[Stacomir-commits] r353 - in pkg: stacomir stacomir/R stacomir/R/po stacomir/data stacomir/inst/config stacomir/inst/tests/testthat stacomir/man stacomirtools/R
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Apr 12 08:17:20 CEST 2017
Author: briand
Date: 2017-04-12 08:17:19 +0200 (Wed, 12 Apr 2017)
New Revision: 353
Removed:
pkg/stacomir/R/RefMsg.r
pkg/stacomir/R/messages.r
pkg/stacomir/data/msg.rda
pkg/stacomir/inst/config/generate_message.r
pkg/stacomir/man/RefMsg-class.Rd
pkg/stacomir/man/charge-RefMsg-method.Rd
pkg/stacomir/man/charge_avec_filtre-RefMsg-method.Rd
pkg/stacomir/man/createmessage-RefMsg-method.Rd
pkg/stacomir/man/messages.Rd
pkg/stacomir/man/msg.Rd
Modified:
pkg/stacomir/DESCRIPTION
pkg/stacomir/NAMESPACE
pkg/stacomir/R/BilanArgentee.r
pkg/stacomir/R/RefCoe.r
pkg/stacomir/R/RefDC.r
pkg/stacomir/R/RefStades.r
pkg/stacomir/R/RefTaxon.r
pkg/stacomir/R/data.r
pkg/stacomir/R/po/R-stacomiR_fr_FR.mo
pkg/stacomir/R/po/R-stacomiR_fr_FR.po
pkg/stacomir/R/stacomi.r
pkg/stacomir/R/utilitaires.r
pkg/stacomir/inst/config/generate_Roxygen2.R
pkg/stacomir/inst/config/generate_data.R
pkg/stacomir/inst/config/stacomi_manual_launch.r
pkg/stacomir/inst/tests/testthat/test-00stacomir.R
pkg/stacomir/man/RefAnnee-class.Rd
pkg/stacomir/man/RefCheckBox-class.Rd
pkg/stacomir/man/RefChoix-class.Rd
pkg/stacomir/man/RefCoe-class.Rd
pkg/stacomir/man/RefDC-class.Rd
pkg/stacomir/man/RefDF-class.Rd
pkg/stacomir/man/RefHorodate-class.Rd
pkg/stacomir/man/RefListe-class.Rd
pkg/stacomir/man/RefStades-class.Rd
pkg/stacomir/man/RefTaxon-class.Rd
pkg/stacomir/man/Refpar-class.Rd
pkg/stacomir/man/Refparqual-class.Rd
pkg/stacomir/man/Refparquan-class.Rd
pkg/stacomir/man/Refperiode-class.Rd
pkg/stacomir/man/bmi.Rd
pkg/stacomir/man/charge-BilanMigrationCar-method.Rd
pkg/stacomir/man/charge-RefChoix-method.Rd
pkg/stacomir/man/chargecsv.Rd
pkg/stacomir/man/envir_stacomi.Rd
pkg/stacomir/man/setasqualitative-BilanMigrationCar-method.Rd
pkg/stacomir/man/stacomi.Rd
pkg/stacomirtools/R/RequeteODBC.r
Log:
Modified: pkg/stacomir/DESCRIPTION
===================================================================
--- pkg/stacomir/DESCRIPTION 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/DESCRIPTION 2017-04-12 06:17:19 UTC (rev 353)
@@ -10,7 +10,7 @@
by the ONEMA institute to centralize data obtained by fishway monitoring.
Version 0.5.1 is available in French English.
