[Stacomir-commits] r418 - in pkg: stacomir stacomir/R 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
Sat Jun 24 22:08:23 CEST 2017
Author: briand
Date: 2017-06-24 22:08:23 +0200 (Sat, 24 Jun 2017)
New Revision: 418
Modified:
pkg/stacomir/DESCRIPTION
pkg/stacomir/NAMESPACE
pkg/stacomir/R/stacomi.R
pkg/stacomir/inst/config/generate_Roxygen2.R
pkg/stacomir/inst/tests/testthat/test-00-stacomir.R
pkg/stacomir/inst/tests/testthat/test-00-zrefclasses.R
pkg/stacomir/inst/tests/testthat/test-01-report_mig_mult.R
pkg/stacomir/inst/tests/testthat/test-02-report_mig.R
pkg/stacomir/inst/tests/testthat/test-05-report_sample_char.R
pkg/stacomir/inst/tests/testthat/test-06-report_mig_interannual.R
pkg/stacomir/inst/tests/testthat/test-07-report_sea_age.R
pkg/stacomir/inst/tests/testthat/test-08-report_silver_eel.R
pkg/stacomir/inst/tests/testthat/test-09-report_annual.R
pkg/stacomir/inst/tests/testthat/test-10-report_env.R
pkg/stacomir/inst/tests/testthat/test-11-report_mig_env.R
pkg/stacomir/inst/tests/testthat/test-12-report_mig_char.R
pkg/stacomir/inst/tests/testthat/test-13-report_species.R
pkg/stacomir/man/stacomiR-package.Rd
pkg/stacomirtools/R/ConnectionODBC.r
pkg/stacomirtools/R/RequeteODBC.r
Log:
Removing assignment to .GlobalEnv and commenting strings so as to pass
check on DESCRIPTION
Modified: pkg/stacomir/DESCRIPTION
===================================================================
--- pkg/stacomir/DESCRIPTION 2017-06-24 18:58:38 UTC (rev 417)
+++ pkg/stacomir/DESCRIPTION 2017-06-24 20:08:23 UTC (rev 418)
@@ -1,14 +1,14 @@
Package: stacomiR
Version: 0.5.3
-Date: 2017-06-19
-Title: Fish Migration Monitoring (stacomiR)
+Date: 2017-06-24
+Title: Fish Migration Monitoring ('stacomiR')
Authors at R: c(person("Cedric", "Briand", role = c("aut", "cre"), email = "cedric.briand00 at gmail.com"),
person("Marion", "Legrand", role = "aut", email="tableau-salt-loire at logrami.fr"),
person("Timothee", "Besse", role = "aut", email="tableau-ang-loire at logrami.fr"))
-Description: Graphical outputs and treatment for a database of fishway
- monitoring. It is a part of the STACOMI open source project developed in
+Description: Graphical outputs and treatment for a database of fish pass
+ monitoring. It is a part of the 'STACOMI' open source project developed in
France by the French Agency for Biodiversity (AFB) institute to centralize
- data obtained by fishway monitoring. Version 0.5.3 is available in French and
+ data obtained by fish pass monitoring. Version 0.5.3 is available in French and
English.
