[CHNOSZ-commits] r86 - in pkg/CHNOSZ: . inst man vignettes

Mon May 18 16:21:17 CEST 2015

Author: jedick
Date: 2015-05-18 16:21:16 +0200 (Mon, 18 May 2015)
New Revision: 86

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/man/CHNOSZ-package.Rd
   pkg/CHNOSZ/vignettes/equilibrium.Rnw
   pkg/CHNOSZ/vignettes/equilibrium.lyx
   pkg/CHNOSZ/vignettes/hotspring.Rnw
   pkg/CHNOSZ/vignettes/hotspring.lyx
Log:
prepare version 1.0.4 for submission to CRAN


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================

--- pkg/CHNOSZ/DESCRIPTION	2015-05-17 09:20:41 UTC (rev 85)
+++ pkg/CHNOSZ/DESCRIPTION	2015-05-18 14:21:16 UTC (rev 86)
@@ -1,10 +1,10 @@
-Date: 2015-05-17
+Date: 2015-05-18
 Package: CHNOSZ
-Version: 1.0.3-23
+Version: 1.0.4
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
-Depends: R (>= 2.12.0)
+Depends: R (>= 3.0.0)
 Suggests: limSolve, parallel, testthat, knitr
 Description: Functions and data sets to support chemical thermodynamic modeling in biochemistry
   and low-temperature geochemistry. The features include calculation of the standard molal

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2015-05-17 09:20:41 UTC (rev 85)
+++ pkg/CHNOSZ/inst/NEWS	2015-05-18 14:21:16 UTC (rev 86)
@@ -1,13 +1,13 @@
-CHANGES IN CHNOSZ 1.0.3-23 (2015-05-17)
----------------------------------------
+CHANGES IN CHNOSZ 1.0.4 (2015-05-18)
+------------------------------------
 
 NEW FEATURES:
 
 - Add mosaic() function for affinity calculations with changing basis
   species. See also new 'mosaic.R' demo.
 
-- Add thermo$opt$varP option as a flag for subcrt() to calculate Gibbs
-  energies of gases using a variable-pressure standard state.
+- Add thermo$opt$varP option for subcrt() to calculate Gibbs energies
+  of gases using a variable-pressure standard state.
 
 - Add 'solubility.R' demo, and add calcite solubility plot to
   anintro.Rnw.
@@ -61,6 +61,8 @@
 - Add 'tplot' argument to diagram() (change to FALSE to use R's default
   plot set-up).
 
+- R version dependency changed to (>= 3.0.0).
+
 CHANGES IN CHNOSZ 1.0.3 (2014-01-12)
 ------------------------------------
 

Modified: pkg/CHNOSZ/man/CHNOSZ-package.Rd
===================================================================
--- pkg/CHNOSZ/man/CHNOSZ-package.Rd	2015-05-17 09:20:41 UTC (rev 85)
+++ pkg/CHNOSZ/man/CHNOSZ-package.Rd	2015-05-18 14:21:16 UTC (rev 86)
@@ -69,7 +69,8 @@
 
 
 \section{Compatibility}{
-  The recommended version of \R is 2.14.0 or greater (to find vignettes in the \code{vignettes} directory, and for availability of \pkg{parallel} in the standard library).
+  As of version 1.0.4, the package depends on \R version 3.0.0 or greater (previous versions use \code{\link{Stangle}} to extract R code from vignettes when installing the source package, leading to failure processing hotspring.Rnw, which now uses knitr instead of Sweave).
+  Before version 1.0.4, the recommended version of \R was 2.14.0 or greater (to find vignettes in the \code{vignettes} directory, and for availability of \pkg{parallel} in the standard library).
   As of version 0.9-9, the package depends on \R version 2.12.0 or greater (so useDynLib in the NAMESPACE can find the shared library on Windows).
   Starting with version 0.9-6 of the package, the dependency was given as \R version 2.10.0 or greater (to read compressed data files).
   Before version 0.9-6 of the package, the dependency was given as \R version 2.7.0 or greater (major update of the X11 device in 2.7.0).

