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-rw-r--r--ChangeLog2
-rw-r--r--R/checkexperiment.R16
-rw-r--r--R/checkplate.R1
-rw-r--r--check.log9
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

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