License: GPL (>= 2)
Collate:
Modified: pkg/stacomir/NAMESPACE
===================================================================
--- pkg/stacomir/NAMESPACE 2017-06-24 18:58:38 UTC (rev 417)
+++ pkg/stacomir/NAMESPACE 2017-06-24 20:08:23 UTC (rev 418)
@@ -16,6 +16,7 @@
export(split_per_day)
export(stacomi)
export(vector_to_listsql)
+export(envir_stacomi)
exportClasses(report_annual)
exportClasses(report_dc)
exportClasses(report_df)
Modified: pkg/stacomir/R/stacomi.R
===================================================================
--- pkg/stacomir/R/stacomi.R 2017-06-24 18:58:38 UTC (rev 417)
+++ pkg/stacomir/R/stacomi.R 2017-06-24 20:08:23 UTC (rev 418)
@@ -358,8 +358,7 @@
stacomi=function(gr_interface=TRUE,login_window=TRUE,database_expected=TRUE){
# first loading of connection and odbc info using chargexml()
# trois variables passees a interface graphique via envir_stacomi :
- envir_stacomi <- new.env(parent = emptyenv())
- assign("envir_stacomi",envir_stacomi,.GlobalEnv)
+ #envir_stacomi <- new.env(parent = asNamespace("stacomiR"))
assign("gr_interface",gr_interface,envir=envir_stacomi)
assign("database_expected",database_expected,envir=envir_stacomi)
assign("login_window",login_window,envir=envir_stacomi)
@@ -537,9 +536,9 @@
# "frame_std","frame_tax","frame_annee","frame_check","frame_choice","ref_year",
# "logw","report_stage_pigm","usrname","usrpwd","notebook","values","ind","progress_bar","progres"))
# Progressbar
-utils::globalVariables(c("progres"))
+#utils::globalVariables(c("progres"))
# environment
-utils::globalVariables(c("envir_stacomi"))
+#utils::globalVariables(c("envir_stacomi"))
# reoxygenize fails if data are not loaded
#setwd("F:/workspace/stacomir/branch0.5/stacomir")
@@ -559,5 +558,5 @@
# "uid", "pwd", "sqldf.uid", "sqldf.pwd", "sqldf.dbname", "sqldf.host",
# "sqldf.port", "pgwd", "datawd", "lang"), class = "data.frame", row.names = c(NA,
# -1L))
-#envir_stacomi <- new.env(parent = emptyenv())
+envir_stacomi <- new.env(parent = asNamespace("stacomiR"))
#calcmig<-data.frame()
\ No newline at end of file
Modified: pkg/stacomir/inst/config/generate_Roxygen2.R
===================================================================
--- pkg/stacomir/inst/config/generate_Roxygen2.R 2017-06-24 18:58:38 UTC (rev 417)
+++ pkg/stacomir/inst/config/generate_Roxygen2.R 2017-06-24 20:08:23 UTC (rev 418)
@@ -40,8 +40,11 @@
roxygen2::roxygenise("C:/workspace/stacomir/pkg/stacomir");warnings()[1:10]
#Pour Marion
+
+# using roxygen with stacomirtools
#roxygen2::roxygenise("C:/Users/logrami/workspace/stacomir/pkg/stacomir");warnings()[1:10]
+require(Rd2roxygen)
+setwd("C:/workspace/stacomir/pkg")
+Rd2roxygen(pkg="stacomirtools")
-
-
\ No newline at end of file
Modified: pkg/stacomir/inst/tests/testthat/test-00-stacomir.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-00-stacomir.R 2017-06-24 18:58:38 UTC (rev 417)
+++ pkg/stacomir/inst/tests/testthat/test-00-stacomir.R 2017-06-24 20:08:23 UTC (rev 418)
@@ -37,7 +37,7 @@
test_that("Test that stacomirtools connects",{
require(stacomiR)
- envir_stacomi <<- new.env(parent = emptyenv())
+ envir_stacomi <- new.env(parent = asNamespace("stacomiR"))
