[adegenet-commits] r972 - pkg pkg/R pkg/man www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Nov 10 16:01:29 CET 2011
Author: jombart
Date: 2011-11-10 16:01:28 +0100 (Thu, 10 Nov 2011)
New Revision: 972
Modified:
pkg/DESCRIPTION
pkg/R/zzz.R
pkg/man/adegenet.package.Rd
www/download.html
www/news.html
Log:
updated website; devel is now 1.3-3
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2011-11-10 11:26:22 UTC (rev 971)
+++ pkg/DESCRIPTION 2011-11-10 15:01:28 UTC (rev 972)
@@ -1,5 +1,5 @@
Package: adegenet
-Version: 1.3-2
+Version: 1.3-3
Date: 2011/11/11
Title: adegenet: an R package for the exploratory analysis of genetic and genomic data.
Author: Thibaut Jombart <t.jombart at imperial.ac.uk>
Modified: pkg/R/zzz.R
===================================================================
--- pkg/R/zzz.R 2011-11-10 11:26:22 UTC (rev 971)
+++ pkg/R/zzz.R 2011-11-10 15:01:28 UTC (rev 972)
@@ -2,7 +2,7 @@
#.initAdegenetClasses()
#.initAdegenetUtils()
library.dynam("adegenet", pkg, lib)
- startup.txt <- " ==========================\n adegenet 1.3-2 is loaded\n ==========================\n\n - to start, type '?adegenet'\n - to browse adegenet website, type 'adegenetWeb()'\n - to post questions/comments: adegenet-forum at lists.r-forge.r-project.org\n\n"
+ startup.txt <- " ==========================\n adegenet 1.3-3 is loaded\n ==========================\n\n - to start, type '?adegenet'\n - to browse adegenet website, type 'adegenetWeb()'\n - to post questions/comments: adegenet-forum at lists.r-forge.r-project.org\n\n"
packageStartupMessage(startup.txt)
}
Modified: pkg/man/adegenet.package.Rd
===================================================================
--- pkg/man/adegenet.package.Rd 2011-11-10 11:26:22 UTC (rev 971)
+++ pkg/man/adegenet.package.Rd 2011-11-10 15:01:28 UTC (rev 972)
@@ -190,7 +190,7 @@
\tabular{ll}{
Package: \tab adegenet\cr
Type: \tab Package\cr
- Version: \tab 1.3-2\cr
+ Version: \tab 1.3-3\cr
Date: \tab 2011-11-11 \cr
License: \tab GPL (>=2)
}
Modified: www/download.html
===================================================================
--- www/download.html 2011-11-10 11:26:22 UTC (rev 971)
+++ www/download.html 2011-11-10 15:01:28 UTC (rev 972)
@@ -1,168 +1,155 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
- <head>
- <meta content="text/html; charset=ISO-8859-1"
- http-equiv="content-type">
- <title>download</title>
- <script type="text/javascript">
-
- var _gaq = _gaq || [];
- _gaq.push(['_setAccount', 'UA-20083187-1']);
- _gaq.push(['_trackPageview']);
-
- (function() {
- var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
- ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
- var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
- })();
-
- </script>
- </head>
- <body>
- <br>
- <br>
- <br>
- <div style="margin-left: 40px;"><img alt="" src="images/bullet.png"
- style="width: 10px; height: 10px;">
- The package adegenet is available from <a
- href="http://cran.r-project.org/mirrors.html">CRAN</a> (stable
- version).<br>
- <br>
- <img alt="" src="images/bullet.png" style="width: 10px; height:
- 10px;">
- The
- <span style="font-weight: bold;">current stable version</span>
- (adegenet_1.3-1)
- is available as:<br>
- - <a href="files/adegenet_1.3-1.tar.gz">linux/unix sources</a><br>
- - <a href="files/adegenet_1.3-1.tgz">MacOS X binary</a><br>
- - <a href="files/adegenet_1.3-1.zip">Windows binary</a><br>
- <br>
- <img alt="" src="images/bullet.png" style="width: 10px; height:
- 10px;">
- The
- <span style="font-weight: bold;">devel version</span>
- (adegenet_1.3-2)
