Version 0.7.2v0.7.2

with fixed checkplate function

4 files changed, 19 insertions, 9 deletions

diff --git a/ChangeLog b/ChangeLog
index 11a12e2..a3efbd1 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -2,6 +2,8 @@
 
 	* DESCRIPTION: New verson 0.7.2
 	* Switch to odbc instead of RODBC
+	* Fix the checkplate function which was not working with this setup,
+	presumably because of different behaviour of mariadb compared to mysql
 
 2017-07-18  Johannes Ranke
 
diff --git a/R/checkexperiment.R b/R/checkexperiment.R
index 7fa1a60..865d678 100644
--- a/R/checkexperiment.R
+++ b/R/checkexperiment.R
@@ -1,7 +1,7 @@
 utils::globalVariables(c("type", "conc", "substance"))
 
-checkexperiment <- function(id, 
-  db = c("ecotox", "cytotox", "enzymes"), 
+checkexperiment <- function(id,
+  db = c("ecotox", "cytotox", "enzymes"),
   endpoint = "%")
 {
   db = match.arg(db)
@@ -27,13 +27,14 @@ checkexperiment <- function(id,
   comment <- as.character(commentdata[[1]])
 
   expquery <- paste0("SELECT ",
-    "experimentator, substance, ", testtype, ", conc, unit,", responsename, ",
-    type, raw_0, duration, performed, ok ",
+    "experimentator, substance, ", testtype, ", conc, unit, ", responsename, ", ",
+    if (db == "ecotox") "type, raw_0, duration, ",
+    "performed, ok ",
     "FROM ", db, " ",
     "WHERE ", exptype, "=", id)
 
   if (db == "ecotox") {
-    expquery <- paste0(expquery, " AND type LIKE '", endpoint, "'") 
+    expquery <- paste0(expquery, " AND type LIKE '", endpoint, "'")
   }
 
   expdata <- dbGetQuery(con, expquery)
@@ -61,7 +62,7 @@ checkexperiment <- function(id,
   } else {
     # Use raw response for ecotox
     expdata$response <- expdata$raw_response
-    
+
     if (nlevels(expdata$type) > 1) {
       message("There are data for more than one type of raw response in your data.\n",
               "The types are ", paste(levels(expdata$type), collapse = " and "), ".\n",
@@ -168,8 +169,7 @@ checkexperiment <- function(id,
   lld <- log10(min(subset(drdata,conc!=0)$conc))
   lhd <- log10(max(drdata$conc))
 
-  ylab <- if (db == "ecotox") endpoint
-          else responsename
+  ylab <- if (db == "ecotox") endpoint else responsename
 
   plot(1,type="n",
       xlim = c(lld - 0.5, lhd + 2),
diff --git a/R/checkplate.R b/R/checkplate.R
index 1421179..d66e1be 100644
--- a/R/checkplate.R
+++ b/R/checkplate.R
@@ -1,4 +1,5 @@
 checkplate <- function(id, db = c("cytotox", "enzymes"))
 {
+  db <- match.arg(db)
   checkexperiment(id, db = db)
 }
diff --git a/check.log b/check.log
index 165a11c..8ccba2d 100644
--- a/check.log
+++ b/check.log
@@ -1,10 +1,13 @@
 * using log directory ‘/home/jranke/git/drfit/drfit.Rcheck’
-* using R version 3.5.1 (2018-07-02)
+* using R Under development (unstable) (2018-10-11 r75429)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * using session charset: UTF-8
+* using option ‘--as-cran’
 * checking for file ‘drfit/DESCRIPTION’ ... OK
 * this is package ‘drfit’ version ‘0.7.2’
 * package encoding: UTF-8
+* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
+Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
 * checking package namespace information ... OK
 * checking package dependencies ... OK
 * checking if this is a source package ... OK
@@ -13,9 +16,11 @@
 * checking for hidden files and directories ... OK
 * checking for portable file names ... OK
 * checking for sufficient/correct file permissions ... OK
+* checking serialization versions ... OK
 * checking whether package ‘drfit’ can be installed ... OK
 * checking installed package size ... OK
 * checking package directory ... OK
+* checking for future file timestanps ... OK
 * checking DESCRIPTION meta-information ... OK
 * checking top-level files ... OK
 * checking for left-over files ... OK
@@ -29,6 +34,7 @@
 * checking whether the namespace can be loaded with stated dependencies ... OK
 * checking whether the namespace can be unloaded cleanly ... OK
 * checking loading without being on the library search path ... OK
+* checking use of S3 registration ... OK
 * checking dependencies in R code ... OK
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
@@ -36,6 +42,7 @@
 * checking R code for possible problems ... OK
 * checking Rd files ... OK
 * checking Rd metadata ... OK
+* checking Rd line widths ... OK
 * checking Rd cross-references ... OK
 * checking for missing documentation entries ... OK
 * checking for code/documentation mismatches ... OK