[CHNOSZ-commits] r418 - in pkg/CHNOSZ: . R inst

[noreply at r-forge.r-project.org]

Author: jedick
Date: 2019-03-02 15:16:57 +0100 (Sat, 02 Mar 2019)
New Revision: 418

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/add.obigt.R
   pkg/CHNOSZ/R/diagram.R
   pkg/CHNOSZ/R/thermo.R
   pkg/CHNOSZ/R/util.data.R
   pkg/CHNOSZ/inst/NEWS
Log:
various fixes to maintain compatibility with R version 3.1.0


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-03-02 11:01:02 UTC (rev 417)
+++ pkg/CHNOSZ/DESCRIPTION	2019-03-02 14:16:57 UTC (rev 418)
@@ -1,6 +1,6 @@
 Date: 2019-03-02
 Package: CHNOSZ
-Version: 1.3.0-2
+Version: 1.3.0-3
 Title: Thermodynamic Calculations and Diagrams for Geochemistry
 Authors at R: c(
     person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),

Modified: pkg/CHNOSZ/R/add.obigt.R
===================================================================
--- pkg/CHNOSZ/R/add.obigt.R	2019-03-02 11:01:02 UTC (rev 417)
+++ pkg/CHNOSZ/R/add.obigt.R	2019-03-02 14:16:57 UTC (rev 418)
@@ -128,7 +128,8 @@
     if(length(isys)==1) file <- system.file(paste0("extdata/OBIGT/", sysfiles[isys]), package="CHNOSZ")
   }
   # read data from the file
-  to2 <- read.csv(file, as.is=TRUE)
+  # we need explicit colClasses here to avoid automatic detection as character for long numeric values in R 3.1.0  20190302
+  to2 <- read.csv(file, as.is=TRUE, colClasses=c(rep("character", 7), rep("numeric", 13)))
   # load only selected species if requested
   if(!is.null(species)) {
     idat <- match(species, to2$name)

Modified: pkg/CHNOSZ/R/diagram.R
===================================================================
--- pkg/CHNOSZ/R/diagram.R	2019-03-02 11:01:02 UTC (rev 417)
+++ pkg/CHNOSZ/R/diagram.R	2019-03-02 14:16:57 UTC (rev 418)
@@ -515,7 +515,8 @@
 	  }
 	}
         # https://stackoverflow.com/questions/34570860/adding-na-to-make-all-list-elements-equal-length 20181029
-        lapply(linesout, `length<-`, max(lengths(linesout)))
+        # for compatibility with R 3.1.0, don't use lengths() here 20190302
+        lapply(linesout, `length<-`, max(sapply(linesout, length)))
       }
       ## label plot function
       plot.names <- function(out, xs, ys, xlim, ylim, names) {

Modified: pkg/CHNOSZ/R/thermo.R
===================================================================
--- pkg/CHNOSZ/R/thermo.R	2019-03-02 11:01:02 UTC (rev 417)
+++ pkg/CHNOSZ/R/thermo.R	2019-03-02 14:16:57 UTC (rev 418)
@@ -44,7 +44,8 @@
   # need explicit "/" for Windows
   sourcefiles <- paste0(OBIGTdir, "/", c(sources_aq, sources_cr, sources_liq, sources_gas), ".csv")
   sourcefiles[!sources=="Berman_cr"] <- paste0(sourcefiles[!sources=="Berman_cr"], ".xz")
-  datalist <- lapply(sourcefiles, read.csv, as.is=TRUE)
+  # we need explicit colClasses here to avoid automatic detection as character for long numeric values in R 3.1.0  20190302
+  datalist <- lapply(sourcefiles, read.csv, as.is=TRUE, colClasses=c(rep("character", 7), rep("numeric", 13)))
   obigt <- do.call(rbind, datalist)
   # also read references file
   refs <- read.csv(file.path(OBIGTdir, "refs.csv"), as.is=TRUE)

Modified: pkg/CHNOSZ/R/util.data.R
===================================================================
--- pkg/CHNOSZ/R/util.data.R	2019-03-02 11:01:02 UTC (rev 417)
+++ pkg/CHNOSZ/R/util.data.R	2019-03-02 14:16:57 UTC (rev 418)
@@ -399,7 +399,7 @@
   # and apply column names depending on the EOS
   if(identical(state, "aq")) {
     # species in the Akinfiev-Diamond model (AkDi) have NA for Z 20190219
-    isAkDi <- is.na(obigt$z.T)
+    isAkDi <- is.na(obigt[, 20])
     # remove scaling factors for the HKF species, but not for the AkDi species
     # protect this by an if statement to workaround error in subassignment to empty subset of data frame in R < 3.6.0
     # (https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17483) 20190302

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2019-03-02 11:01:02 UTC (rev 417)
+++ pkg/CHNOSZ/inst/NEWS	2019-03-02 14:16:57 UTC (rev 418)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.3.0-1 (2019-03-02)
+CHANGES IN CHNOSZ 1.3.0-3 (2019-03-02)
 --------------------------------------
 
 - Fix unexported function obigt2eos(), which was affected by "Assignment
@@ -7,6 +7,10 @@
   caused errors in R-release (3.5.2) but not R-devel, when using info()
   for species with the AkDi model.
 
+- Various fixes to maintain compatibility with R version 3.1.0 (don't
+  use lengths(), and provide explicit colClasses to read.csv() to avoid
+  automatic detection of character for long numeric values).
+
 CHANGES IN CHNOSZ 1.3.0 (2019-02-26)
 ------------------------------------