[CHNOSZ-commits] r675 - in pkg/CHNOSZ: . man vignettes

[noreply at r-forge.r-project.org]

Author: jedick
Date: 2021-04-22 02:02:02 +0200 (Thu, 22 Apr 2021)
New Revision: 675

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/man/extdata.Rd
   pkg/CHNOSZ/man/taxonomy.Rd
   pkg/CHNOSZ/vignettes/anintro.Rmd
Log:
Don't use ftp:// in help pages and vignettes


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2021-04-21 12:19:45 UTC (rev 674)
+++ pkg/CHNOSZ/DESCRIPTION	2021-04-22 00:02:02 UTC (rev 675)
@@ -1,6 +1,6 @@
 Date: 2021-04-21
 Package: CHNOSZ
-Version: 1.4.1-2
+Version: 1.4.1-3
 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/man/extdata.Rd
===================================================================
--- pkg/CHNOSZ/man/extdata.Rd	2021-04-21 12:19:45 UTC (rev 674)
+++ pkg/CHNOSZ/man/extdata.Rd	2021-04-22 00:02:02 UTC (rev 675)
@@ -57,7 +57,7 @@
 
   Files in \code{taxonomy} contain taxonomic data files:
   \itemize{
-    \item \code{names.dmp} and \code{nodes.dmp} are excerpts of the taxonomy files available on the NCBI ftp site (\url{ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz}, accessed 2010-02-15). These files contain only the entries for \emph{Escherichia coli} K-12, \emph{Saccharomyces cerevisiae}, \emph{Homo sapiens}, \emph{Pyrococcus furisosus} and \emph{Methanocaldococcus jannaschii} (taxids 83333, 4932, 9606, 186497, 243232) and the higher-ranking nodes (genus, family, etc.) in the respective lineages. See \code{\link{taxonomy}} for examples that use these files.
+    \item \code{names.dmp} and \code{nodes.dmp} are excerpts of NCBI taxonomy files (\url{https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz}, accessed 2010-02-15). These files contain only the entries for \emph{Escherichia coli} K-12, \emph{Saccharomyces cerevisiae}, \emph{Homo sapiens}, \emph{Pyrococcus furisosus} and \emph{Methanocaldococcus jannaschii} (taxids 83333, 4932, 9606, 186497, 243232) and the higher-ranking nodes (genus, family, etc.) in the respective lineages. See \code{\link{taxonomy}} for examples that use these files.
   }
 
   Files in \code{adds} contain additional thermodynamic data and group additivity definitions:

Modified: pkg/CHNOSZ/man/taxonomy.Rd
===================================================================
--- pkg/CHNOSZ/man/taxonomy.Rd	2021-04-21 12:19:45 UTC (rev 674)
+++ pkg/CHNOSZ/man/taxonomy.Rd	2021-04-22 00:02:02 UTC (rev 675)
@@ -32,7 +32,7 @@
 
 \details{
 
-  These functions provide a convenient way to read data from NCBI taxonomy files (i.e., the contents of \code{taxdump.tar.gz}, which can be downloaded from \url{ftp://ftp.ncbi.nih.gov/pub/taxonomy/}). 
+  These functions provide a convenient way to read data from NCBI taxonomy files (i.e., the contents of \code{taxdump.tar.gz}, which is available from \url{https://ftp.ncbi.nih.gov/pub/taxonomy/}). 
 
   The \code{taxdir} argument is used to specify the directory where the \code{nodes.dmp} and \code{names.dmp} files are located. \code{getnodes} and \code{getnames} read these files into data frames. \code{getrank} returns the rank (species, genus, etc) of the node with the given taxonomic \code{id}. \code{parent} returns the taxonomic ID of the next-lowest node below that specified by the \code{id} in the argument, unless \code{rank} is supplied, in which case the function descends the tree until a node with that rank is found. \code{allparents} returns all the taxonomic IDs of all nodes between that specified by \code{id} and the root of the tree, inclusive. \code{sciname} returns the scientific name of the node with the given \code{id}.
   

Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd	2021-04-21 12:19:45 UTC (rev 674)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd	2021-04-22 00:02:02 UTC (rev 675)
@@ -1763,7 +1763,7 @@
 
 * <span style="color:green">`eqdata()`</span> reads data, including concentrations of aqueous species, numbers of moles of solid phases, and mineral saturation states (affinities), from an EQ6 output file [@Wol92].
 
-* Some functions are available (see <span style="color:blue">`?taxonomy`</span>) to read data from [NCBI taxonomy files](ftp://ftp.ncbi.nih.gov/pub/taxonomy/), traverse taxonomic ranks, and get scientific names of taxonomic nodes.
+* Some functions are available (see <span style="color:blue">`?taxonomy`</span>) to read data from [NCBI taxonomy files](https://www.ncbi.nlm.nih.gov/taxonomy), traverse taxonomic ranks, and get scientific names of taxonomic nodes.
 
 # Citation and contact information