License: GPL (>= 2)
-Collate:
+Collate:
'create_generic.r'
'Refpar.r'
'RefHorodate.r'
@@ -45,7 +45,6 @@
'RefCoe.r'
'Bilan_poids_moyen.r'
'RefCheckBox.r'
- 'RefMsg.r'
'Refperiode.r'
'data.r'
'fn_EcritBilanMensuel.r'
@@ -71,7 +70,6 @@
'interface_Bilan_carlot.r'
'interface_Bilan_taille.r'
'interface_bilan_poids_moyen.r'
- 'messages.r'
'setAs.r'
'stacomi.r'
LazyLoad: yes
Modified: pkg/stacomir/NAMESPACE
===================================================================
--- pkg/stacomir/NAMESPACE 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/NAMESPACE 2017-04-12 06:17:19 UTC (rev 353)
@@ -24,7 +24,6 @@
export(hCamembert)
export(hTableBilanEspeces)
export(interface_BilanEspeces)
-export(messages)
export(mygtkProgressBar)
export(split_per_day)
export(stacomi)
@@ -45,18 +44,17 @@
exportClasses(Bilan_carlot)
exportClasses(Bilan_poids_moyen)
exportMethods(DateFin)
-exportMethods(setasqualitative)
exportMethods(barplot)
exportMethods(calcule)
exportMethods(charge)
exportMethods(charge_avec_filtre)
exportMethods(choice_c)
exportMethods(connect)
-exportMethods(createmessage)
exportMethods(getvalue)
exportMethods(model)
exportMethods(plot)
exportMethods(print)
+exportMethods(setasqualitative)
exportMethods(summary)
exportMethods(supprime)
exportMethods(write_database)
Modified: pkg/stacomir/R/BilanArgentee.r
===================================================================
--- pkg/stacomir/R/BilanArgentee.r 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/R/BilanArgentee.r 2017-04-12 06:17:19 UTC (rev 353)
@@ -414,7 +414,7 @@
xlab=gettext("Month",domain="R-stacomiR"),
ylab=gettext("Number",domain="R-stacomiR"),
par.strip.text=list(col="white", font=2),
- auto.key=list(title=gettext("Number by pigmentation stage",domain="R-stacomiR"),
+ auto.key=list(title=gettext("Number by silvering stage",domain="R-stacomiR"),
cex.title=1.2,
space="top",
columns=6,
Modified: pkg/stacomir/R/RefCoe.r
===================================================================
--- pkg/stacomir/R/RefCoe.r 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/R/RefCoe.r 2017-04-12 06:17:19 UTC (rev 353)
@@ -74,8 +74,8 @@
requete at colonnedebut<-"coe_date_debut"
requete at colonnefin<-"coe_date_fin"
requete at select=stringr::str_c("DELETE from ",get("sch",envir=envir_stacomi),"tj_coefficientconversion_coe ")
- requete at and=" and coe_tax_code='2038' and coe_std_code='CIV' and coe_qte_code='1'"
- invisible(utils::capture.output(requete<-stacomirtools::connect(requete)))
+ requete at and=str_c(" and coe_tax_code='",tax,"' and coe_std_code='",std,"' and coe_qte_code='1'")
+ requete<-stacomirtools::connect(requete)
if (!silent) funout(gettextf("%s rows deleted from table tj_coefficientconversion_coe",nrow(object at data),domain="R-stacomiR"))
return(invisible(NULL))
})
Modified: pkg/stacomir/R/RefDC.r
===================================================================
--- pkg/stacomir/R/RefDC.r 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/R/RefDC.r 2017-04-12 06:17:19 UTC (rev 353)
@@ -216,7 +216,6 @@
# group(ggroup)[nb(notebook)[groupdc(ggroup&tab)[[frameDCsource(gframe)[tbsourcedc(gtable)],frameDCdest(gframe)[tbdcdest(gtable)]],OKbutton]]
DC=object at data[,c("dc","dis_commentaires","type_dc")]
- #TODO addmsg
groupdc<-ggroup(container=notebook, label="dc") ## "add" called by constructor this is a tab of the notebook
assign("groupdc",groupdc,envir=.GlobalEnv)
frameDCsource<-gframe(gettext("Counting devices choice",domain="R-stacomiR"),container=groupdc)
Deleted: pkg/stacomir/R/RefMsg.r
===================================================================
--- pkg/stacomir/R/RefMsg.r 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/R/RefMsg.r 2017-04-12 06:17:19 UTC (rev 353)
@@ -1,125 +0,0 @@
-#' RefMsg referential class to load message according to the language chosen
-#'
-#' @slot data A data.frame
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-setClass(Class="RefMsg",representation= representation(messager="data.frame",messagerlang="data.frame" ))
-
-
-#' Loading method for RefMsg referential objects
-#'
-#' loads the common table ts_messager_msr
-#' @return An S4 object of class RefMsg
-#' @param object An object of class \link{RefMsg-class}
-#' @family Referential objects
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @examples
-#' \dontrun{
-#' object=new("RefMsg")
-#' charge(object)
-#' }
-setMethod("charge",signature=signature("RefMsg"),definition=function(object) {
- req=new("RequeteODBC")
- req at baseODBC<-get("baseODBC",envir=envir_stacomi)
- req at sql="SELECT * from ref.ts_messager_msr ORDER BY msr_id ASC ;"
- req<-stacomirtools::connect(req) # appel de la methode connect de l'object requeteODBC
- object at messager<-req at query
- return(object)
- })
-
-#' Loading method for RefMsg referential objects
-#'