Modified: pkg/CHNOSZ/vignettes/equilibrium.Rnw
===================================================================
--- pkg/CHNOSZ/vignettes/equilibrium.Rnw	2015-05-17 09:20:41 UTC (rev 85)
+++ pkg/CHNOSZ/vignettes/equilibrium.Rnw	2015-05-18 14:21:16 UTC (rev 86)
@@ -1,4 +1,4 @@
-%% LyX 2.1.0beta2 created this file.  For more info, see http://www.lyx.org/.
+%% LyX 2.1.3 created this file.  For more info, see http://www.lyx.org/.
 %% Do not edit unless you really know what you are doing.
 \documentclass[english,noae]{article}
 \usepackage{mathpazo}
@@ -78,12 +78,10 @@
 the molar formula by the balancing coefficients. This normalization
 has been referred to previously as using the residue equivalents of
 proteins \citep{Dic08}; here the terminology of \emph{normalize}
-will be used preferentially%
-\footnote{The older style of function call using \texttt{diagram(..., residue=TRUE)}
+will be used preferentially\footnote{The older style of function call using \texttt{diagram(..., residue=TRUE)}
 has been replaced by \texttt{equilibrate(..., normalize=TRUE)} or
 \texttt{diagram(..., normalize=TRUE)} starting with version 0.9-9
-of CHNOSZ.%
-}.
+of CHNOSZ.}.
 
 Two different methods of calculating the equilibrium activities of
 species in a system are described below. These are referred to as
@@ -580,20 +578,14 @@
 distribution.
 
 
-\section{Document Information}
+\section{Document revision history}
 
-Revision history
 \begin{itemize}
 \item 2009-11-29 Initial version containing CSG example (title: Calculating
 relative abundances of proteins)
 \item 2012-09-30 Renamed from previous ``protactiv.Rnw'': Remove activity
-comparisons, add maximum affinity method.
-\end{itemize}
-R session information
+comparisons, add maximum affinity method.\end{itemize}
 
-<<SessionInfo>>=
-sessionInfo()
-@
 
 \bibliographystyle{plainnat}
 \bibliography{vig}

Modified: pkg/CHNOSZ/vignettes/equilibrium.lyx
===================================================================
--- pkg/CHNOSZ/vignettes/equilibrium.lyx	2015-05-17 09:20:41 UTC (rev 85)
+++ pkg/CHNOSZ/vignettes/equilibrium.lyx	2015-05-18 14:21:16 UTC (rev 86)
@@ -2302,17 +2302,13 @@
 \end_layout
 
 \begin_layout Section
-Document Information
+Document revision history
 \end_layout
 
 \begin_layout Standard
 \begin_inset Branch stuff
 status open
 
-\begin_layout Standard
-Revision history
-\end_layout
-
 \begin_layout Itemize
 2009-11-29 Initial version containing CSG example (title: Calculating relative
  abundances of proteins)
@@ -2330,38 +2326,11 @@
 : Remove activity comparisons, add maximum affinity method.
 \end_layout
 
-\begin_layout Standard
-R session information
-\end_layout
-
-\begin_layout Standard
-\begin_inset Flex Chunk
-status open
-
-\begin_layout Plain Layout
-
-\begin_inset Argument 1
-status open
-
-\begin_layout Plain Layout
-SessionInfo
-\end_layout
-
 \end_inset
 
-sessionInfo()
-\end_layout
 
-\end_inset
-
-
 \end_layout
 
-\end_inset
-
-
-\end_layout
-
 \begin_layout Standard
 \begin_inset CommandInset bibtex
 LatexCommand bibtex

Modified: pkg/CHNOSZ/vignettes/hotspring.Rnw
===================================================================
--- pkg/CHNOSZ/vignettes/hotspring.Rnw	2015-05-17 09:20:41 UTC (rev 85)
+++ pkg/CHNOSZ/vignettes/hotspring.Rnw	2015-05-18 14:21:16 UTC (rev 86)
@@ -330,7 +330,7 @@
 
 This 1-2-4 progression of stabilities is visualized below; for some
 groups of proteins, an update to the thermodynamic properties of the
-methionine sidechain causes site 3 also to become stable.
+methionine sidechain causes proteins from site 3 also to become stable.
 
 
 \subsection{Relative stabilities along a chemical gradient}

Modified: pkg/CHNOSZ/vignettes/hotspring.lyx
===================================================================
--- pkg/CHNOSZ/vignettes/hotspring.lyx	2015-05-17 09:20:41 UTC (rev 85)
+++ pkg/CHNOSZ/vignettes/hotspring.lyx	2015-05-18 14:21:16 UTC (rev 86)
@@ -1364,7 +1364,7 @@
 \begin_layout Standard
 This 1-2-4 progression of stabilities is visualized below; for some groups
  of proteins, an update to the thermodynamic properties of the methionine
- sidechain causes site 3 also to become stable.
+ sidechain causes proteins from site 3 also to become stable.
 \end_layout
 
 \begin_layout Subsection