mylinks=chargecsv(database_expected=TRUE)
baseODBC=mylinks[["baseODBC"]]
con=new("ConnectionODBC")
@@ -46,7 +46,7 @@
expect_is(connect(con),'ConnectionODBC')
expect_equal(con at etat,"Connection in progress")
odbcCloseAll()
- rm("envir_stacomi",envir =.GlobalEnv)
+ rm("envir_stacomi")
})
@@ -65,13 +65,13 @@
# expect_is(connect(con),'ConnectionODBC')
# expect_equal(con at etat,"Connection in progress")
# odbcCloseAll()
-# rm("envir_stacomi",envir =.GlobalEnv)
+# rm("envir_stacomi")
# })
test_that("Test that positive count for nrow(ref.tr_taxon_tax)",{
require(stacomiR)
- envir_stacomi <<- new.env(parent = emptyenv())
+ envir_stacomi <- new.env(parent = asNamespace("stacomiR"))
mylinks=chargecsv(database_expected=TRUE)
baseODBC=mylinks[["baseODBC"]]
requete=new("RequeteODBC")
@@ -80,12 +80,12 @@
requete<-stacomirtools::connect(requete)
expect_true(as.numeric(requete at query)>0)
odbcCloseAll()
- rm("envir_stacomi",envir =.GlobalEnv)
+ rm("envir_stacomi")
})
test_that("Tests positive count for sch.t_operation_ope",{
require(stacomiR)
- envir_stacomi <<- new.env(parent = emptyenv())
+ envir_stacomi <- new.env(parent = asNamespace("stacomiR"))
mylinks=chargecsv(database_expected=TRUE)
baseODBC=mylinks[["baseODBC"]]
sch<-paste(baseODBC[2],".",sep="")
@@ -95,7 +95,7 @@
requete<-stacomirtools::connect(requete)
expect_true(as.numeric(requete at query)>0)
odbcCloseAll()
- rm("envir_stacomi",envir =.GlobalEnv)
+ rm("envir_stacomi")
})
context("Loading program")
@@ -106,7 +106,6 @@
stacomi(gr_interface=TRUE,login_window=TRUE,database_expected=TRUE)
expect_true(exists("envir_stacomi"))
dispose(get("logw",envir_stacomi))
- rm("envir_stacomi",envir =.GlobalEnv)
})
test_that("Test that gWidget loginwindow is loaded ",{
@@ -114,7 +113,6 @@
stacomi(gr_interface=TRUE,login_window=TRUE,database_expected=TRUE)
expect_true(exists("logw",envir_stacomi))
dispose(get("logw",envir_stacomi))
- rm("envir_stacomi",envir =.GlobalEnv)
})
test_that("Test that gWidget gr_interface is loaded, without database_expected, nor login window",{
@@ -122,7 +120,6 @@
stacomi(gr_interface=TRUE,login_window=FALSE,database_expected=FALSE)
expect_true(exists("win",envir_stacomi))
dispose(get("win",envir_stacomi))
- rm("envir_stacomi",envir =.GlobalEnv)
})
test_that("gWidget gr_interface is loaded, with pre launch_test, but without login window",{
@@ -130,7 +127,6 @@
stacomi(gr_interface=TRUE,login_window=FALSE,database_expected=TRUE)
expect_true(exists("win",envir_stacomi))
dispose(get("win",envir_stacomi))
- rm("envir_stacomi",envir =.GlobalEnv)
})
Modified: pkg/stacomir/inst/tests/testthat/test-00-zrefclasses.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-00-zrefclasses.R 2017-06-24 18:58:38 UTC (rev 417)
+++ pkg/stacomir/inst/tests/testthat/test-00-zrefclasses.R 2017-06-24 20:08:23 UTC (rev 418)
@@ -17,7 +17,6 @@
horodate="01-01-2013"),prints_text("^\\[1\\].+date.+"))
expect_error(ref_horodate<-choice_c(ref_horodate,
horodate="2013/01/01 00:00:00"))
- rm("envir_stacomi",envir =.GlobalEnv)
})
Modified: pkg/stacomir/inst/tests/testthat/test-01-report_mig_mult.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-01-report_mig_mult.R 2017-06-24 18:58:38 UTC (rev 417)
