[Seqinr-commits] r1769 - in pkg: . R src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Feb 22 11:15:54 CET 2012
Author: simonpenel
Date: 2012-02-22 11:15:53 +0100 (Wed, 22 Feb 2012)
New Revision: 1769
Modified:
pkg/DESCRIPTION
pkg/R/AAstat.R
pkg/R/db.growth.R
pkg/R/modifylist.R
pkg/R/query.r
pkg/R/zscore.R
pkg/src/alignment.c
pkg/src/deflate.c
pkg/src/trees.c
pkg/src/zutil.c
Log:
Small modifications : supression of stderr C stuff, and partial match problems
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2012-02-20 12:00:59 UTC (rev 1768)
+++ pkg/DESCRIPTION 2012-02-22 10:15:53 UTC (rev 1769)
@@ -1,6 +1,6 @@
Package: seqinr
Version: 3.0-6
-Date: 2012-02-17
+Date: 2012-02-22
Title: Biological Sequences Retrieval and Analysis
Author: Delphine Charif and Jean R. Lobry and Anamaria Necsulea and Leonor Palmeira and Simon Penel and Guy Perriere
Maintainer: Simon Penel <simon.penel at univ-lyon1.fr>
Modified: pkg/R/AAstat.R
===================================================================
--- pkg/R/AAstat.R 2012-02-20 12:00:59 UTC (rev 1768)
+++ pkg/R/AAstat.R 2012-02-22 10:15:53 UTC (rev 1769)
@@ -14,8 +14,8 @@
plot(c(0, n.res), c(0, n.items + 1), type = "n", axes = FALSE,
ann = FALSE, xlim = c(0, n.res + 1))
title(xlab = "Position of the residues along the sequence")
- axis(2, at = seq(1.5, 10, 1), lab = names(tutu), col.lab = "blue", las = 1, cex.axis = 0.8)
- axis(1, at = seq(0, n.res, 15), lab = seq(0, n.res, 15), col.axis = "blue")
+ axis(2, at = seq(1.5, 10, 1), labels = names(tutu), col.lab = "blue", las = 1, cex.axis = 0.8)
+ axis(1, at = seq(0, n.res, 15), labels = seq(0, n.res, 15), col.axis = "blue")
lapply(seq_len(n.items), function(x){
segments(tutu[[x]], x, tutu[[x]], x + 1, col = coul[x], lwd = 2)
rect(0, x, n.res, 1, lwd = 2)
Modified: pkg/R/db.growth.R
===================================================================
--- pkg/R/db.growth.R 2012-02-20 12:00:59 UTC (rev 1768)
+++ pkg/R/db.growth.R 2012-02-22 10:15:53 UTC (rev 1769)
@@ -5,7 +5,7 @@
ftp.proxy.bck <- Sys.getenv("ftp_proxy")
if (ftp.proxy.bck != "") {
warning("I'am trying to neutralize proxies")
- Sys.putenv("no_proxy" = "")
+ Sys.setenv("no_proxy" = "")
}
embl <- where
@@ -76,13 +76,13 @@
for( i in seq(-10,10,by=0.5) )
if( i != 0 )
abline( coef=c(b+i, a), col="black" )
- legend( x = 1990, y = 7, leg= c(paste("Observed doubling time:",
+ legend( x = 1990, y = 7, legend= c(paste("Observed doubling time:",
round(dbt,1),"months"),"Moore's doubling time : 18 months"),
lty = c(1,1), col = c("yellow","black"))
}
else
{
- legend( x = 1990, y = 7, leg=paste("Observed doubling time:",
+ legend( x = 1990, y = 7, legend=paste("Observed doubling time:",
round(dbt,1), "months"), lty = 1, col = "yellow")
}
par( op )
Modified: pkg/R/modifylist.R
===================================================================
--- pkg/R/modifylist.R 2012-02-20 12:00:59 UTC (rev 1768)
+++ pkg/R/modifylist.R 2012-02-22 10:15:53 UTC (rev 1769)
@@ -85,6 +85,6 @@
result <- list(call = match.call(), name = modlistname, nelem = mlcount, typelist = NA,
req = req, socket = socket)
class(result) <- c("qaw")
- assign(modlistname, result, env = .GlobalEnv)
+ assign(modlistname, result, envir = .GlobalEnv)
}
Modified: pkg/R/query.r
===================================================================
--- pkg/R/query.r 2012-02-20 12:00:59 UTC (rev 1768)
+++ pkg/R/query.r 2012-02-22 10:15:53 UTC (rev 1769)
@@ -116,7 +116,7 @@
result <- list(call = match.call(), name = listname, nelem = nelem, typelist = typelist,
req = req, socket = socket)