- is also available
- from <a href="https://r-forge.r-project.org/scm/?group_id=120"
- target="_top">R-Forge's
- daily snapshots</a>.<br>
- It can be installed directly from R console using: <br>
- <span style="font-family: monospace;">install.packages("adegenet",repos="http://r-forge.r-project.org")<br>
- <br>
- </span><img alt="" src="images/bullet.png" style="width: 10px;
- height: 10px;">
- <span style="font-weight: bold;">Patches</span> <br>
- Patches correct minor bugs or
- implement new functionnalities, and will be included into the next
- CRAN
- release. It is recommended to use these versions instead of the
- current
- (CRAN) ones. Simply download the file (right click -> 'Save
- link
- as') in your working directory and
- type <span style="font-family: monospace;">source("[your-patch-file.R]")</span>
- to
- use
- a
- patch.<br>
- <a href="files/patches/addedFeatures.R"><span style="font-family:
- monospace;">addedFeatures.R</span></a>:
- (for
- adegenet_1.3-1)
- added features not included in the CRAN version of the package;
- includes conversion from <span style="font-family: monospace;">seqTrack
- </span>outputs to <span style="font-family: monospace;">graphNEL
- </span>objects.<br>
- <a href="files/patches/export.R"><span style="font-family:
- monospace;"></span></a><br>
- <img alt="" src="images/bullet.png" style="width: 10px; height:
- 10px;">
- <span style="font-weight: bold;">Older
- versions</span>:<br>
- adegenet_1.3-0<br>
- - <a href="files/adegenet_1.3-0.tar.gz">linux/unix sources</a><br>
- - <a href="files/adegenet_1.3-0.tgz">MacOS X binary</a><br>
- - <a href="files/adegenet_1.3-0.zip">Windows binary<br>
- </a><a href="files/adegenet_1.3-0.zip"></a><br>
- adegenet_1.2-9: there is no adegenet_1.2-9...<br>
- <br>
- adegenet_1.2-8<br>
- - <a href="files/adegenet_1.2-8.tar.gz">linux/unix sources</a><br>
- - <a href="files/adegenet_1.2-8.tgz">MacOS X binary</a><br>
- - <a href="files/adegenet_1.2-8.zip">Windows binary</a><br>
- <br>
- adegenet_1.2-7<br>
- - <a href="files/adegenet_1.2-7.tar.gz">linux/unix sources</a><br>
- - <a href="files/adegenet_1.2-7.tgz">MacOS X binary</a><br>
- - <a href="files/adegenet_1.2-7.zip">Windows binary</a><br>
- <br>
- adegenet_1.2-6<br>
- - <a href="files/adegenet_1.2-6.tar.gz">linux/unix sources</a><br>
- - <a href="files/adegenet_1.2-6.tgz">MacOS X binary</a><br>
- - <a href="files/adegenet_1.2-6.zip">Windows binary</a><br>
- <br>
- adegenet_1.2-5<br>
- - <a href="files/adegenet_1.2-5.tar.gz">linux/unix sources</a><br>
- - <a href="files/adegenet_1.2-5.tgz">MacOS X binary</a><br>
- - <a href="files/adegenet_1.2-5.zip">Windows binary</a><br>
- <br>
- adegenet_1.2-4<br>
- - <a href="files/adegenet_1.2-4.tar.gz">linux/unix sources</a><br>
- - <a href="files/adegenet_1.2-4.tgz">MacOS X binary</a><br>
- - <a href="files/adegenet_1.2-4.zip">Windows binary</a><br>
- <br>
- adegenet_1.3-3<br>
- - <a href="files/adegenet_1.2-3.tar.gz">linux/unix sources</a><br>
- - <a href="files/adegenet_1.2-3.tgz">MacOS X binary</a><br>
- - <a href="files/adegenet_1.2-3.zip">Windows binary</a><br>
- <br>
- adegenet_1.2-2<br>
- - <a href="files/adegenet_1.2-2.tar.gz">linux/unix sources</a><br>
- - <a href="files/adegenet_1.2-2.tgz">MacOS X binary</a><br>
- - <a href="files/adegenet_1.2-2.zip">Windows binary</a><br>
- <br>
- adegenet_1.2-1<br>
- - <a href="files/adegenet_1.2-1.tar.gz">linux/unix sources</a><br>
- - <a href="files/adegenet_1.2-1.tgz">MacOS X binary</a><br>
- - <a href="files/adegenet_1.2-1.zip">Windows binary</a><br>
- <br>
- adegenet_1.2-0<br>
- - <a href="files/adegenet_1.2-0.tar.gz">linux/unix sources</a><br>