+++ pkg/stacomir/inst/tests/testthat/test-01-report_mig_mult.R 2017-06-24 20:08:23 UTC (rev 418)
@@ -68,7 +68,7 @@
silent=TRUE)
options(warn = 0)
report_mig_mult<-charge(report_mig_mult,silent=TRUE)
-
+ rm(list=ls(envir=envir_stacomi),envir=envir_stacomi)
})
test_that("Test connect method for report_mig_mult",
@@ -107,6 +107,7 @@
source(example_path)
options(warn = 0)
summary(r_mig_mult,silent=TRUE)
+ rm(list=ls(envir=envir_stacomi),envir=envir_stacomi)
})
Modified: pkg/stacomir/inst/tests/testthat/test-02-report_mig.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-02-report_mig.R 2017-06-24 18:58:38 UTC (rev 417)
+++ pkg/stacomir/inst/tests/testthat/test-02-report_mig.R 2017-06-24 20:08:23 UTC (rev 418)
@@ -19,7 +19,7 @@
options(warn = 0)
expect_s4_class(report_mig,
"report_mig")
- rm("envir_stacomi",envir =.GlobalEnv)
+ rm(list=ls(envir=envir_stacomi),envir=envir_stacomi)
})
@@ -50,7 +50,7 @@
# the rest are in 1998
expect_equal(round(sum(report_mig at calcdata[["dc_6"]][["data"]]$Effectif_total)),
8614)
- rm("envir_stacomi",envir =.GlobalEnv)
+ rm(list=ls(envir=envir_stacomi),envir=envir_stacomi)
})
test_that("Test another instance of report_mig, check that operations accross two years are split correcly",{
@@ -80,7 +80,7 @@
# the rest are in 1998
expect_equal(round(sum(report_mig at calcdata[["dc_6"]][["data"]]$Effectif_total)),
26454)
- rm("envir_stacomi",envir =.GlobalEnv)
+ rm(list=ls(envir=envir_stacomi),envir=envir_stacomi)
})
test_that("Test connect method",{
@@ -105,7 +105,7 @@
r_mig<-connect(r_mig,silent=TRUE)
expect_length(r_mig at data,11)
- rm("envir_stacomi",envir =.GlobalEnv)
+ rm(list=ls(envir=envir_stacomi),envir=envir_stacomi)
})
test_that("Test example 02_report_mig",
@@ -135,7 +135,7 @@
data("r_mig")
r_mig<-calcule(r_mig,silent=TRUE)
summary(r_mig,silent=TRUE)
- rm("envir_stacomi",envir =.GlobalEnv)
+ rm(list=ls(envir=envir_stacomi),envir=envir_stacomi)
})
test_that("Test writing an example to the database",
@@ -153,7 +153,7 @@
data("r_mig")
r_mig<-calcule(r_mig,silent=TRUE)
write_database(object=r_mig,silent=TRUE)
- rm("envir_stacomi",envir =.GlobalEnv)
+ rm(list=ls(envir=envir_stacomi),envir=envir_stacomi)
})
test_that("Test that different sums are the same, for report_mig, report_mig_interannual, report_annual",
@@ -193,7 +193,7 @@
sum(bili at data$bjo_valeur[bili at data$bjo_labelquantite=="Effectif_total"]),
label="The sum of number in the report_mig are different to the
number in the report_mig_interannual")
- rm("envir_stacomi",envir =.GlobalEnv)
+ rm(list=ls(envir=envir_stacomi),envir=envir_stacomi)
})
@@ -211,7 +211,7 @@
# this chunk is not launched from examples but loads the r_mig dataset if connection works
data("r_mig")
expect_output(print(r_mig), "report_mig=choice_c",info = NULL)
- rm("envir_stacomi",envir =.GlobalEnv)
+ rm(list=ls(envir=envir_stacomi),envir=envir_stacomi)
})
@@ -240,7 +240,7 @@
bM_EclusierVaux<-calcule(bM_EclusierVaux,silent=TRUE)
plot(bM_EclusierVaux,silent=TRUE)
summary(bM_EclusierVaux,silent=TRUE)
- rm("envir_stacomi",envir =.GlobalEnv)
+ rm(list=ls(envir=envir_stacomi),envir=envir_stacomi)
})
