #merge incidence and population

diff --git a/conf/tables/r/Rcan_slide.r b/conf/tables/r/Rcan_slide.r
@@ -17,7 +17,7 @@ tryCatch({
 
   #load dependency packages
   canreg_load_packages(c("data.table", "ggplot2", "gridExtra", "scales", "Cairo","officer","flextable", "zip", "bmp", "jpeg", "png","shiny.i18n", "Rcan"))
-	i18n <- Translator(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
+	i18n <- Translator$new(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
 	i18n$set_translation_language(ls_args$lang)
 
   #merge incidence and population

diff --git a/conf/tables/r/Rcan_time_trend.r b/conf/tables/r/Rcan_time_trend.r
@@ -17,7 +17,7 @@ tryCatch({
 
   #load dependency packages
 	canreg_load_packages(c("data.table", "ggplot2", "gridExtra", "scales", "Cairo","bmp", "jpeg", "shiny.i18n", "Rcan"))
-	i18n <- Translator(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
+	i18n <- Translator$new(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
 	i18n$set_translation_language(ls_args$lang)
 
   #merge incidence and population

diff --git a/conf/tables/r/r-packages/Rcan_1.3.64.tar.gz b/conf/tables/r/r-packages/Rcan_1.3.64.tar.gz
diff --git a/conf/tables/r/shiny/global.r b/conf/tables/r/shiny/global.r
@@ -4,7 +4,7 @@ source(paste(sep="/", script.basename, "Rcan_core.r"))
 ls_args <- canreg_args(Args)
 
 
-i18n <- Translator(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
+i18n <- Translator$new(translation_csvs_path  = (paste(sep="/", script.basename, "r-translations")))
 i18n$set_translation_language(ls_args$lang)
 
 

diff --git a/doc/CanReg5-Future/CanReg5-Future.lyx b/doc/CanReg5-Future/CanReg5-Future.lyx
@@ -1,5 +1,5 @@
-#LyX 2.2 created this file. For more info see http://www.lyx.org/
-\lyxformat 508
+#LyX 2.3 created this file. For more info see http://www.lyx.org/
+\lyxformat 544
 \begin_document
 \begin_header
 \save_transient_properties true
@@ -21,6 +21,8 @@
 \font_osf false
 \font_sf_scale 100 100
 \font_tt_scale 100 100
+\use_microtype false
+\use_dash_ligatures true
 \graphics default
 \default_output_format default
 \output_sync 0
@@ -50,6 +52,7 @@
 \suppress_date false
 \justification true
 \use_refstyle 0
+\use_minted 0
 \index Index
 \shortcut idx
 \color #008000
@@ -58,7 +61,10 @@
 \tocdepth 3
 \paragraph_separation indent
 \paragraph_indentation default
-\quotes_language english
+\is_math_indent 0
+\math_numbering_side default
+\quotes_style english
+\dynamic_quotes 0
 \papercolumns 1
 \papersides 1
 \paperpagestyle default
@@ -82,7 +88,7 @@ By: Morten Johannes Ervik, CSU, IARC
 \begin_layout Standard
 \align center
 \begin_inset Graphics
-	filename CanReg5-Instructions/LogoBetaNewer.png
+	filename ../CanReg5-Instructions/LogoBetaNewer.png
 	lyxscale 33
 	width 50line%
 
@@ -251,7 +257,7 @@ Group by other meta variables for frequencies by year (age group, 2 digit
 \end_layout
 
 \begin_layout Itemize
-Export report automatically opened in the System?
+Export report automatically opened in the System? [DONE]
 \end_layout
 
 \begin_layout Itemize
@@ -415,19 +421,9 @@ Pending bugs
 \end_layout
 
 \begin_layout Itemize
-Bug in R script:
-\begin_inset Separator latexpar
-\end_inset
-
-
-\end_layout
-
-\begin_deeper
-\begin_layout Itemize
-drops cases when highest age group cutoff < 85?
+Merge issues
 \end_layout
 
-\end_deeper
 \begin_layout Section*
 (Computer) Code related improvements
 \end_layout
@@ -533,7 +529,7 @@ Data Entry related
 \end_layout
 
 \begin_layout Itemize
-Let user enter dates in the format they wish?
+Let user enter dates in the format they wish? [DONE]
 \end_layout
 
 \begin_layout Itemize
@@ -733,6 +729,10 @@ Using Spark? http://www.sparkjava.com/index.html
 \end_layout
 
 \end_deeper
+\begin_layout Itemize
+Capture/recapture analysis
+\end_layout
+
 \begin_layout Section*
 Management related
 \end_layout

diff --git a/doc/CanReg5-Future/CanReg5-Future.pdf b/doc/CanReg5-Future/CanReg5-Future.pdf
diff --git a/doc/CanReg5-Instructions/CanReg5-Instructions.lyx b/doc/CanReg5-Instructions/CanReg5-Instructions.lyx
@@ -14196,7 +14196,7 @@ Copyright
 \end_layout
 
 \begin_layout Standard
-© 2008-2019 International Agency for Research on Cancer World Health Organizatio
+© 2008-2020 International Agency for Research on Cancer World Health Organizatio
 n All rights reserved.
 \end_layout
 

diff --git a/inno-settings.txt b/inno-settings.txt
@@ -1 +1 @@
-#define MyAppVersion "5.00.44d"
+#define MyAppVersion "5.00.44e"
diff --git a/nbproject/jnlp-impl.xml b/nbproject/jnlp-impl.xml
@@ -306,7 +306,7 @@ made subject to such option by the copyright holder.
 
     <target name="-copy-tmp-manifest" if="manifest.file">
         <property name="tmp.manifest.file" value="${build.dir}/manifest.mf"/>
-        <copy file="${manifest.file}" tofile="${build.dir}/manifest.mf" encoding="UTF-8" outputencoding="UTF-8"/>
+        <copy file="${manifest.file}" tofile="${build.dir}/manifest.mf" encoding="${manifest.encoding}" outputencoding="UTF-8"/>
     </target>
 
     <target name="-set-mixed-code-properties" depends="-check-signing-possible" if="jnlp.signed.true+signjars.task.available">

diff --git a/version.txt b/version.txt
@@ -1 +1 @@
-5.00.44d
+5.00.44e