[CHNOSZ-commits] r517 - in pkg/CHNOSZ: . R inst tests/testthat

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Thu Dec 5 02:29:39 CET 2019 

Author: jedick
Date: 2019-12-05 02:29:39 +0100 (Thu, 05 Dec 2019)
New Revision: 517

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/add.obigt.R
   pkg/CHNOSZ/R/basis.R
   pkg/CHNOSZ/R/objective.R
   pkg/CHNOSZ/R/util.args.R
   pkg/CHNOSZ/R/util.blast.R
   pkg/CHNOSZ/R/util.expression.R
   pkg/CHNOSZ/R/util.fasta.R
   pkg/CHNOSZ/R/util.matrix.R
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/tests/testthat/test-revisit.R
Log:
change class() to inherits() (fix for R-devel)


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-11-16 03:14:04 UTC (rev 516)
+++ pkg/CHNOSZ/DESCRIPTION	2019-12-05 01:29:39 UTC (rev 517)
@@ -1,6 +1,6 @@
-Date: 2019-11-16
+Date: 2019-12-05
 Package: CHNOSZ
-Version: 1.3.3-13
+Version: 1.3.3-14
 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	2019-11-16 03:14:04 UTC (rev 516)
+++ pkg/CHNOSZ/R/add.obigt.R	2019-12-05 01:29:39 UTC (rev 517)
@@ -145,7 +145,7 @@
   id2 <- paste(to2$name,to2$state)
   # check if the data is compatible with thermo$obigt
   tr <- try(rbind(to1,to2),silent=TRUE)
-  if(identical(class(tr),'try-error')) stop(paste(file,"is not compatible with thermo$obigt data table."))
+  if(inherits(tr, "try-error")) stop(paste(file, "is not compatible with thermo$obigt data table."))
   # match the new species to existing ones
   does.exist <- id2 %in% id1
   ispecies.exist <- na.omit(match(id2, id1))

Modified: pkg/CHNOSZ/R/basis.R
===================================================================
--- pkg/CHNOSZ/R/basis.R	2019-11-16 03:14:04 UTC (rev 516)
+++ pkg/CHNOSZ/R/basis.R	2019-12-05 01:29:39 UTC (rev 517)
@@ -118,7 +118,7 @@
     else stop("the number of basis species is less than the number of elements")
   }
   # the second test: matrix is invertible
-  if(class(try(solve(comp), silent=TRUE))=='try-error') 
+  if(inherits(try(solve(comp), silent=TRUE), "try-error")) 
     stop("singular stoichiometric matrix")
   # store the basis definition in thermo$basis, including
   # both numeric and character data, so we need to use a data frame

Modified: pkg/CHNOSZ/R/objective.R
===================================================================
--- pkg/CHNOSZ/R/objective.R	2019-11-16 03:14:04 UTC (rev 516)
+++ pkg/CHNOSZ/R/objective.R	2019-12-05 01:29:39 UTC (rev 517)
@@ -54,7 +54,7 @@
     qqrfun <- function(x) {
       # this is to catch errors from qqnorm
       qqn <- try(qqnorm(x, plot.it=FALSE), silent=TRUE)
-      if(class(qqn)=="try-error") qqr <- NA
+      if(inherits(qqn, "try-error")) qqr <- NA
       else qqr <- cor(qqn[[1]], qqn[[2]])
     }
     # apply the function to the rows of loga1

Modified: pkg/CHNOSZ/R/util.args.R
===================================================================
--- pkg/CHNOSZ/R/util.args.R	2019-11-16 03:14:04 UTC (rev 516)
+++ pkg/CHNOSZ/R/util.args.R	2019-12-05 01:29:39 UTC (rev 517)
@@ -46,7 +46,7 @@
     # 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(class(name)=="try-error") name <- character()
+    if(inherits(name, "try-error")) name <- character()
   }
   return(name)
 }

Modified: pkg/CHNOSZ/R/util.blast.R
===================================================================
--- pkg/CHNOSZ/R/util.blast.R	2019-11-16 03:14:04 UTC (rev 516)
+++ pkg/CHNOSZ/R/util.blast.R	2019-12-05 01:29:39 UTC (rev 517)
@@ -6,7 +6,7 @@
 ## E-value and max hits per query
 read.blast <- function(file, similarity=30, evalue=1e-5, max.hits=1, min.length=NA, quiet=FALSE) {
   # display some information about the file
-  if("connection" %in% class(file)) fname <- summary(file)$description
+  if(inherits(file, "connection")) fname <- summary(file)$description
   else fname <- basename(file)
   cat(paste("read.blast: reading", fname, "\n"))
   # read the blast tabular file