@@ -270,7 +270,7 @@
# some additional arguments passed to plot via ...
plot(bM_Arzal_civ,silent=TRUE,bty="n")
summary(bM_Arzal_civ,silent=TRUE)
- rm("envir_stacomi",envir =.GlobalEnv)
+ rm(list=ls(envir=envir_stacomi),envir=envir_stacomi)
})
# here require setting a connection to logrami server under the name BD_CONTMIG_NAT_SERVEUR
#test_that("test connexion to logrami server",
Modified: pkg/stacomir/inst/tests/testthat/test-05-report_sample_char.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-05-report_sample_char.R 2017-06-24 18:58:38 UTC (rev 417)
+++ pkg/stacomir/inst/tests/testthat/test-05-report_sample_char.R 2017-06-24 20:08:23 UTC (rev 418)
@@ -36,7 +36,6 @@
#options(warn = 0)
expect_s4_class(r_sample_char,
"report_sample_char")
- rm("envir_stacomi",envir =.GlobalEnv)
})
@@ -65,7 +64,6 @@
r_sample_char<-connect(r_sample_char,silent=TRUE)
expect_true(nrow(r_sample_char at data)>0,label="No data for r_sample_char")
r_sample_char<-calcule(r_sample_char,silent=TRUE)
- rm("envir_stacomi",envir =.GlobalEnv)
})
@@ -94,7 +92,6 @@
r_sample_char<-connect(r_sample_char,silent=TRUE)
r_sample_char<-charge(r_sample_char)
r_sample_char<-calcule(r_sample_char,silent=TRUE)
- rm("envir_stacomi",envir =.GlobalEnv)
})
Modified: pkg/stacomir/inst/tests/testthat/test-06-report_mig_interannual.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-06-report_mig_interannual.R 2017-06-24 18:58:38 UTC (rev 417)
+++ pkg/stacomir/inst/tests/testthat/test-06-report_mig_interannual.R 2017-06-24 20:08:23 UTC (rev 418)
@@ -26,7 +26,6 @@
# three warning produced, none shown due to silent=TRUE
options(warn = 0)
expect_s4_class(r_mig_interannual,"report_mig_interannual")
- rm("envir_stacomi",envir =.GlobalEnv)
})
@@ -54,7 +53,6 @@
r_mig_interannual<-connect(r_mig_interannual,silent=TRUE)
summary(object=r_mig_interannual,silent=TRUE)
# two warning produced
- rm("envir_stacomi",envir =.GlobalEnv)
})
@@ -180,5 +178,4 @@
label="The sum of number in the report_mig are different to the
number in the report_annual class"
)
- rm("envir_stacomi",envir =.GlobalEnv)
})
Modified: pkg/stacomir/inst/tests/testthat/test-07-report_sea_age.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-07-report_sea_age.R 2017-06-24 18:58:38 UTC (rev 417)
+++ pkg/stacomir/inst/tests/testthat/test-07-report_sea_age.R 2017-06-24 20:08:23 UTC (rev 418)
@@ -21,7 +21,6 @@
))
# warnings No data for par 1786No data for par 1785
r_seaa<-connect(r_seaa,silent=TRUE)
- rm("envir_stacomi",envir =.GlobalEnv)
})
test_that("test that loading bad limits fails",{
Modified: pkg/stacomir/inst/tests/testthat/test-08-report_silver_eel.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-08-report_silver_eel.R 2017-06-24 18:58:38 UTC (rev 417)
+++ pkg/stacomir/inst/tests/testthat/test-08-report_silver_eel.R 2017-06-24 20:08:23 UTC (rev 418)
@@ -26,7 +26,6 @@
plot(r_silver, plot.type=4)
# print a summary statistic, and save the output in a list for later use
stats<-summary(r_silver,silent=TRUE)
- rm("envir_stacomi",envir =.GlobalEnv)
})
Modified: pkg/stacomir/inst/tests/testthat/test-09-report_annual.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-09-report_annual.R 2017-06-24 18:58:38 UTC (rev 417)
+++ pkg/stacomir/inst/tests/testthat/test-09-report_annual.R 2017-06-24 20:08:23 UTC (rev 418)
@@ -20,7 +20,6 @@
silent=TRUE)
r_ann<-connect(r_ann,silent=TRUE)
expect_s4_class(r_ann,"report_annual")
- rm("envir_stacomi",envir =.GlobalEnv)
})
@@ -45,8 +44,7 @@
dev.new()
plot(r_ann,silent=TRUE)
dev.new()
- barplot(r_ann)
- rm("envir_stacomi",envir =.GlobalEnv)
+ barplot(r_ann)
})
test_that("Test example report_mig_annual-example",
Modified: pkg/stacomir/inst/tests/testthat/test-10-report_env.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-10-report_env.R 2017-06-24 18:58:38 UTC (rev 417)
+++ pkg/stacomir/inst/tests/testthat/test-10-report_env.R 2017-06-24 20:08:23 UTC (rev 418)