-#' searching ref.ts_messagerlang_mrl for the lines corresponding to lang
-#' @param object An object of class \link{RefMsg-class}
-#' @param lang A language, either "French" or "English" or "Spanish"
-#' @return An S4 object of class RefMsg
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @examples
-#' \dontrun{
-#' object=new("RefMsg")
-#' charge_avec_filtre(object,lang='French')
-#' }
-setMethod("charge_avec_filtre",signature=signature("RefMsg"),definition=function(object,lang) {
- requete=new("RequeteODBCwhere")
- requete at baseODBC<-get("baseODBC",envir=envir_stacomi)
- requete at select=stringr::str_c("SELECT mrl_id,mrl_msr_id, mrl_text",
- " FROM ref.ts_messagerlang_mrl")
- requete at where=stringr::str_c("where mrl_lang='",lang,"'")
- requete at order_by="ORDER BY mrl_msr_id ASC"
- requete<-stacomirtools::connect(requete)
- object at messagerlang<-requete at query
- return(object)
- })
-
-#' createmessage method for RefMsg referential objects
-#' @param ojbect An object of class RefMsg
-#' @param database_expected Default to TRUE, if FALSE, no database connection is expected and the messages will be loaded from msg dataset within the package
-#' @return An S4 object of class RefMsg
-#' @note When coming from the database, doublequotes are now escaped with an antislash (/"), those at the beginning and end are left as doublequotes,
-#' the others are single quote when they are to be pasted within the text as code example. The remainder "c("a","b","c") are rebuilt into vectors by the function
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @export
-#' @keywords internal
-setMethod("createmessage",signature=signature("RefMsg"),definition=function(object,database_expected) {
- if (database_expected){
- #object=new("RefMsg")
- object<-charge(object)
- object<-charge_avec_filtre(object,lang=get("lang",envir=envir_stacomi))
- if (nrow(object at messager)!=nrow(object at messagerlang)) stop("internal error, check messager and messagerlang length, they should match")
- msg=list()
- buildmsg<-merge(object at messager,object at messagerlang,by.x="msr_id",by.y="mrl_msr_id")
- buildmsg$msr_endofline2<-ifelse(as.logical(buildmsg$"msr_endofline"),"\n","")
- buildmsg1<-apply(buildmsg,1,function(X)stringr::str_c(X["msr_element"],
- ".",
- as.integer(X["msr_number"])))
- # special case for graphical interface which contains number like 2.1 ...
- buildmsg1[buildmsg$msr_element=="interface_graphique_menu"]<-apply(buildmsg[buildmsg$msr_element=="interface_graphique_menu",],1,function(X)stringr::str_c(X["msr_element"],
- ".",
- as.character(X["msr_number"])))
- buildmsg1<-gsub(' ', '', buildmsg1)
- buildmsg2<-apply(buildmsg,1,function(X)stringr::str_c(
- X["mrl_text"],
- X["msr_endofline2"]))
- nettoye<-function(X){
- X<-gsub(".00","",X)
- X<-gsub("0","",X)
- return(X)
- }
- buildmsg1[buildmsg$msr_element=="interface_graphique_menu"]<-nettoye(buildmsg1[buildmsg$msr_element=="interface_graphique_menu"])
-
-
-
- # internal problem patch
- buildmsg1[match("interface_graphique_menu.2.9",buildmsg1)+1]<-"interface_graphique_menu.2.10"
- # here I'm dealing with "\" but only at the beginning and ending of strings
- list<-gregexpr("(\")", buildmsg2)
- for (i in 1:length(buildmsg2)){
- if (length(list[[i]])<=2) buildmsg2[i]<-gsub("\"","", buildmsg2[i])
- }
- # dealing with the special problems of vectors which I want as vector c("toto","titi") and not as "c(toto,titi)"
- #
- create_vector<-function(m){
- # expressions contenant get
- index<-grep("(c\\()",m)
- # debug j<-index[1]
- for (j in index){
- list<-gregexpr("(\")", m[[j]])
- # getting vector elements and coalescing them in a vector
- m[[j]]<-do.call(c,lapply(2*(1:(length(list[[1]])/2))-1,function(i){
- substring(m[[j]],list[[1]][i]+1,list[[1]][i+1]-1)
- }))
- }
- return(m)
-
- }
-
- for (i in 1:length(buildmsg1)){
- msg[buildmsg1[i]]<-buildmsg2[i]
- }
- msg<-create_vector(msg)
- assign("msg",msg,envir=envir_stacomi)
- } else { # !database_expected
- utils::data("msg")
- assign("msg",msg,envir=envir_stacomi)
- }
- invisible(NULL)
- })
Modified: pkg/stacomir/R/RefStades.r
===================================================================
--- pkg/stacomir/R/RefStades.r 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/R/RefStades.r 2017-04-12 06:17:19 UTC (rev 353)
@@ -223,7 +223,6 @@
# below the widget structure [=> within (=> type
# group(ggroup)[notebook(notebook)[groupstd(ggroup&tab)[[framestdsource(gframe)[tbsourcestd(gtable)],framestddest(gframe)[tbdeststd(gtable)]],OKbutton]]
if (!exists("notebook")) notebook <- gnotebook(container=group)
- #TODO addmsg
std_libelle=fun_char_spe(object at data$std_libelle)
groupstd<-ggroup()
assign("goupstd",groupstd,envir=.GlobalEnv)
@@ -231,7 +230,6 @@
framestdsource<-gframe(gettext("Stage selection",domain="R-stacomiR"),container=groupstd)
