[CHNOSZ-commits] r751 - in pkg/CHNOSZ: . R inst

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

Author: jedick
Date: 2022-10-16 02:14:48 +0200 (Sun, 16 Oct 2022)
New Revision: 751

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/util.fasta.R
   pkg/CHNOSZ/inst/NEWS.Rd
Log:
Remove parallel calculations in read.fasta() and count.aa()


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2022-10-15 11:09:52 UTC (rev 750)
+++ pkg/CHNOSZ/DESCRIPTION	2022-10-16 00:14:48 UTC (rev 751)
@@ -1,6 +1,6 @@
 Date: 2022-10-15
 Package: CHNOSZ
-Version: 1.9.9-42
+Version: 1.9.9-43
 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/R/util.fasta.R
===================================================================
--- pkg/CHNOSZ/R/util.fasta.R	2022-10-15 11:09:52 UTC (rev 750)
+++ pkg/CHNOSZ/R/util.fasta.R	2022-10-16 00:14:48 UTC (rev 751)
@@ -66,7 +66,7 @@
   # protein/gene name is from header line for entry
   # (strip the ">" and go to the first space)
   missid <- missing(id)
-  if(is.null(id)) id <- as.character(palply("", iseq, function(j) {
+  if(is.null(id)) id <- as.character(lapply(iseq, function(j) {
     # get the text of the line
     f1 <- linefun(ihead[j],ihead[j])
     # stop if the first character is not ">"
@@ -179,7 +179,7 @@
     return(counts)
   }
   # counts for each sequence
-  counts <- palply("", seq, countfun, start, stop)
+  counts <- lapply(seq, countfun, start, stop)
   counts <- do.call(rbind, counts)
   # check for letters that aren't in our alphabet
   ina <- colSums(counts[, -ilett, drop=FALSE]) > 0

Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd	2022-10-15 11:09:52 UTC (rev 750)
+++ pkg/CHNOSZ/inst/NEWS.Rd	2022-10-16 00:14:48 UTC (rev 751)
@@ -12,7 +12,7 @@
 % links to vignettes 20220723
 \newcommand{\viglink}{\ifelse{html}{\out{<a href="../CHNOSZ/doc/#1.html"><strong>#1.Rmd</strong></a>}}{\bold{#1.Rmd}}}
 
-\section{Changes in CHNOSZ version 1.9.9-42 (2022-10-15)}{
+\section{Changes in CHNOSZ version 1.9.9-43 (2022-10-15)}{
 
   \subsection{MAJOR USER-VISIBLE CHANGES}{
     \itemize{
@@ -135,6 +135,9 @@
       \item \code{EOSregress()} and the associated demo and vignette have been
       removed.
 
+      \item Remove parallel calculations in \code{read.fasta()} and
+      \code{count.aa()} (they just made things slower in my tests).
+
     }
   }