@@ -12,7 +12,6 @@
silent=TRUE)
r_env<-connect(r_env,silent=TRUE)
expect_true(nrow(r_env at data)>0,"The is a problem when loading data in the data slot" )
- rm("envir_stacomi",envir =.GlobalEnv)
})
test_that("test plot method",{
@@ -26,7 +25,6 @@
silent=TRUE)
r_env<-connect(r_env,silent=TRUE)
r_env<-plot(r_env)
- rm("envir_stacomi",envir =.GlobalEnv)
})
Modified: pkg/stacomir/inst/tests/testthat/test-11-report_mig_env.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-11-report_mig_env.R 2017-06-24 18:58:38 UTC (rev 417)
+++ pkg/stacomir/inst/tests/testthat/test-11-report_mig_env.R 2017-06-24 20:08:23 UTC (rev 418)
@@ -17,7 +17,6 @@
r_mig_env<-connect(r_mig_env,silent=TRUE)
expect_true(nrow(r_mig_env at report_env@data)>0,"Data not loaded in the report_env part of the object" )
expect_true(nrow(r_mig_env at report_mig_mult@data)>0,"Data not loaded in the report_mig_mult part of the object" )
- rm("envir_stacomi",envir =.GlobalEnv)
})
test_that("test plot method",{
@@ -39,7 +38,6 @@
suppressWarnings(plot(r_mig_env,
color_station=c("temp_gabion"="red","coef_maree"="blue","phases_lune"="pink"),
color_dc=c("5"="yellow","6"="orange","12"="purple"),silent=TRUE))
- rm("envir_stacomi",envir =.GlobalEnv)
})
Modified: pkg/stacomir/inst/tests/testthat/test-12-report_mig_char.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-12-report_mig_char.R 2017-06-24 18:58:38 UTC (rev 417)
+++ pkg/stacomir/inst/tests/testthat/test-12-report_mig_char.R 2017-06-24 20:08:23 UTC (rev 418)
@@ -27,7 +27,6 @@
r_mig_char<-connect(r_mig_char)
expect_true(is.null(r_mig_char at data$parqual),label="there should be no data in parqual when not qualitative parm are selected")
expect_true(nrow(r_mig_char at data$parquan)>0,"There should be data in the parquan slot when quantitative parm are selected" )
- rm("envir_stacomi",envir =.GlobalEnv)
})
test_that("test setasqualitative method",{
@@ -64,7 +63,6 @@
expect_false(r_mig_char at parquan@par_selected=='A124', label="The parameter A124 should have been removed from quant parm")
expect_true('A124'%in%r_mig_char at data$parqual$car_par_code)
expect_false('A124'%in%r_mig_char at data$parquan$car_par_code)
- rm("envir_stacomi",envir =.GlobalEnv)
})
@@ -99,8 +97,7 @@
silent=TRUE,breaks=c(0,1.5,2.5,10),label=c("age 1","age 2","age 3"))
r_mig_char<-calcule(r_mig_char,silent=TRUE)
expect_true(any(!is.na(r_mig_char at calcdata$car_par_code_qual))&any(!is.na(r_mig_char at calcdata$car_par_code_quan)), label="The merge function works and returns both qualitative and quantitative parameters")
-
- rm("envir_stacomi",envir =.GlobalEnv)
+
})
Modified: pkg/stacomir/inst/tests/testthat/test-13-report_species.R
===================================================================
--- pkg/stacomir/inst/tests/testthat/test-13-report_species.R 2017-06-24 18:58:38 UTC (rev 417)
+++ pkg/stacomir/inst/tests/testthat/test-13-report_species.R 2017-06-24 20:08:23 UTC (rev 418)
@@ -72,8 +72,7 @@
mycolorrampyellow(5),
mycolorrampred(5))
plot(bilesp,plot.type="barplot",color=color,silent=TRUE)
- rm("envir_stacomi",envir =.GlobalEnv)
- })
+ })
test_that("test that summary method works",{
require(stacomiR)
@@ -93,6 +92,5 @@
bilesp<-connect(bilesp,silent=TRUE)
bilesp<-calcule(bilesp,silent=TRUE)
summary(bilesp,silent=TRUE)
- rm("envir_stacomi",envir =.GlobalEnv)
})
Modified: pkg/stacomir/man/stacomiR-package.Rd
===================================================================
--- pkg/stacomir/man/stacomiR-package.Rd 2017-06-24 18:58:38 UTC (rev 417)
+++ pkg/stacomir/man/stacomiR-package.Rd 2017-06-24 20:08:23 UTC (rev 418)
@@ -3,15 +3,15 @@
\docType{package}
\title{package Fish Migration Monitoring (stacomiR)- Stations de Controle des Migrations}
\description{
-Stacomi enables to read informations in a database about fish migrations to build overviews of fish migrations and creating charts, plots, and summaries.