- - <a href="files/adegenet_1.2-0.tgz">MacOS X binary</a><br>
- - <a href="files/adegenet_1.2-0.zip">Windows binary</a><br>
- <br>
- adegenet_1.1-2<br>
- - <a href="files/adegenet_1.1-2.tar.gz">linux/unix sources</a><br>
- - <a href="files/adegenet_1.1-2.tgz">MacOS X binary</a><br>
- - <a href="files/adegenet_1.1-2.zip">Windows binary</a><br>
- <br>
- adegenet_1.1-1<br>
- - <a href="files/adegenet_1.1-1.tar.gz">linux/unix sources</a><br>
- - <a href="files/adegenet_1.1-1.tgz">MacOS X binary</a><br>
- - <a href="files/adegenet_1.1-1.zip">Windows binary</a><br>
- <br>
- adegenet_1.1-0<br>
- - <a href="files/adegenet_1.1-0.tar.gz">linux/unix sources</a><br>
- - <a href="files/adegenet_1.1-0.tgz">MacOS X binary</a><br>
- - <a href="files/adegenet_1.1-0.zip">Windows binary</a><br>
- <br>
- adegenet_1.0-2<br>
- - <a href="files/adegenet_1.0-2.tar.gz">linux/unix sources</a><br>
- - <a href="files/adegenet_1.0-2.tgz">MacOS X binary</a><br>
- - <a href="files/adegenet_1.0-2.zip">Windows binary</a><br>
- <br>
- adegenet_1.0-1<br>
- - <a href="files/adegenet_1.0-1.tar.gz">linux/unix sources</a><br>
- - <a href="files/adegenet_1.0-1.tgz">MacOS X binary</a><br>
- - <a href="files/adegenet_1.0-1.zip">Windows binary</a><span
- style="text-decoration: underline;"><br>
- <br>
- </span>adegenet_1.0-0<br>
- - <a href="files/adegenet_1.0-0.tar.gz">linux/unix sources</a><br>
- - <a href="files/adegenet_1.0-0.tgz">MacOS X binary</a> <br>
- - <a href="files/adegenet_1.0-0.zip">Windows binary</a><br>
- <span style="font-weight: bold;"></span><br>
- </div>
- </body>
-</html>
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+ <meta content="text/html; charset=ISO-8859-1"
+ http-equiv="content-type">
+ <title>download</title>
+ <script type="text/javascript">
+
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-20083187-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+
+ </script>
+</head>
+<body>
+<br>
+<br>
+<br>
+<div style="margin-left: 40px;"><img alt="" src="images/bullet.png"
+ style="width: 10px; height: 10px;"> The package adegenet is available
+from <a href="http://cran.r-project.org/mirrors.html">CRAN</a> (stable
+version).<br>
+<br>
+<img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
+The <span style="font-weight: bold;">current stable version</span>
+(adegenet_1.3-2) is available as:<br>
+- <a href="files/adegenet_1.3-2.tar.gz">linux/unix sources</a><br>
+- MacOS X binary<br>
+- Windows binary<br>
+<br>
+<img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
+The <span style="font-weight: bold;">devel version</span>
+(adegenet_1.3-3) is also available from <a
+ href="https://r-forge.r-project.org/scm/?group_id=120" target="_top">R-Forge's
+
+daily snapshots</a>.<br>
+It can be installed directly from R console using: <br>
+<span style="font-family: monospace;">install.packages("adegenet",repos="http://r-forge.r-project.org")<br>
+<br>
+</span><img alt="" src="images/bullet.png"
+ style="width: 10px; height: 10px;"> <span style="font-weight: bold;">Patches</span>
+<br>
+Patches correct minor bugs or implement new functionnalities, and will
+be included into the next CRAN release. It is recommended to use these
+versions instead of the current (CRAN) ones. Simply download the file
+(right click -> 'Save link as') in your working directory and type <span
+ style="font-family: monospace;">source("[your-patch-file.R]")</span>
+
+to use a patch.<br>
+<a href="files/patches/addedFeatures.R"><span
+ style="font-family: monospace;">addedFeatures.R</span></a>: (for