class(result) <- c("qaw")
- assign(listname, result, env = .GlobalEnv)
+ assign(listname, result, envir = .GlobalEnv)
}
#
Modified: pkg/R/zscore.R
===================================================================
--- pkg/R/zscore.R 2012-02-20 12:00:59 UTC (rev 1768)
+++ pkg/R/zscore.R 2012-02-22 10:15:53 UTC (rev 1769)
@@ -37,7 +37,7 @@
split <- splitseq(sequence)
n <- length(split)
pos <- sort(c(seq(3,length(sequence)-1,by=3),seq(4,length(sequence),by=3))) #position3-1 codons
- xy <- table(factor(splitseq(sequence[pos],w=2),levels=words(2)))
+ xy <- table(factor(splitseq(sequence[pos],word=2),levels=words(2)))
n1 <- sapply(s2c('acgt'), function(x){length(which(substring(split,3,3)==x))})
n1 <- rep(n1,each=4)
n2 <- sapply(s2c('acgt'), function(x){length(which(substring(split,1,1)==x))})
Modified: pkg/src/alignment.c
===================================================================
--- pkg/src/alignment.c 2012-02-20 12:00:59 UTC (rev 1768)
+++ pkg/src/alignment.c 2012-02-22 10:15:53 UTC (rev 1769)
@@ -115,8 +115,8 @@
lgs = strlen(string);
if(lgs >= (MAXSTRING - 1)) {
- fprintf(stderr, "\n Too long line in alignment (> %d).\n", MAXSTRING);
- error("increase MAXSTRING and recompile.\n");
+ REprintf("\n Fatal Error. Too long line in alignment (> %d).\n", MAXSTRING);
+ REprintf("Increase MAXSTRING and recompile.\n");
}
c2 = string[0];
@@ -183,7 +183,7 @@
rem_blank(string);
if((int) strlen(string) >= (MAXMNMASE - 1)) {
- fprintf(stderr, "max %d characters\n", MAXMNMASE);
+ REprintf("Error. Maximum sequance name is %d characters\n", MAXMNMASE);
error("sequence name too long!");
}
strcpy(aln[ii].mn, string);
Modified: pkg/src/deflate.c
===================================================================
--- pkg/src/deflate.c 2012-02-20 12:00:59 UTC (rev 1768)
+++ pkg/src/deflate.c 2012-02-22 10:15:53 UTC (rev 1769)
@@ -1221,15 +1221,15 @@
/* check that the match is indeed a match */
if (zmemcmp(s->window + match,
s->window + start, length) != EQUAL) {
- fprintf(stderr, " start %u, match %u, length %d\n",
+ REprintf(" start %u, match %u, length %d\n",
start, match, length);
do {
- fprintf(stderr, "%c%c", s->window[match++], s->window[start++]);
+ REprintf("%c%c", s->window[match++], s->window[start++]);
} while (--length != 0);
z_error("invalid match");
}
if (z_verbose > 1) {
- fprintf(stderr,"\\[%d,%d]", start-match, length);
+ REprintf("\\[%d,%d]", start-match, length);
do { putc(s->window[start++], stderr); } while (--length != 0);
}
}
Modified: pkg/src/trees.c
===================================================================
--- pkg/src/trees.c 2012-02-20 12:00:59 UTC (rev 1768)
+++ pkg/src/trees.c 2012-02-22 10:15:53 UTC (rev 1769)
@@ -169,7 +169,7 @@
#else /* DEBUG */
# define send_code(s, c, tree) \
- { if (z_verbose>2) fprintf(stderr,"\ncd %3d ",(c)); \
+ { if (z_verbose>2) REprintf("\ncd %3d ",(c)); \
send_bits(s, tree[c].Code, tree[c].Len); }
#endif
@@ -689,7 +689,7 @@
tree[n].Dad = tree[m].Dad = (ush)node;
#ifdef DUMP_BL_TREE
if (tree == s->bl_tree) {
- fprintf(stderr,"\nnode %d(%d), sons %d(%d) %d(%d)",
+ REprintf("\nnode %d(%d), sons %d(%d) %d(%d)",
node, tree[node].Freq, n, tree[n].Freq, m, tree[m].Freq);
}
#endif
Modified: pkg/src/zutil.c
===================================================================
--- pkg/src/zutil.c 2012-02-20 12:00:59 UTC (rev 1768)
+++ pkg/src/zutil.c 2012-02-22 10:15:53 UTC (rev 1769)
@@ -122,7 +122,7 @@
void z_error (m)
char *m;
{
- fprintf(stderr, "%s\n", m);
+ REprintf("%s\n", m);
exit(1);
}
#endif
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