[med-svn] [r-cran-ape] 01/02: Added patch to fix phyml binary location.

[Dylan Aïssi]

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bob.dybian-guest pushed a commit to branch master
in repository r-cran-ape.

commit a244d8fe392e27c2a596c058ac60fb4107e26b85
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date:   Sat Jun 14 09:10:44 2014 +0200

    Added patch to fix phyml binary location.
---
 debian/patches/01_Fix_PhyML_bin_location.patch | 20 ++++++++++++++++++++
 debian/patches/series                          |  1 +
 2 files changed, 21 insertions(+)

diff --git a/debian/patches/01_Fix_PhyML_bin_location.patch b/debian/patches/01_Fix_PhyML_bin_location.patch
new file mode 100644
index 0000000..01c39a0
--- /dev/null
+++ b/debian/patches/01_Fix_PhyML_bin_location.patch
@@ -0,0 +1,20 @@
+Author: Dylan Aïssi <bob.dybian at gmail.com>
+Description: Fix PhyML binary location in Debian.
+ Fix PhyML location for Debian and Fedora packages and maybe for
+ others distributions.
+
+--- a/R/phymltest.R
++++ b/R/phymltest.R
+@@ -26,7 +26,11 @@
+     os <- Sys.info()[1]
+     ## default names of PhyML:
+     if (is.null(execname)) {
+-        if (os == "Linux") execname <- "phyml_3.0.1_linux32"
++        if (os == "Linux") {
++		 # PhyML location for Debian and Fedora packages and maybe for others distributions
++		if (file.exists("/usr/bin/phyml")) execname <- "/usr/bin/phyml"
++		else execname <- "phyml_3.0.1_linux32"
++	}
+         if (os == "Darwin") execname <- "phyml_3.0.1_macintel"
+         if (os == "Windows") execname <- "phyml_3.0.1_win32"
+     }
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..bb25a51
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+01_Fix_PhyML_bin_location.patch

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