+adegenet_1.3-1) added features not included in the CRAN version of the
+package; includes conversion from <span style="font-family: monospace;">seqTrack
+
+</span>outputs to <span style="font-family: monospace;">graphNEL </span>objects.<br>
+<a href="files/patches/export.R"><span style="font-family: monospace;"></span></a><br>
+<img alt="" src="images/bullet.png" style="width: 10px; height: 10px;">
+<span style="font-weight: bold;">Older versions</span>:<br>
+adegenet_1.3-1<br>
+- <a href="files/adegenet_1.3-1.tar.gz">linux/unix sources</a><br>
+- <a href="files/adegenet_1.3-1.tgz">MacOS X binary</a><br>
+- <a href="files/adegenet_1.3-1.zip">Windows binary</a><br>
+<br>
+adegenet_1.3-0<br>
+- <a href="files/adegenet_1.3-0.tar.gz">linux/unix sources</a><br>
+- <a href="files/adegenet_1.3-0.tgz">MacOS X binary</a><br>
+- <a href="files/adegenet_1.3-0.zip">Windows binary<br>
+</a><a href="files/adegenet_1.3-0.zip"></a><br>
+adegenet_1.2-9: there is no adegenet_1.2-9...<br>
+<br>
+adegenet_1.2-8<br>
+- <a href="files/adegenet_1.2-8.tar.gz">linux/unix sources</a><br>
+- <a href="files/adegenet_1.2-8.tgz">MacOS X binary</a><br>
+- <a href="files/adegenet_1.2-8.zip">Windows binary</a><br>
+<br>
+adegenet_1.2-7<br>
+- <a href="files/adegenet_1.2-7.tar.gz">linux/unix sources</a><br>
+- <a href="files/adegenet_1.2-7.tgz">MacOS X binary</a><br>
+- <a href="files/adegenet_1.2-7.zip">Windows binary</a><br>
+<br>
+adegenet_1.2-6<br>
+- <a href="files/adegenet_1.2-6.tar.gz">linux/unix sources</a><br>
+- <a href="files/adegenet_1.2-6.tgz">MacOS X binary</a><br>
+- <a href="files/adegenet_1.2-6.zip">Windows binary</a><br>
+<br>
+adegenet_1.2-5<br>
+- <a href="files/adegenet_1.2-5.tar.gz">linux/unix sources</a><br>
+- <a href="files/adegenet_1.2-5.tgz">MacOS X binary</a><br>
+- <a href="files/adegenet_1.2-5.zip">Windows binary</a><br>
+<br>
+adegenet_1.2-4<br>
+- <a href="files/adegenet_1.2-4.tar.gz">linux/unix sources</a><br>
+- <a href="files/adegenet_1.2-4.tgz">MacOS X binary</a><br>
+- <a href="files/adegenet_1.2-4.zip">Windows binary</a><br>
+<br>
+adegenet_1.3-3<br>
+- <a href="files/adegenet_1.2-3.tar.gz">linux/unix sources</a><br>
+- <a href="files/adegenet_1.2-3.tgz">MacOS X binary</a><br>
+- <a href="files/adegenet_1.2-3.zip">Windows binary</a><br>
+<br>
+adegenet_1.2-2<br>
+- <a href="files/adegenet_1.2-2.tar.gz">linux/unix sources</a><br>
+- <a href="files/adegenet_1.2-2.tgz">MacOS X binary</a><br>
+- <a href="files/adegenet_1.2-2.zip">Windows binary</a><br>
+<br>
+adegenet_1.2-1<br>
+- <a href="files/adegenet_1.2-1.tar.gz">linux/unix sources</a><br>
+- <a href="files/adegenet_1.2-1.tgz">MacOS X binary</a><br>
+- <a href="files/adegenet_1.2-1.zip">Windows binary</a><br>
+<br>
+adegenet_1.2-0<br>
+- <a href="files/adegenet_1.2-0.tar.gz">linux/unix sources</a><br>
+- <a href="files/adegenet_1.2-0.tgz">MacOS X binary</a><br>
+- <a href="files/adegenet_1.2-0.zip">Windows binary</a><br>
+<br>
+adegenet_1.1-2<br>
+- <a href="files/adegenet_1.1-2.tar.gz">linux/unix sources</a><br>
+- <a href="files/adegenet_1.1-2.tgz">MacOS X binary</a><br>
+- <a href="files/adegenet_1.1-2.zip">Windows binary</a><br>
+<br>
+adegenet_1.1-1<br>
+- <a href="files/adegenet_1.1-1.tar.gz">linux/unix sources</a><br>
+- <a href="files/adegenet_1.1-1.tgz">MacOS X binary</a><br>
+- <a href="files/adegenet_1.1-1.zip">Windows binary</a><br>
+<br>
+adegenet_1.1-0<br>
+- <a href="files/adegenet_1.1-0.tar.gz">linux/unix sources</a><br>
+- <a href="files/adegenet_1.1-0.tgz">MacOS X binary</a><br>
+- <a href="files/adegenet_1.1-0.zip">Windows binary</a><br>
+<br>
+adegenet_1.0-2<br>
