From noreply at r-forge.r-project.org  Sat Jul  4 06:27:43 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sat,  4 Jul 2015 06:27:43 +0200 (CEST)
Subject: [CHNOSZ-commits] r90 - in pkg/CHNOSZ: . inst
Message-ID: <20150704042743.4C417187A6B@r-forge.r-project.org>

Author: jedick
Date: 2015-07-04 06:27:42 +0200 (Sat, 04 Jul 2015)
New Revision: 90

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/NAMESPACE
   pkg/CHNOSZ/inst/NEWS
Log:
add importFrom for functions from default packages


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2015-06-13 17:27:56 UTC (rev 89)
+++ pkg/CHNOSZ/DESCRIPTION	2015-07-04 04:27:42 UTC (rev 90)
@@ -1,11 +1,12 @@
-Date: 2015-06-13
+Date: 2015-07-04
 Package: CHNOSZ
-Version: 1.0.5-2
+Version: 1.0.5-3
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
 Depends: R (>= 3.1.0)
 Suggests: limSolve, testthat, knitr
+Imports: grDevices, graphics, stats, utils
 Description: Functions and data sets to support chemical thermodynamic modeling in biochemistry
   and low-temperature geochemistry. The features include calculation of the standard molal
   thermodynamic properties and chemical affinities of reactions involving minerals and/or

Modified: pkg/CHNOSZ/NAMESPACE
===================================================================
--- pkg/CHNOSZ/NAMESPACE	2015-06-13 17:27:56 UTC (rev 89)
+++ pkg/CHNOSZ/NAMESPACE	2015-07-04 04:27:42 UTC (rev 90)
@@ -3,3 +3,15 @@
 
 # Load shared objects
 useDynLib(CHNOSZ)
+
+# Imports from default packages
+importFrom("grDevices", "dev.cur", "dev.off", "extendrange",
+  "heat.colors", "png", "rainbow")
+importFrom("graphics", "abline", "axTicks", "axis", "barplot", "box",
+  "contour", "image", "legend", "lines", "mtext", "par", "plot",
+  "plot.new", "plot.window", "points", "rect", "text", "title")
+importFrom("stats", "D", "as.formula", "cor", "lm", "loess.smooth",
+  "na.omit", "qqline", "qqnorm", "sd", "splinefun", "uniroot")
+importFrom("utils", "browseURL", "capture.output", "combn", "demo",
+  "example", "head", "installed.packages", "read.csv", "tail",
+  "write.csv", "write.table")

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2015-06-13 17:27:56 UTC (rev 89)
+++ pkg/CHNOSZ/inst/NEWS	2015-07-04 04:27:42 UTC (rev 90)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.5-2 (2015-06-13)
+CHANGES IN CHNOSZ 1.0.5-3 (2015-07-04)
 --------------------------------------
 
 - Rewrite rho.IAPWS95() to be able to invert density from IAPWS-95
@@ -30,6 +30,9 @@
   of basis species when blend=TRUE. Thanks to Grayson Boyer for the bug
   report that led to this fix.
 
+- Add grDevices, graphics, stats, utils to Imports: in DESCRIPTION, and
+  add specific importsFrom lines in NAMESPACE.
+
 CHANGES IN CHNOSZ 1.0.5 (2015-05-19)
 ------------------------------------
 


From noreply at r-forge.r-project.org  Fri Jul 10 14:00:15 2015
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 10 Jul 2015 14:00:15 +0200 (CEST)
Subject: [CHNOSZ-commits] r91 - in pkg/CHNOSZ: . R data inst
Message-ID: <20150710120015.6A9521878F6@r-forge.r-project.org>

Author: jedick
Date: 2015-07-10 14:00:15 +0200 (Fri, 10 Jul 2015)
New Revision: 91

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/diagram.R
   pkg/CHNOSZ/data/OBIGT.csv
   pkg/CHNOSZ/inst/NEWS
Log:
fix incorrect entry for entropy (S) of aqueous methionine and [Met]


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2015-07-04 04:27:42 UTC (rev 90)
+++ pkg/CHNOSZ/DESCRIPTION	2015-07-10 12:00:15 UTC (rev 91)
@@ -1,6 +1,6 @@
-Date: 2015-07-04
+Date: 2015-07-10
 Package: CHNOSZ
-Version: 1.0.5-3
+Version: 1.0.5-4
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/R/diagram.R
===================================================================
--- pkg/CHNOSZ/R/diagram.R	2015-07-04 04:27:42 UTC (rev 90)
+++ pkg/CHNOSZ/R/diagram.R	2015-07-10 12:00:15 UTC (rev 91)
@@ -391,8 +391,8 @@
         else if(any(grepl(names(dev.cur()), c("X11cairo", "quartz", "windows")))) fill <- "heat"
       }
       if(is.null(fill)) fill <- "transparent"
-      else if(fill[1]=="rainbow") fill <- rainbow(ngroups)
-      else if(fill[1]=="heat") fill <- heat.colors(ngroups)
+      else if(isTRUE(fill[1]=="rainbow")) fill <- rainbow(ngroups)
+      else if(isTRUE(fill[1]=="heat")) fill <- heat.colors(ngroups)
       fill <- rep(fill, length.out=ngroups)
       # the x and y values 
       xs <- eout$vals[[1]]

