[Seqinr-commits] r1899 - pkg/man

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

Author: jeanlobry
Date: 2016-06-02 14:58:01 +0200 (Thu, 02 Jun 2016)
New Revision: 1899

Modified:
   pkg/man/read.fasta.Rd
Log:
file updates

Modified: pkg/man/read.fasta.Rd
===================================================================
--- pkg/man/read.fasta.Rd	2016-06-02 12:43:37 UTC (rev 1898)
+++ pkg/man/read.fasta.Rd	2016-06-02 12:58:01 UTC (rev 1899)
@@ -7,7 +7,7 @@
   Read nucleic or amino-acid sequences from a file in FASTA format.
 }
 \usage{
-read.fasta(file = "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.fasta", 
+read.fasta(file = system.file("sequences/ct.fasta.gz", package = "seqinr"), 
   seqtype = c("DNA", "AA"), as.string = FALSE, forceDNAtolower = TRUE,
   set.attributes = TRUE, legacy.mode = TRUE, seqonly = FALSE, strip.desc = FALSE,
   bfa = FALSE, sizeof.longlong = .Machine$sizeof.longlong,
@@ -17,7 +17,7 @@
   \item{file}{ The name of the file which the sequences in fasta format are to be 
   read from. If it does not contain an absolute or relative path, the file name is relative 
     to the current working directory, \code{\link{getwd}}. The default here is to
-    read the \code{ct.fasta} file which is present in the \code{sequences} folder
+    read the \code{ct.fasta.gz} file which is present in the \code{sequences} folder
    of the seqinR package.}
   \item{seqtype}{ the nature of the sequence: \code{DNA} or \code{AA}, defaulting
     to \code{DNA} }
@@ -157,7 +157,7 @@
 # on a platform where .Platform$endian == "little" and .Machine$sizeof.longlong == 8
 #
 \dontrun{
-  fastafile <- "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.fasta"
+  fastafile <- system.file("sequences/ct.fasta.gz", package = "seqinr")
   bfafile <- "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.bfa"
 
   original <- read.fasta(fastafile, as.string = TRUE, set.att = FALSE)