+- <a href="files/adegenet_1.0-2.tar.gz">linux/unix sources</a><br>
+- <a href="files/adegenet_1.0-2.tgz">MacOS X binary</a><br>
+- <a href="files/adegenet_1.0-2.zip">Windows binary</a><br>
+<br>
+adegenet_1.0-1<br>
+- <a href="files/adegenet_1.0-1.tar.gz">linux/unix sources</a><br>
+- <a href="files/adegenet_1.0-1.tgz">MacOS X binary</a><br>
+- <a href="files/adegenet_1.0-1.zip">Windows binary</a><span
+ style="text-decoration: underline;"><br>
+<br>
+</span>adegenet_1.0-0<br>
+- <a href="files/adegenet_1.0-0.tar.gz">linux/unix sources</a><br>
+- <a href="files/adegenet_1.0-0.tgz">MacOS X binary</a> <br>
+- <a href="files/adegenet_1.0-0.zip">Windows binary</a><br>
+<span style="font-weight: bold;"></span><br>
+</div>
+</body>
+</html>
Modified: www/news.html
===================================================================
--- www/news.html 2011-11-10 11:26:22 UTC (rev 971)
+++ www/news.html 2011-11-10 15:01:28 UTC (rev 972)
@@ -28,14 +28,14 @@
<br>
<span style="font-weight: bold;"><big><br>
</big></span><span style="font-weight: bold;"><big>Coming soon</big></span><br>
-Next release (1.3-2) is under development.<br>
+Next release (1.3-3) is under development.<br>
<br>
<br>
<span style="font-weight: bold;"><big>Today</big> </span><span
style="font-weight: bold;"></span><span style="font-weight: bold;"></span><br>
<span style="font-weight: bold;"></span>Current
stable version of <span style="color: rgb(255, 0, 0);">adegenet is
-1.3-1 </span>for R.2.13.1.<br>
+1.3-2 </span>for R.2.14.0.<br>
You can install the devel version from <a
href="https://r-forge.r-project.org/scm/?group_id=120">R-Forge</a>.<br>
See the current <a
@@ -43,9 +43,34 @@
for a list of
all modifications.<br>
<br>
-<span style="font-weight: bold;">02/09/2011 </span><span
+<span style="font-weight: bold;">11/11/2011 </span><span
style="font-weight: bold;"></span><img
style="width: 80px; height: 37px;" alt="" src="images/new.png"><br>
+<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.3-2</span>)
+has
+been
+released
+for
+R-2.14.0!</big> This minor release fixes some issues in the detection
+of the number of cores occuring on some platforms, as well as a few
+fixes in manpages. Function <span
+ style="font-family: monospace; color: rgb(255, 0, 0);">fstat</span> is
+now gone for good as <span style="font-style: italic;">hierfstat </span>package
+seems to be gone for good from CRAN, but the documentation shows how to
+use <span style="color: rgb(255, 0, 0); font-family: monospace;">Fst</span>
+from the <span style="font-style: italic;">pegas </span>package
+instead. <span style="color: rgb(255, 0, 0);"><span
+ style="color: rgb(0, 0, 0);">See
+the </span></span><span style="color: rgb(255, 0, 0);"><span
+ style="color: rgb(0, 0, 0);"></span></span><a
+ href="http://cran.r-project.org/web/packages/adegenet/ChangeLog">ChangeLog</a><span
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);"></span></span><span
+ style="color: rgb(255, 0, 0);"><span style="color: rgb(0, 0, 0);">
+file for more details.</span></span><br>
+<br>
+<br>
+<span style="font-weight: bold;">02/09/2011 </span><span
+ style="font-weight: bold;"></span><br>
<big>New adegenet version (<span style="color: rgb(255, 0, 0);">1.3-1</span>)
has
been
@@ -360,7 +385,8 @@
in
an
analysis.
-A new georeferenced genetic dataset is also available
+A
+new georeferenced genetic dataset is also available
(dataset <span style="color: rgb(255, 0, 0); font-family: monospace;">rupica</span>).
And...
<a href="files/ChangeLog">several other things</a>!<br>
More information about the adegenet-commits
mailing list