tbsourcestd = gtable(std_libelle,container=framestdsource,expand = TRUE, fill = TRUE)
size(tbsourcestd)<-c(160,300)
- #TODO addmsg
framestddest<-gframe(gettext("drop here",domain="R-stacomiR"),container=groupstd)
# need for a fixed size data.frame otherwise errors when adding new lines
xx<-data.frame(choice=rep("",8))
Modified: pkg/stacomir/R/RefTaxon.r
===================================================================
--- pkg/stacomir/R/RefTaxon.r 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/R/RefTaxon.r 2017-04-12 06:17:19 UTC (rev 353)
@@ -151,7 +151,6 @@
tbsourcetaxon = gtable(tax_libelle,container=frametaxonsource,expand = TRUE, fill = TRUE)
size(tbsourcetaxon)<-c(160,300) # les dimensions sont testees a la main
# pour s'ajuster aux dimensions du notebook (largeur 400)
- #TODO addmsg
frametaxondest<-gframe(gettext("drop here",domain="R-stacomiR"),container=grouptaxon)
# need for a fixed size data.frame otherwise errors when adding new lines
xx<-data.frame(choice=rep("",8))
Modified: pkg/stacomir/R/data.r
===================================================================
--- pkg/stacomir/R/data.r 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/R/data.r 2017-04-12 06:17:19 UTC (rev 353)
@@ -1,3 +1,12 @@
+#' Working environment for stacomiR created when launching stacomi()
+#'
+#' This is where the graphical interface stores its objects
+#' try \code{ls(envir=envir_stacomi)}
+#' @keywords environment
+"envir_stacomi"
+
+
+
#' Anguilla migration at the Arzal station (BilanMigrationMult-class)
#'
#' This data corresponds to the data collected from three fishways
@@ -31,13 +40,6 @@
#' @keywords data
"bMM_Arzal"
-#' Messages
-#'
-#' In english
-#'
-#'
-#' @keywords data
-"msg"
#' Video counting of thin lipped mullet (Liza ramada) in 2015 on the Vilaine (France)
#'
Deleted: pkg/stacomir/R/messages.r
===================================================================
--- pkg/stacomir/R/messages.r 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/R/messages.r 2017-04-12 06:17:19 UTC (rev 353)
@@ -1,38 +0,0 @@
-# messages.r
-# last changes 3 april 2011
-# Author: cedric
-###############################################################################
-
-
-
-
-
-
-
-#' Function used at the beginning of the program to display the first messages
-#' collected by method RODBC Attention all msgs are starting with a letter "l"
-#' numbers are wrong when used as msgs within a list
-#'
-#' Function used at the beginning of the program to display the first messages
-#' collected by method RODBC Attention all msgs are starting with a letter "l"
-#' numbers are wrong when used as msgs within a list
-#'
-#'
-#' @param lang one of "French","Spanish","English"
-#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-#' @export
-# exported for test_that
-messages=function(){
- msg=list()
-# RequeteODBC
- msg$RequeteODBC.1<-gettext("Error ODBC =>Define a vector baseODBC with the name of the ODBC link, user and password")
- msg$RequeteODBC.2<-gettext("Connection trial :")
- msg$RequeteODBC.3<-gettext("Connection failure :")
- msg$RequeteODBC.4<-gettext("Connection successful")
- msg$RequeteODBC.5<-gettext("Trying query")
- msg$RequeteODBC.6<-gettext("Query succeded")
-# RequeteODBCwhere
-# RequeteODBCwheredate
-
- assign("msg",msg,envir=envir_stacomi)
-}
Modified: pkg/stacomir/R/po/R-stacomiR_fr_FR.mo
===================================================================
(Binary files differ)
Modified: pkg/stacomir/R/po/R-stacomiR_fr_FR.po
===================================================================
--- pkg/stacomir/R/po/R-stacomiR_fr_FR.po 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/R/po/R-stacomiR_fr_FR.po 2017-04-12 06:17:19 UTC (rev 353)
@@ -2,7 +2,7 @@
msgstr ""
"Project-Id-Version: stacomiR 0.5.0\n"
"POT-Creation-Date: 2017-04-03 15:22+0200\n"
-"PO-Revision-Date: 2017-04-03 15:27+0200\n"
+"PO-Revision-Date: 2017-04-11 15:37+0200\n"
"Last-Translator: \n"
"Language-Team: \n"
"Language: fr_FR\n"
@@ -134,7 +134,7 @@
msgstr "Effectif"
msgid "Number by pigmentation stage"
-msgstr "Effectif par stade pigmentaire"
+msgstr "Effectif par stade d'Argenture"
msgid "Size (mm)"
msgstr "Taille (mm)"
Modified: pkg/stacomir/R/stacomi.r
===================================================================
--- pkg/stacomir/R/stacomi.r 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/R/stacomi.r 2017-04-12 06:17:19 UTC (rev 353)
@@ -254,8 +254,6 @@
#' through the command line.}
#' }
#' When \code{database_expected=FALSE} a connection to the database is not expected. Therefore test are run by calling examples object stored in Rdata.
-#' And also messages are downloaded from the database in several languages. These are loaded from the data directory of the package instead, and
-#' are only avalaible in english.
