[CHNOSZ-commits] r518 - in pkg/CHNOSZ: . R tests/testthat

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

Author: jedick
Date: 2019-12-08 16:50:00 +0100 (Sun, 08 Dec 2019)
New Revision: 518

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/objective.R
   pkg/CHNOSZ/R/util.args.R
   pkg/CHNOSZ/tests/testthat/test-revisit.R
Log:
apply Martin Maechler's fixes for issues under R-devel


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-12-05 01:29:39 UTC (rev 517)
+++ pkg/CHNOSZ/DESCRIPTION	2019-12-08 15:50:00 UTC (rev 518)
@@ -1,6 +1,6 @@
 Date: 2019-12-05
 Package: CHNOSZ
-Version: 1.3.3-14
+Version: 1.3.3-15
 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/objective.R
===================================================================
--- pkg/CHNOSZ/R/objective.R	2019-12-05 01:29:39 UTC (rev 517)
+++ pkg/CHNOSZ/R/objective.R	2019-12-08 15:50:00 UTC (rev 518)
@@ -53,9 +53,8 @@
     # first, a function to calculate qqr
     qqrfun <- function(x) {
       # this is to catch errors from qqnorm
-      qqn <- try(qqnorm(x, plot.it=FALSE), silent=TRUE)
-      if(inherits(qqn, "try-error")) qqr <- NA
-      else qqr <- cor(qqn[[1]], qqn[[2]])
+      qqn <- tryCatch(qqnorm(x, plot.it=FALSE), error=identity)
+      qqr <- if(inherits(qqn, "error")) NA else cor(qqn[[1]], qqn[[2]])
     }
     # apply the function to the rows of loga1
     qqr <- apply(loga1, 1, qqrfun)

Modified: pkg/CHNOSZ/R/util.args.R
===================================================================
--- pkg/CHNOSZ/R/util.args.R	2019-12-05 01:29:39 UTC (rev 517)
+++ pkg/CHNOSZ/R/util.args.R	2019-12-08 15:50:00 UTC (rev 518)
@@ -42,11 +42,10 @@
   if(sys.nframe() < n) name <- character()
   else {
     sc <- sys.call(-n)[[1]]
-    name <- try(as.character(sc),silent=TRUE)
+    name <- tryCatch(as.character(sc), error = function(e) character())
     # also return character() if the value from sys.call is
     # the function itself (why does this sometimes happen,
     # e.g. when called from affinity()?)
-    if(inherits(name, "try-error")) name <- character()
   }
   return(name)
 }

Modified: pkg/CHNOSZ/tests/testthat/test-revisit.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-revisit.R	2019-12-05 01:29:39 UTC (rev 517)
+++ pkg/CHNOSZ/tests/testthat/test-revisit.R	2019-12-08 15:50:00 UTC (rev 518)
@@ -37,7 +37,7 @@
   r2.qqr <- revisit(e2, "qqr", plot.it=FALSE)
   r3.qqr <- revisit(e3, "qqr", plot.it=FALSE)
   # check that we get the same values
-  expect_equivalent(c(r0.qqr$H), tail(r1.qqr$H, 1))
+  expect_equal(c(r0.qqr$H), c(tail(r1.qqr$H, 1)))
   expect_equal(c(r0.qqr$H), r3.qqr$H[4, 3, 2])
   # check that we get the same index and same optimum
   expect_equal(r1.qqr$ixopt, r2.qqr$ixopt, check.attributes=FALSE)
@@ -62,7 +62,7 @@
   # the referenced objectives compare the logarithms of activities (loga1) to reference values (loga2)
   # the spearman correlation coefficient
   r1.spearman <- revisit(e1, "spearman", c(1, 2, 3), plot.it=FALSE)
-  expect_equivalent(head(r1.spearman$H, 1), -1) # perfect anti-rank correlation
+  expect_equal(c(head(r1.spearman$H, 1)), -1) # perfect anti-rank correlation
   expect_equal(max(r1.spearman$H), 1)  # perfect rank correlation
   # where logarithm of activity of the 3rd species (glutamic acid) maximizes
   r1.logact <- revisit(e1, "logact", 3, plot.it=FALSE)