[CHNOSZ-commits] r51 - in pkg/CHNOSZ: . R inst man

Thu Mar 28 16:57:07 CET 2013

Author: jedick
Date: 2013-03-28 16:57:07 +0100 (Thu, 28 Mar 2013)
New Revision: 51

Modified:
   pkg/CHNOSZ/.Rinstignore
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/util.blast.R
   pkg/CHNOSZ/inst/CHECKLIST
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/man/CHNOSZ-package.Rd
Log:
prepare version 1.0.0 for release on CRAN


Modified: pkg/CHNOSZ/.Rinstignore
===================================================================

--- pkg/CHNOSZ/.Rinstignore	2013-03-27 00:03:51 UTC (rev 50)
+++ pkg/CHNOSZ/.Rinstignore	2013-03-28 15:57:07 UTC (rev 51)
@@ -1,5 +1,2 @@
-chnosz_new.pdf
-rxn_.*.pdf
-EF-Tu_.*.pdf
 vig.bib
 .*.lyx

Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2013-03-27 00:03:51 UTC (rev 50)
+++ pkg/CHNOSZ/DESCRIPTION	2013-03-28 15:57:07 UTC (rev 51)
@@ -1,6 +1,6 @@
-Date: 2013-03-27
+Date: 2013-03-28
 Package: CHNOSZ
-Version: 0.9-9.11
+Version: 1.0.0
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey M. Dick
 Maintainer: Jeffrey M. Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/R/util.blast.R
===================================================================
--- pkg/CHNOSZ/R/util.blast.R	2013-03-27 00:03:51 UTC (rev 50)
+++ pkg/CHNOSZ/R/util.blast.R	2013-03-28 15:57:07 UTC (rev 51)
@@ -79,12 +79,12 @@
   it <- which(nt/sum(nt) >= min.taxon)
   itt <- which(blast$taxid %in% names(nt)[it])
   blast <- blast[itt,]
-  cat(paste("  min taxon abundance filtering leaves",length(unique(blast$query)),
+  cat(paste("  min taxon abundance filtering leaves",length(unique(blast$queryId)),
     "query sequences,",length(unique(blast$phylum)),"phyla,",length(unique(blast$taxid)),"taxa\n"))
   # only take phylum assignments that make up at least a certain 
   # fraction ('amin') of hits to the query sequence
-  uquery <- unique(blast$query)
-  iquery <- match(uquery,blast$query)
+  uquery <- unique(blast$queryId)
+  iquery <- match(uquery,blast$queryId)
   # function to select the (highest) represented phylum for each query
   iqfun <- function(i) {
     if((i-1)%%1000==0) cat(paste(i,""))

Modified: pkg/CHNOSZ/inst/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST	2013-03-27 00:03:51 UTC (rev 50)
+++ pkg/CHNOSZ/inst/CHECKLIST	2013-03-28 15:57:07 UTC (rev 51)
@@ -37,8 +37,6 @@
   (CFLAGS=-ffloat-store ./configure --disable-long-double)
 
 - build the package on the source directory:
-  R CMD build --compact-vignettes chnosz
+  R CMD build --compact-vignettes chnosz/
     don't use --no-vignettes, that keeps the Rnw files from being copied to inst/doc,
       causing vignettes to disappear from CRAN webpage
-    don't use --compact-vignettes=both, that results in smaller PDFs (using ghostscript),
-      but erases some metadata

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2013-03-27 00:03:51 UTC (rev 50)
+++ pkg/CHNOSZ/inst/NEWS	2013-03-28 15:57:07 UTC (rev 51)
@@ -1,11 +1,12 @@
-CHANGES IN CHNOSZ 0.9-9.11 (2013-03-26)
----------------------------------------
+CHANGES IN CHNOSZ 1.0.0 (2013-03-28)
+------------------------------------
 
 MAJOR USER-VISIBLE CHANGE:
 
 - On attaching the package, the user is asked to load the 'thermo'
-  object using data(thermo). This is required because packages are not
-  permitted to alter the search path (but the user may).
+  object, containing thermodynamic data and system settings, using
+  data(thermo). This is required because packages are not permitted to
+  alter the search path (but the user may).
 
 OTHER CHANGES:
 
@@ -59,9 +60,6 @@
 
 - Simplify EOSplot() somewhat (don't group data by pressure ranges).
 
-- [temporary] Deactivate code using 'central' method in guess()
-  (wjd.Rnw) as limSolve package on not available on R-Forge for windows.
-
 - EOSlab() gets label from attribute (if present) of user-defined
   function.
 
@@ -73,7 +71,8 @@
 
 - Remove read.supcrt() and write.supcrt().
 
-- guess() now defaults to "stoich" method, not "central".
+- guess() now defaults to "stoich" method, not "central". (Needed since
+  limSolve package is not found during R-Forge checks on Windows.)
 
 
 CHANGES IN CHNOSZ 0.9-9 (2013-01-01)

Modified: pkg/CHNOSZ/man/CHNOSZ-package.Rd
===================================================================
--- pkg/CHNOSZ/man/CHNOSZ-package.Rd	2013-03-27 00:03:51 UTC (rev 50)
+++ pkg/CHNOSZ/man/CHNOSZ-package.Rd	2013-03-28 15:57:07 UTC (rev 51)
@@ -74,7 +74,7 @@
 
   \code{\link{subcrt}} does not correctly identify the stable polymorph of some minerals at high temperature.
 
-  \code{\link{diagram}} causes an error while plotting stability field boundaries if the x and y resolutions are not identical. (\code{diagram(..., plot.it=FALSE)} can still be used to retrieve the results of the equilibrium calculation.)
+  \code{\link{diagram}} causes an error while plotting stability field boundaries if the x and y resolutions are not identical.
 }
 
 \seealso{
@@ -82,8 +82,10 @@
 }
 
 \examples{
-\dontshow{data(thermo)}
 ### Getting Started
+## the 'thermo' object contains thermodynamic data and is also where
+## user's settings (definition of chemical system) are stored
+data(thermo)
 
 ## standard thermodynamic properties of species
 subcrt("H2O")
@@ -122,9 +124,9 @@
 subcrt(c("k-feldspar", "kaolinite"), c(-2, 1))
 
 ## chemical affinities
-# basis species and their activities or fugacities
+# set basis species and their activities or fugacities
 basis(c("CO2", "H2O", "O2"), c(-3, 0, -80))
-# species of interest
+# set species of interest
 species(c("CH4", "C2H4O2", "CO2"))
 # chemical affinities of formation reactions
 # take off $values for complete output