#'
#' @param gr_interface Boolean, if \code{TRUE} the program will launch the graphical interface
#' @param login_window Boolean, if \code{TRUE} a login window will be displayed asking the user to specify
@@ -331,8 +329,6 @@
assign("gr_interface",gr_interface,envir=envir_stacomi)
assign("database_expected",database_expected,envir=envir_stacomi)
assign("login_window",login_window,envir=envir_stacomi)
- # the first messages are necessary for the first access to the database, they are in French
- msg<-messages()
mylinks=chargecsv(database_expected)
baseODBC=mylinks[["baseODBC"]]
datawd=mylinks[["datawd"]]
@@ -346,10 +342,6 @@
assign("baseODBC",baseODBC,envir=envir_stacomi)
assign("sch",paste(baseODBC[2],".",sep=""),envir=envir_stacomi)
- refMsg=new("RefMsg")
- createmessage(refMsg,database_expected)
-
- msg=get("msg",envir=envir_stacomi)
#libraries()
options(sqldf.RPostgreSQL.user = sqldf.options["sqldf.uid"],
sqldf.RPostgreSQL.password =sqldf.options["sqldf.pwd"],
@@ -396,7 +388,6 @@
#' are assigned in the user environment \code{.GlobalEnv}.
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
interface_graphique=function(){
- msg=get("msg",envir=envir_stacomi) # appel dans chaque sous fonction
if (exists("graphes")) rm(list=c("graphes"),envir=.GlobalEnv)
if (exists("ggroupboutonsbas")) rm(list=c("ggroupboutonsbas"),envir=.GlobalEnv)
if (exists("group")) rm(list=c("group"),envir=.GlobalEnv)
@@ -511,15 +502,10 @@
utils::globalVariables(c("envir_stacomi"))
# reoxygenize fails if data are not loaded
#setwd("F:/workspace/stacomir/branch0.5/stacomir")
-#data("bMM_Arzal")
-#' Working environment for stacomiR created when launching stacomi()
-#'
-#' This is where the graphical interface stores its objects
-#' try \code{ls(envir=envir_stacomi)}
-#' @keywords environment
-"envir_stacomi"
-## using dput
+
+
+## THESE LINES MUST BE UNCOMMENTED IN ORDER TO MAKE THE DOCUMENT METHOD FROM DEVTOOL WORK
#calcmig<-
# structure(list(lienODBC = structure(1L, .Label = "bd_contmig_nat", class = "factor"),
# uid = structure(1L, .Label = "iav", class = "factor"), pwd = structure(1L, .Label = "iav", class = "factor"),
Modified: pkg/stacomir/R/utilitaires.r
===================================================================
--- pkg/stacomir/R/utilitaires.r 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/R/utilitaires.r 2017-04-12 06:17:19 UTC (rev 353)
@@ -22,7 +22,7 @@
if (exists("envir_stacomi")){
miettes=ls(envir=envir_stacomi)
if (length(miettes)> 0 ) {
- miettes=miettes[!miettes%in%c("msg","datawd","sch","lang","baseODBC","usrname","usrpwd","database_expected","gr_interface","login_window")]
+ miettes=miettes[!miettes%in%c("datawd","sch","baseODBC","usrname","usrpwd","database_expected","gr_interface","login_window")]
rm(list=miettes,envir=envir_stacomi)
}
}
@@ -116,8 +116,8 @@
#' source if you plan not to use the compiler but run manually using inst/config/stacomi_manual_launch.R for development.\cr
#' \code{datawd}, is the
#' directory where you want to place the outputs, mostly tables, from the
-#' program, default to ~//CalcmigData lang, is either one of French, English or
-#' Spanish
+#' program, default to ~//CalcmigData
+#' \code{lang}, is either one of French, English or Spanish (deprecated)
#' other fields correspond to sqldf options.
