[Seqinr-commits] r1893 - pkg/R

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

Author: jeanlobry
Date: 2016-06-02 13:36:34 +0200 (Thu, 02 Jun 2016)
New Revision: 1893

Modified:
   pkg/R/oriloc.R
   pkg/R/read.fasta.R
   pkg/R/rearranged.oriloc.R
Log:
using the gzipped ct.fasta.gz

Modified: pkg/R/oriloc.R
===================================================================
--- pkg/R/oriloc.R	2016-06-02 11:36:01 UTC (rev 1892)
+++ pkg/R/oriloc.R	2016-06-02 11:36:34 UTC (rev 1893)
@@ -6,7 +6,7 @@
 ########################################################################
 
 oriloc <- function(
-  seq.fasta = system.file("sequences/ct.fasta", package ="seqinr"),
+  seq.fasta = system.file("sequences/ct.fasta.gz", package ="seqinr"),
   g2.coord = system.file("sequences/ct.predict", package = "seqinr"),
   glimmer.version = 3,
   oldoriloc = FALSE,

Modified: pkg/R/read.fasta.R
===================================================================
--- pkg/R/read.fasta.R	2016-06-02 11:36:01 UTC (rev 1892)
+++ pkg/R/read.fasta.R	2016-06-02 11:36:34 UTC (rev 1893)
@@ -1,4 +1,4 @@
-read.fasta <- function(file = "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.fasta", 
+read.fasta <- function(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,

Modified: pkg/R/rearranged.oriloc.R
===================================================================
--- pkg/R/rearranged.oriloc.R	2016-06-02 11:36:01 UTC (rev 1892)
+++ pkg/R/rearranged.oriloc.R	2016-06-02 11:36:34 UTC (rev 1893)
@@ -6,8 +6,8 @@
 #############################################################################
 
 rearranged.oriloc <- function(
-    seq.fasta = "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.fasta" ,
-    g2.coord = "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.coord" )
+    seq.fasta = system.file("sequences/ct.fasta.gz", package = "seqinr") ,
+    g2.coord = system.file("sequences/ct.predict", package = "seqinr") )
   {
     
     seq.fasta <- read.fasta(seq.fasta)[[1]]