-The stacomi project comprises an open source Postgres database, and a java interface to fill in data. Please contact the author if you want to try it out.
+'Stacomi' enables to read informations in a database about fish migrations to build overviews of fish migrations and creating charts, plots, and summaries.
+The 'stacomi' project comprises an open source 'Postgres' database, and a 'java' interface to fill in data. Please contact the author if you want to try it out.
}
\details{
\tabular{ll}{
Package: \tab stacomiR\cr
Type: \tab Package\cr
Version: \tab 0.5.3\cr
-Date: \tab 2017-06-19\cr
+Date: \tab 2017-06-24\cr
License: \tab GPL (>= 2)\cr
LazyLoad: \tab yes\cr
Depends: \tab methods\cr
Modified: pkg/stacomirtools/R/ConnectionODBC.r
===================================================================
--- pkg/stacomirtools/R/ConnectionODBC.r 2017-06-24 18:58:38 UTC (rev 417)
+++ pkg/stacomirtools/R/ConnectionODBC.r 2017-06-24 20:08:23 UTC (rev 418)
@@ -49,7 +49,7 @@
if (exists("baseODBC",envir=envir_stacomi)){
object at baseODBC<-get("baseODBC",envir=envir_stacomi)
} else {
- if(exists("envir_stacomi")){# the program is called within stacomiR
+ if (exists("envir_stacomi")){# the program is called within stacomiR
funout(gettext("You need to define a baseODBC vector with the 'ODBC' link, the user and the password\n"),arret=TRUE)
} else {
stop("you need to define a vector baseODBC with the 'ODBC' link, user and password")
@@ -62,14 +62,14 @@
case = "tolower",
believeNRows = FALSE))
if (!exists("odbcConnect")) {
- if(exists("envir_stacomi")){
+ if (exists("envir_stacomi")){
funout("The RODBC library is necessary, please load the package",arret=TRUE)
} else {
stop("the RODBC library is necessary, please load the package")
}
}
if (!object at silent) {
- if(exists("envir_stacomi")){
+ if (exists("envir_stacomi")){
print(paste("connection trial, warning this class should only be used for test: ",object at baseODBC[1]))
} else {
print(paste("connection trial, warning this class should only be used for test: ",object at baseODBC[1]))
@@ -77,7 +77,7 @@
}
# sends the result of a trycatch connection in the
#l'object (current connection), e.g. a character vector
- connection_error<-if(exists("envir_stacomi")){
+ connection_error<-if (exists("envir_stacomi")){
error=paste(gettext("Connection failed :\n",object at baseODBC[1]))
} else {
error="impossible connection"
Modified: pkg/stacomirtools/R/RequeteODBC.r
===================================================================
--- pkg/stacomirtools/R/RequeteODBC.r 2017-06-24 18:58:38 UTC (rev 417)
+++ pkg/stacomirtools/R/RequeteODBC.r 2017-06-24 20:08:23 UTC (rev 418)
@@ -146,7 +146,7 @@
}
if ((class(resultatRequete)=="data.frame")[1]) {
if (!object at silent) funout(msg6)
- object at query=killfactor(query) # instead of query 11/08/2009 11:55:20
+ object at query=killfactor(query)
object at etat=msg6
} else {
if (!object at silent) print(resultatRequete)
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