#' @param database expected Are the program (stacomi directory) and database expected to be installed,
#' this argument is necessary to pass tests on system where stacomi is not installed (e.g. R-forge)
Deleted: pkg/stacomir/data/msg.rda
===================================================================
(Binary files differ)
Modified: pkg/stacomir/inst/config/generate_Roxygen2.R
===================================================================
--- pkg/stacomir/inst/config/generate_Roxygen2.R 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/inst/config/generate_Roxygen2.R 2017-04-12 06:17:19 UTC (rev 353)
@@ -30,7 +30,6 @@
setwd("F:/workspace/stacomir/pkg/stacomir")
#data("bMM_Arzal")
#data("bM_Arzal")
-#data("msg")
envir_stacomi <- new.env(parent = emptyenv())
#
require(stacomiR)
Modified: pkg/stacomir/inst/config/generate_data.R
===================================================================
--- pkg/stacomir/inst/config/generate_data.R 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/inst/config/generate_data.R 2017-04-12 06:17:19 UTC (rev 353)
@@ -19,22 +19,7 @@
setwd("F:/workspace/stacomir/pkg/stacomir")
devtools::use_data(calcmig,internal=FALSE,overwrite=TRUE)
-
-
#################################
-# generates messages as generated by RefMesssage()
-# the message are in the default langage (english)
-# from iav three dc with eels
-##################################
-require(stacomiR)
-stacomi(FALSE,FALSE,FALSE)
-assign("lang","English",envir=envir_stacomi)
-refMsg=new("RefMsg")
-createmessage(refMsg,database_expected=TRUE)
-msg=get("msg",envir=envir_stacomi)
-devtools::use_data(msg,internal=FALSE,overwrite=TRUE)
-
-#################################
# generates a dataset with Durif coefficients
# source Laurent Beaulaton
##################################
Deleted: pkg/stacomir/inst/config/generate_message.r
===================================================================
--- pkg/stacomir/inst/config/generate_message.r 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/inst/config/generate_message.r 2017-04-12 06:17:19 UTC (rev 353)
@@ -1,7 +0,0 @@
-# see http://w3.eptb-vilaine.fr:8080/tracstacomi/wiki/Stacomi%20gettext?action=edit
-
-assign("lang","English",envir=envir_stacomi)
-mmmm=new("RefMsg")
-createmessage(mmmm,TRUE)
-msg<-get("msg",envir=envir_stacomi)
-str(msg)
Modified: pkg/stacomir/inst/config/stacomi_manual_launch.r
===================================================================
--- pkg/stacomir/inst/config/stacomi_manual_launch.r 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/inst/config/stacomi_manual_launch.r 2017-04-12 06:17:19 UTC (rev 353)
@@ -56,7 +56,6 @@
source("RefStationMesure.r")
source("Refperiode.r")
source("RefHorodate.r")
-source("RefMsg.r")
source("BilanFonctionnementDC.r")
source("BilanFonctionnementDF.r")
source("BilanOperation.r")
@@ -104,7 +103,6 @@
source("stacomi.r")
# interface_BilanEspeces dans BilanEspeces
setwd("F:/workspace/stacomir/pkg/stacomir")
-data("msg")
stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
Modified: pkg/stacomir/inst/tests/testthat/test-00stacomir.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-00stacomir.R 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/inst/tests/testthat/test-00stacomir.R 2017-04-12 06:17:19 UTC (rev 353)
@@ -30,7 +30,6 @@
test_that("Test that stacomirtools connects",{
require(stacomiR)
envir_stacomi <<- new.env(parent = emptyenv())
- msg<-messages()
mylinks=chargecsv(database_expected=TRUE)
baseODBC=mylinks[["baseODBC"]]
con=new("ConnectionODBC")
@@ -45,7 +44,6 @@
test_that("Test that positive count for nrow(ref.tr_taxon_tax)",{
require(stacomiR)
envir_stacomi <<- new.env(parent = emptyenv())
- msg<-messages()
mylinks=chargecsv(database_expected=TRUE)
baseODBC=mylinks[["baseODBC"]]
requete=new("RequeteODBC")
@@ -60,7 +58,6 @@
test_that("Tests positive count for sch.t_operation_ope",{
require(stacomiR)
envir_stacomi <<- new.env(parent = emptyenv())
- msg<-messages()
mylinks=chargecsv(database_expected=TRUE)
baseODBC=mylinks[["baseODBC"]]
sch<-paste(baseODBC[2],".",sep="")
@@ -108,37 +105,7 @@
rm("envir_stacomi",envir =.GlobalEnv)
})
-context("Messages")
-test_that("Test that messages are loaded from the database",
- {
- envir_stacomi <<- new.env(parent = emptyenv())
- msg<-messages()
- mylinks=chargecsv(database_expected=TRUE)
- baseODBC=mylinks[["baseODBC"]]
- assign("baseODBC",baseODBC,envir=envir_stacomi)
- object=new("RefMsg")
- object<-charge(object)
- expect_true(nrow(object at messager)>0)
- rm("envir_stacomi",envir =.GlobalEnv)
- })
-
-test_that("Test that messages without connection are loaded and of the same length",
- {
- require(stacomiR)
- stacomi(gr_interface=FALSE,login_window=FALSE,database_expected=FALSE)
- assign("lang","English",envir=envir_stacomi)