Modified: pkg/CHNOSZ/R/util.expression.R
===================================================================
--- pkg/CHNOSZ/R/util.expression.R	2019-11-16 03:14:04 UTC (rev 516)
+++ pkg/CHNOSZ/R/util.expression.R	2019-12-05 01:29:39 UTC (rev 517)
@@ -19,7 +19,7 @@
     elements <- suppressWarnings(try(makeup(species), TRUE))
   } else elements <- split.formula(species)
   # if species can't be parsed as a chemical formula, we don't do the formula formatting
-  if(identical(class(elements), "try-error") | !is.numeric(elements)) expr <- species
+  if(inherits(elements, "try-error") | !is.numeric(elements)) expr <- species
   else {
     # where we'll put the expression
     expr <- ""

Modified: pkg/CHNOSZ/R/util.fasta.R
===================================================================
--- pkg/CHNOSZ/R/util.fasta.R	2019-11-16 03:14:04 UTC (rev 516)
+++ pkg/CHNOSZ/R/util.fasta.R	2019-12-05 01:29:39 UTC (rev 517)
@@ -16,7 +16,7 @@
   #   otherwise ID is parsed from FASTA header (can take a while)
   
   # check if the file is in an archive (https://github.com/jimhester/archive)
-  if("archive_read" %in% class(file)) {
+  if(inherits(file, "archive_read")) {
     is.archive <- TRUE
     filebase <- gsub("]", "", basename(summary(file)$description))
   } else {
@@ -115,7 +115,7 @@
   oldopt <- options(warn=-1)
   URLstuff <- try(readLines(proteinURL),TRUE)
   options(oldopt)
-  if(class(URLstuff)=="try-error") {
+  if(inherits(URLstuff, "try-error")) {
     message(" ::: FAILED :::")
     return(NA)
   }

Modified: pkg/CHNOSZ/R/util.matrix.R
===================================================================
--- pkg/CHNOSZ/R/util.matrix.R	2019-11-16 03:14:04 UTC (rev 516)
+++ pkg/CHNOSZ/R/util.matrix.R	2019-12-05 01:29:39 UTC (rev 517)
@@ -15,7 +15,7 @@
   for(i in 1:nrow(combs)) {
     # a slow method, actually calculating the inverse
     #tt <- try(solve(A[combs[i,],]),silent=TRUE)
-    #if(class(tt)!="try-error") ic <- c(ic,i)
+    #if(!inherits(tt, "try-error")) ic <- c(ic,i)
     # it's faster just to test if the determinant is non-zero
     d <- det(A[combs[i,],])
     if(abs(d) > zero) ic <- c(ic, i)

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2019-11-16 03:14:04 UTC (rev 516)
+++ pkg/CHNOSZ/inst/NEWS	2019-12-05 01:29:39 UTC (rev 517)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.3.3-12 (2019-11-11)
+CHANGES IN CHNOSZ 1.3.3-14 (2019-12-05)
 ---------------------------------------
 
 - describe.reaction(): remove the Unicode double arrow. A simple equals
@@ -42,6 +42,13 @@
   to -999, and vice versa. Thanks to Feng Lai for the request and test
   case.
 
+- Fix a bug where berman() returned NA values for K-feldspar below
+  298.15 K, due to improperly initialized values for the disorder
+  properties. Thanks to Kaustubh Hakim for the bug report.
+
+- Use inherits() instead of class() for checking try() errors (don't
+  use conditions of length > 1 in if() statements -- fix for R-devel).
+
 CHANGES IN CHNOSZ 1.3.3 (2019-08-02)
 ------------------------------------
 

Modified: pkg/CHNOSZ/tests/testthat/test-revisit.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-revisit.R	2019-11-16 03:14:04 UTC (rev 516)
+++ pkg/CHNOSZ/tests/testthat/test-revisit.R	2019-12-05 01:29:39 UTC (rev 517)
@@ -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_equal(c(r0.qqr$H), tail(r1.qqr$H, 1))
+  expect_equivalent(c(r0.qqr$H), tail(r1.qqr$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_equal(head(r1.spearman$H, 1), -1) # perfect anti-rank correlation
+  expect_equivalent(head(r1.spearman$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)

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