From noreply at r-forge.r-project.org  Sun Mar 23 03:53:50 2014
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sun, 23 Mar 2014 03:53:50 +0100 (CET)
Subject: [CHNOSZ-commits] r66 - in pkg/CHNOSZ: . inst inst/tests man
Message-ID: <20140323025350.DEEB518670A@r-forge.r-project.org>

Author: jedick
Date: 2014-03-23 03:53:46 +0100 (Sun, 23 Mar 2014)
New Revision: 66

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/inst/tests/test-EOSregress.R
   pkg/CHNOSZ/man/revisit.Rd
Log:
use full spelling of check.attributes argument in all.equal (via expect_equal)


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2014-02-01 08:39:09 UTC (rev 65)
+++ pkg/CHNOSZ/DESCRIPTION	2014-03-23 02:53:46 UTC (rev 66)
@@ -1,6 +1,6 @@
-Date: 2014-02-01
+Date: 2014-03-23
 Package: CHNOSZ
-Version: 1.0.3-3
+Version: 1.0.3-4
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2014-02-01 08:39:09 UTC (rev 65)
+++ pkg/CHNOSZ/inst/NEWS	2014-03-23 02:53:46 UTC (rev 66)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.3-3 (2014-02-01)
+CHANGES IN CHNOSZ 1.0.3-4 (2014-03-23)
 --------------------------------------
 
 - Add files with average amino acid compositions of proteins from Bison

Modified: pkg/CHNOSZ/inst/tests/test-EOSregress.R
===================================================================
--- pkg/CHNOSZ/inst/tests/test-EOSregress.R	2014-02-01 08:39:09 UTC (rev 65)
+++ pkg/CHNOSZ/inst/tests/test-EOSregress.R	2014-03-23 02:53:46 UTC (rev 66)
@@ -34,15 +34,15 @@
   ## the tests: did we get the HKF parameters that are in the database?
   CH4.par <- info(info("CH4"))
   # c1 and c2
-  expect_equal(Cp.coeff[1], CH4.par$c1, check.attr=FALSE)
-  expect_equal(Cp.coeff[2], CH4.par$c2, check.attr=FALSE)
+  expect_equal(Cp.coeff[1], CH4.par$c1, check.attributes=FALSE)
+  expect_equal(Cp.coeff[2], CH4.par$c2, check.attributes=FALSE)
   # omega (from Cp)
-  expect_equal(Cp.coeff[3], CH4.par$omega, check.attr=FALSE)
+  expect_equal(Cp.coeff[3], CH4.par$omega, check.attributes=FALSE)
   # a1, a2, a3 and a4
-  expect_equal(V.coeff[1], CH4.par$a1, check.attr=FALSE)
-  expect_equal(V.coeff[2], CH4.par$a2, check.attr=FALSE)
-  expect_equal(V.coeff[3], CH4.par$a3, check.attr=FALSE)
-  expect_equal(V.coeff[4], CH4.par$a4, check.attr=FALSE)
+  expect_equal(V.coeff[1], CH4.par$a1, check.attributes=FALSE)
+  expect_equal(V.coeff[2], CH4.par$a2, check.attributes=FALSE)
+  expect_equal(V.coeff[3], CH4.par$a3, check.attributes=FALSE)
+  expect_equal(V.coeff[4], CH4.par$a4, check.attributes=FALSE)
   # omega (from V) - note negative sign
-  expect_equal(-V.coeff[5], CH4.par$omega, check.attr=FALSE)
+  expect_equal(-V.coeff[5], CH4.par$omega, check.attributes=FALSE)
 })

Modified: pkg/CHNOSZ/man/revisit.Rd
===================================================================
--- pkg/CHNOSZ/man/revisit.Rd	2014-02-01 08:39:09 UTC (rev 65)
+++ pkg/CHNOSZ/man/revisit.Rd	2014-03-23 02:53:46 UTC (rev 66)
@@ -72,7 +72,7 @@
 In this case, plotting is disabled, since the names of the variables are not in the input.
 
 \samp{revisit} is a partial anagram of \samp{diversity}, which was the provisional name of the function but was changed in CHNOSZ-0.9.
-While the \code{\link[vegan]{diversity}} function (in \pkg{vegan}) operates on a matrix with (biological) species on the columns, \code{revisit} operates on a list with (chemical) species as the elements of the list.
+While the \code{diversity} function (in \pkg{vegan}) operates on a matrix with (biological) species on the columns, \code{revisit} operates on a list with (chemical) species as the elements of the list.
 The name of the \samp{H} output value is the conventional symbol for the Shannon diversity index, which was the first target statistic to be implemented in \code{revisit}.
 
 }