- object=new("RefMsg")
- object<-createmessage(object,TRUE)
- msgbase<-get("msg",envir=envir_stacomi)
-
-
- msg<-get("msg",envir=envir_stacomi)
- # objects should have the same length but different languages
- expect_identical(length(msg),length(msgbase))
- rm("envir_stacomi",envir =.GlobalEnv)
- })
-
# pour schema get("sch",envir=envir_stacomi)
context(stringr::str_c("Database integrity"))
Modified: pkg/stacomir/man/RefAnnee-class.Rd
===================================================================
--- pkg/stacomir/man/RefAnnee-class.Rd 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/man/RefAnnee-class.Rd 2017-04-12 06:17:19 UTC (rev 353)
@@ -31,8 +31,7 @@
\code{\link{Refparqual-class}},
\code{\link{Refparquan-class}},
\code{\link{Refperiode-class}},
- \code{\link{charge,RefChoix-method}},
- \code{\link{charge,RefMsg-method}}
+ \code{\link{charge,RefChoix-method}}
}
\author{
cedric.briand"at"eptb-vilaine.fr
Modified: pkg/stacomir/man/RefCheckBox-class.Rd
===================================================================
--- pkg/stacomir/man/RefCheckBox-class.Rd 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/man/RefCheckBox-class.Rd 2017-04-12 06:17:19 UTC (rev 353)
@@ -33,8 +33,7 @@
\code{\link{Refparqual-class}},
\code{\link{Refparquan-class}},
\code{\link{Refperiode-class}},
- \code{\link{charge,RefChoix-method}},
- \code{\link{charge,RefMsg-method}}
+ \code{\link{charge,RefChoix-method}}
}
\author{
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
Modified: pkg/stacomir/man/RefChoix-class.Rd
===================================================================
--- pkg/stacomir/man/RefChoix-class.Rd 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/man/RefChoix-class.Rd 2017-04-12 06:17:19 UTC (rev 353)
@@ -36,8 +36,7 @@
\code{\link{Refparqual-class}},
\code{\link{Refparquan-class}},
\code{\link{Refperiode-class}},
- \code{\link{charge,RefChoix-method}},
- \code{\link{charge,RefMsg-method}}
+ \code{\link{charge,RefChoix-method}}
}
\author{
cedric.briand"at"eptb-vilaine.fr
Modified: pkg/stacomir/man/RefCoe-class.Rd
===================================================================
--- pkg/stacomir/man/RefCoe-class.Rd 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/man/RefCoe-class.Rd 2017-04-12 06:17:19 UTC (rev 353)
@@ -40,8 +40,7 @@
\code{\link{Refparqual-class}},
\code{\link{Refparquan-class}},
\code{\link{Refperiode-class}},
- \code{\link{charge,RefChoix-method}},
- \code{\link{charge,RefMsg-method}}
+ \code{\link{charge,RefChoix-method}}
}
\author{
cedric.briand"at"eptb-vilaine.fr
Modified: pkg/stacomir/man/RefDC-class.Rd
===================================================================
--- pkg/stacomir/man/RefDC-class.Rd 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/man/RefDC-class.Rd 2017-04-12 06:17:19 UTC (rev 353)
@@ -38,8 +38,7 @@
\code{\link{Refparqual-class}},
\code{\link{Refparquan-class}},
\code{\link{Refperiode-class}},
- \code{\link{charge,RefChoix-method}},
- \code{\link{charge,RefMsg-method}}
+ \code{\link{charge,RefChoix-method}}
}
\author{
cedric.briand"at"eptb-vilaine.fr
Modified: pkg/stacomir/man/RefDF-class.Rd
===================================================================
--- pkg/stacomir/man/RefDF-class.Rd 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/man/RefDF-class.Rd 2017-04-12 06:17:19 UTC (rev 353)
@@ -30,8 +30,7 @@
\code{\link{Refparqual-class}},
\code{\link{Refparquan-class}},
\code{\link{Refperiode-class}},
- \code{\link{charge,RefChoix-method}},
- \code{\link{charge,RefMsg-method}}
+ \code{\link{charge,RefChoix-method}}
}
\author{
cedric.briand"at"eptb-vilaine.fr
Modified: pkg/stacomir/man/RefHorodate-class.Rd
===================================================================
--- pkg/stacomir/man/RefHorodate-class.Rd 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/man/RefHorodate-class.Rd 2017-04-12 06:17:19 UTC (rev 353)
@@ -29,8 +29,7 @@
\code{\link{Refparqual-class}},
\code{\link{Refparquan-class}},
\code{\link{Refperiode-class}},
- \code{\link{charge,RefChoix-method}},
- \code{\link{charge,RefMsg-method}}
+ \code{\link{charge,RefChoix-method}}
}
\author{
Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
Modified: pkg/stacomir/man/RefListe-class.Rd
===================================================================
--- pkg/stacomir/man/RefListe-class.Rd 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/man/RefListe-class.Rd 2017-04-12 06:17:19 UTC (rev 353)
@@ -31,8 +31,7 @@
\code{\link{Refparqual-class}},
\code{\link{Refparquan-class}},
\code{\link{Refperiode-class}},
- \code{\link{charge,RefChoix-method}},
- \code{\link{charge,RefMsg-method}}
+ \code{\link{charge,RefChoix-method}}
}
\author{
cedric.briand"at"eptb-vilaine.fr
Deleted: pkg/stacomir/man/RefMsg-class.Rd
===================================================================