Modified: pkg/CHNOSZ/data/OBIGT.csv
===================================================================
--- pkg/CHNOSZ/data/OBIGT.csv	2015-07-04 04:27:42 UTC (rev 90)
+++ pkg/CHNOSZ/data/OBIGT.csv	2015-07-10 12:00:15 UTC (rev 91)
@@ -1523,7 +1523,7 @@
 lysine,Lys,C6H14N2O2,aq,AH97b,DLH06,25.Aug.06,-80680,-159330,57.91,63.8,108.6,24.56,8.3,24.43,-9.53,86.6,-10.9,0.07,0
 lysinium,Lys+,C6H15N2O2+,aq,AH97b,DLH06,25.Aug.06,-92890,-170370,61.82,67.9,107.5,28.62,-1.51,4.47,-3.99,95.2,-8,1.21,0
 lysinate,Lys-,C6H13N2O2-,aq,AH97b,DLH06,25.Aug.06,-66310,-146340,53.27,72.8,112.2,28.29,10.53,2.97,-7.61,133.7,-18,2.67,0
-methionine,Met,C5H11NO2S,aq,LD12,DLH06,12.Sep.11,-76959.8,-135210.3,62.36,70.7,105.4,24.95,6.9,13.59,-7.77,85.3,-6.6,0.13,0
+methionine,Met,C5H11NO2S,aq,LD12,DLH06,10.Jul.15,-76959.8,-135210.3,62.81,70.7,105.4,24.95,6.9,13.59,-7.77,85.3,-6.6,0.13,0
 phenylalanine,Phe,C9H11NO2,aq,AH97b,DLH06,25.Aug.06,-49430,-108900,56.6,93.8,122.1,28.27,8.8,19.34,-9.38,108.1,-6.5,0.12,0
 proline,Pro,C5H9NO2,aq,AH97b,DLH06,25.Aug.06,-73560,-124100,49.83,43,82.6,19.39,4.87,11.88,-5.68,63.6,-9.5,0.14,0
 serine,Ser,C3H7NO3,aq,AH97b,DLH06,25.Aug.06,-123930,-172420,47.24,27.8,60.6,15.69,0.73,3.87,-3.49,48.5,-9.4,0.18,0
@@ -1550,7 +1550,7 @@
 [Leu],NA,C4H9,aq,DLH06,NA,25.Aug.06,675,-34390,28.43,97.21,74.2,15.21,9.37,17.16,-6.6,81.1,7.3,-0.14,0
 [Lys],NA,C4H10N,aq,DLH06,NA,25.Aug.06,5657,-37650,39.3,65.848,75.048,15.09,10.16,21.66,-7.76,65,-0.3,-0.16,0
 [Lys+],NA,C4H11N+,aq,DLH06,NA,25.Aug.06,-8014,-51160,39.84,69.955,73.89,19.15,0.35,1.7,-2.22,73.6,2.6,0.98,0
-[Met],NA,C3H7S,aq,LD12,DLH06,12.Sep.11,7911.1,-16001.4,40.38,72.739,71.832,15.48,8.76,10.82,-6,63.7,4,-0.1,0
+[Met],NA,C3H7S,aq,LD12,DLH06,10.Jul.15,7911.1,-16001.4,40.82,72.739,71.832,15.48,8.76,10.82,-6,63.7,4,-0.1,0
 [Phe],NA,C7H7,aq,DLH06,NA,25.Aug.06,35444,10310,34.62,95.834,88.545,18.8,10.66,16.57,-7.61,86.5,4.1,-0.11,0
 [Pro],NA,C3H5,aq,DLH06,NA,25.Aug.06,11314,-4890,27.85,45.055,49.049,9.92,6.73,9.11,-3.91,42,1.1,-0.09,0
 [Ser],NA,CH3O,aq,DLH06,NA,25.Aug.06,-39054,-53210,25.26,29.794,27.042,6.22,2.59,1.1,-1.72,26.9,1.2,-0.05,0

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2015-07-04 04:27:42 UTC (rev 90)
+++ pkg/CHNOSZ/inst/NEWS	2015-07-10 12:00:15 UTC (rev 91)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.5-3 (2015-07-04)
+CHANGES IN CHNOSZ 1.0.5-4 (2015-07-10)
 --------------------------------------
 
 - Rewrite rho.IAPWS95() to be able to invert density from IAPWS-95
@@ -33,6 +33,9 @@
 - Add grDevices, graphics, stats, utils to Imports: in DESCRIPTION, and
   add specific importsFrom lines in NAMESPACE.
 
+- Fix incorrect entry for entropy of aqueous methionine and [Met] in
+  OBIGT.csv. Thanks to Apar Prasad for spotting this.
+
 CHANGES IN CHNOSZ 1.0.5 (2015-05-19)
 ------------------------------------