[Seqinr-commits] r2153 - in pkg: . man

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

Author: simonpenel
Date: 2022-11-28 16:06:10 +0100 (Mon, 28 Nov 2022)
New Revision: 2153

Modified:
   pkg/DESCRIPTION
   pkg/man/ECH.Rd
   pkg/man/JLO.Rd
   pkg/man/read.abif.Rd
Log:
Updating other urls

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2022-11-28 14:42:34 UTC (rev 2152)
+++ pkg/DESCRIPTION	2022-11-28 15:06:10 UTC (rev 2153)
@@ -1,6 +1,6 @@
 Encoding: UTF-8
 Package: seqinr
-Version: 4.2-22
+Version: 4.2-23
 Date: 2022-11-28
 Title: Biological Sequences Retrieval and Analysis
 Authors at R: c(person("Delphine", "Charif", role = "aut"),

Modified: pkg/man/ECH.Rd
===================================================================
--- pkg/man/ECH.Rd	2022-11-28 14:42:34 UTC (rev 2152)
+++ pkg/man/ECH.Rd	2022-11-28 15:06:10 UTC (rev 2153)
@@ -21,12 +21,12 @@
   \code{citation("seqinr")}
 
   Anonymous (2006) Applied Biosystem Genetic Analysis Data File Format.
-  Available at \url{https://www.thermofisher.com/at/en/home/brands/applied-biosystems.html}.
+  Available at \url{https://www.thermofisher.com/de/de/home/brands/applied-biosystems.html}.
   Last visited on 03-NOV-2008.
 }
 \author{J.R. Lobry}
 \seealso{
-  function \code{\link{read.abif}} to import files in ABIF format, 
+  function \code{\link{read.abif}} to import files in ABIF format,
   data \code{\link{gs500liz}} for internal size standards,
   data \code{\link{identifiler}} for allele names in the allelic ladder,
   data \code{\link{JLO}} for an example of an individual sample file.
@@ -34,4 +34,3 @@
 \examples{
 data(JLO)
 }
-

Modified: pkg/man/JLO.Rd
===================================================================
--- pkg/man/JLO.Rd	2022-11-28 14:42:34 UTC (rev 2152)
+++ pkg/man/JLO.Rd	2022-11-28 15:06:10 UTC (rev 2153)
@@ -33,12 +33,12 @@
   \code{citation("seqinr")}
 
   Anonymous (2006) Applied Biosystem Genetic Analysis Data File Format.
-  Available at \url{https://www.thermofisher.com/at/en/home/brands/applied-biosystems.html}.
+  Available at \url{https://www.thermofisher.com/de/de/home/brands/applied-biosystems.html}.
   Last visited on 03-NOV-2008.
 }
 \author{J.R. Lobry}
 \seealso{
-  function \code{\link{read.abif}} to import files in ABIF format, 
+  function \code{\link{read.abif}} to import files in ABIF format,
   data \code{\link{gs500liz}} for internal size standards,
   data \code{\link{ECH}} for the corresponding allelic ladder,
   data \code{\link{identifiler}} for allele names in the allelic ladder.
@@ -46,4 +46,3 @@
 \examples{
 data(JLO)
 }
-

Modified: pkg/man/read.abif.Rd
===================================================================
--- pkg/man/read.abif.Rd	2022-11-28 14:42:34 UTC (rev 2152)
+++ pkg/man/read.abif.Rd	2022-11-28 15:06:10 UTC (rev 2153)
@@ -6,14 +6,14 @@
 Corresponding files usually have an \code{*.ab1} or \code{*.fsa} extension.
 }
 \usage{
-read.abif(filename, max.bytes.in.file = file.info(filename)$size, 
+read.abif(filename, max.bytes.in.file = file.info(filename)$size,
  pied.de.pilote = 1.2, verbose = FALSE)
 }
 \arguments{
   \item{filename}{The name of the file.}
-  \item{max.bytes.in.file}{The size in bytes of the file, defaulting to what is returned by \code{\link{file.info}}}	
-  \item{pied.de.pilote}{Safety factor: the argument \code{n} to \code{\link{readBin}} is set as \code{pied.de.pilote*max.bytes.in.file}.}	
-  \item{verbose}{logical [FALSE]. If TRUE verbose mode is on.}	
+  \item{max.bytes.in.file}{The size in bytes of the file, defaulting to what is returned by \code{\link{file.info}}}
+  \item{pied.de.pilote}{Safety factor: the argument \code{n} to \code{\link{readBin}} is set as \code{pied.de.pilote*max.bytes.in.file}.}
+  \item{verbose}{logical [FALSE]. If TRUE verbose mode is on.}
 }
 \details{
 All data are imported into memory, there is no attempt to read items on the fly.
@@ -24,13 +24,13 @@
 the offset to find the location of the directory. \code{Directory} is a data.frame for the directory
 of the file with the number of row being the number of elements in the directory and the 7
 columns describing various low-level information about the elements. \code{Data} is a list
-with the number of components equal to the number of elements in the directory. 
+with the number of components equal to the number of elements in the directory.
 }
-\references{ 
+\references{
 \code{citation("seqinR")}
 
 Anonymous (2006) Applied Biosystem Genetic Analysis Data File Format.
-Available at \url{https://www.thermofisher.com/at/en/home/brands/applied-biosystems.html}.
+Available at \url{https://www.thermofisher.com/de/de/home/brands/applied-biosystems.html}.
 Last visited on 03-NOV-2008.
 
 The figure in the example section is an attempt to reproduce figure 1A from:
@@ -53,7 +53,7 @@
 #
 
 data(JLO)
-JLO.check <- read.abif(system.file("abif/2_FAC321_0000205983_B02_004.fsa", 
+JLO.check <- read.abif(system.file("abif/2_FAC321_0000205983_B02_004.fsa",
   package = "seqinr"))
 stopifnot(identical(JLO, JLO.check))
 
@@ -61,7 +61,7 @@
 # Try to reproduce figure 1A from Krawczyk et al. 2009:
 #
 
-Krawczyk <- read.abif(system.file("abif/samplefsa2ps.fsa", 
+Krawczyk <- read.abif(system.file("abif/samplefsa2ps.fsa",
   package = "seqinr"))$Data
 x <- 1:length(Krawczyk[["DATA.1"]])
 par(mar = c(2,4,2,0)+0.1, cex = 0.5)