--- pkg/stacomir/man/RefMsg-class.Rd 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/man/RefMsg-class.Rd 2017-04-12 06:17:19 UTC (rev 353)
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/RefMsg.r
-\docType{class}
-\name{RefMsg-class}
-\alias{RefMsg-class}
-\title{RefMsg referential class to load message according to the language chosen}
-\description{
-RefMsg referential class to load message according to the language chosen
-}
-\section{Slots}{
-
-\describe{
-\item{\code{data}}{A data.frame}
-}}
-
-\author{
-Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
-}
Modified: pkg/stacomir/man/RefStades-class.Rd
===================================================================
--- pkg/stacomir/man/RefStades-class.Rd 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/man/RefStades-class.Rd 2017-04-12 06:17:19 UTC (rev 353)
@@ -26,8 +26,7 @@
\code{\link{Refparqual-class}},
\code{\link{Refparquan-class}},
\code{\link{Refperiode-class}},
- \code{\link{charge,RefChoix-method}},
- \code{\link{charge,RefMsg-method}}
+ \code{\link{charge,RefChoix-method}}
}
\author{
cedric.briand"at"eptb-vilaine.fr
Modified: pkg/stacomir/man/RefTaxon-class.Rd
===================================================================
--- pkg/stacomir/man/RefTaxon-class.Rd 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/man/RefTaxon-class.Rd 2017-04-12 06:17:19 UTC (rev 353)
@@ -31,8 +31,7 @@
\code{\link{Refparqual-class}},
\code{\link{Refparquan-class}},
\code{\link{Refperiode-class}},
- \code{\link{charge,RefChoix-method}},
- \code{\link{charge,RefMsg-method}}
+ \code{\link{charge,RefChoix-method}}
}
\author{
cedric.briand"at"eptb-vilaine.fr
Modified: pkg/stacomir/man/Refpar-class.Rd
===================================================================
--- pkg/stacomir/man/Refpar-class.Rd 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/man/Refpar-class.Rd 2017-04-12 06:17:19 UTC (rev 353)
@@ -37,8 +37,7 @@
\code{\link{Refparqual-class}},
\code{\link{Refparquan-class}},
\code{\link{Refperiode-class}},
- \code{\link{charge,RefChoix-method}},
- \code{\link{charge,RefMsg-method}}
+ \code{\link{charge,RefChoix-method}}
}
\author{
cedric.briand"at"eptb-vilaine.fr
Modified: pkg/stacomir/man/Refparqual-class.Rd
===================================================================
--- pkg/stacomir/man/Refparqual-class.Rd 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/man/Refparqual-class.Rd 2017-04-12 06:17:19 UTC (rev 353)
@@ -35,8 +35,7 @@
\code{\link{RefTaxon-class}}, \code{\link{Refpar-class}},
\code{\link{Refparquan-class}},
\code{\link{Refperiode-class}},
- \code{\link{charge,RefChoix-method}},
- \code{\link{charge,RefMsg-method}}
+ \code{\link{charge,RefChoix-method}}
}
\author{
cedric.briand"at"eptb-vilaine.fr
Modified: pkg/stacomir/man/Refparquan-class.Rd
===================================================================
--- pkg/stacomir/man/Refparquan-class.Rd 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/man/Refparquan-class.Rd 2017-04-12 06:17:19 UTC (rev 353)
@@ -27,8 +27,7 @@
\code{\link{RefTaxon-class}}, \code{\link{Refpar-class}},
\code{\link{Refparqual-class}},
\code{\link{Refperiode-class}},
- \code{\link{charge,RefChoix-method}},
- \code{\link{charge,RefMsg-method}}
+ \code{\link{charge,RefChoix-method}}
}
\author{
cedric.briand"at"eptb-vilaine.fr
Modified: pkg/stacomir/man/Refperiode-class.Rd
===================================================================
--- pkg/stacomir/man/Refperiode-class.Rd 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/man/Refperiode-class.Rd 2017-04-12 06:17:19 UTC (rev 353)
@@ -32,7 +32,6 @@
\code{\link{RefTaxon-class}}, \code{\link{Refpar-class}},
\code{\link{Refparqual-class}},
\code{\link{Refparquan-class}},
- \code{\link{charge,RefChoix-method}},
- \code{\link{charge,RefMsg-method}}
+ \code{\link{charge,RefChoix-method}}
}
\keyword{classes}
Modified: pkg/stacomir/man/bmi.Rd
===================================================================
--- pkg/stacomir/man/bmi.Rd 2017-04-10 18:28:50 UTC (rev 352)
+++ pkg/stacomir/man/bmi.Rd 2017-04-12 06:17:19 UTC (rev 353)
@@ -3,7 +3,7 @@
\docType{data}
\name{bmi}
\alias{bmi}
-\title{Daily glass eel and elver migration from 1984 to 2016 in the Sèvre Niortaise}
+\title{Daily glass eel and elver migration from 1984 to 2016 in the S \u0168 vre Niortaise}
\format{An object of class \link{BilanMigrationInterAnnuelle-class} with data loaded.}
\usage{
bmi
Modified: pkg/stacomir/man/charge-BilanMigrationCar-method.Rd
===================================================================
--- pkg/stacomir/man/charge-BilanMigrationCar-method.Rd 2017-04-10 18:28:50 UTC (rev 352)
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/stacomir -r 353
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