[med-svn] [mothur] 01/01: d/patches: drop a patch that changes how .pat files are sought

[Tomasz Buchert]

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tomasz pushed a commit to branch master
in repository mothur.

commit c90a011565828dbdc5f55ef430400322699b842b
Author: Tomasz Buchert <tomasz at debian.org>
Date:   Sat Sep 12 10:29:30 2015 +0200

    d/patches: drop a patch that changes how .pat files are sought
---
 debian/patches/0007-Fix-file-searching-logic.patch | 62 ----------------------
 debian/patches/series                              |  1 -
 2 files changed, 63 deletions(-)

diff --git a/debian/patches/0007-Fix-file-searching-logic.patch b/debian/patches/0007-Fix-file-searching-logic.patch
deleted file mode 100644
index 6017314..0000000
--- a/debian/patches/0007-Fix-file-searching-logic.patch
+++ /dev/null
@@ -1,62 +0,0 @@
-From: Tim Booth <tbooth at ceh.ac.uk>
-Date: Fri, 4 Sep 2015 00:01:52 +0200
-Subject: Fix file searching logic
-
-Mothur ships with some .pat files which are needed by a couple of
-commands.  Default behaviour is to fall back to looking in the exec dir,
-which makes no sense in a package, so redirect it.
----
- source/commands/sffmultiplecommand.cpp |  6 +++---
- source/commands/shhhercommand.cpp      | 12 ++++++------
- 2 files changed, 9 insertions(+), 9 deletions(-)
-
-diff --git a/source/commands/sffmultiplecommand.cpp b/source/commands/sffmultiplecommand.cpp
-index abd012d..5a77bec 100644
---- a/source/commands/sffmultiplecommand.cpp
-+++ b/source/commands/sffmultiplecommand.cpp
-@@ -316,10 +316,10 @@ SffMultipleCommand::SffMultipleCommand(string option)  {
- 				for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
- 				exepath = exepath.substr(0, (tempPath.find_last_of('m')));
-                 
--				string tryPath = m->getFullPathName(exepath) + m->getSimpleName(lookupFileName);
--				m->mothurOut("Unable to open " + lookupFileName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine();
-+				string tryPath = "/usr/share/mothur/";
-+				m->mothurOut("Unable to open " + lookupFileName + ". Trying default location " + tryPath); m->mothurOutEndLine();
- 				ifstream in2;
--				int ableToOpen = m->openInputFile(tryPath, in2, "noerror");
-+				int ableToOpen = m->openInputFile(tryPath + m->getSimpleName(lookupFileName), in2, "noerror");
- 				in2.close();
- 				lookupFileName = tryPath;
- 				
-diff --git a/source/commands/shhhercommand.cpp b/source/commands/shhhercommand.cpp
-index e20a309..90786ae 100644
---- a/source/commands/shhhercommand.cpp
-+++ b/source/commands/shhhercommand.cpp
-@@ -315,10 +315,10 @@ ShhherCommand::ShhherCommand(string option) {
- 					for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
- 					exepath = exepath.substr(0, (tempPath.find_last_of('m')));
- 					
--					string tryPath = m->getFullPathName(exepath) + m->getSimpleName(lookupFileName);
--					m->mothurOut("Unable to open " + lookupFileName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine();
-+					string tryPath = "/usr/share/mothur/";
-+					m->mothurOut("Unable to open " + lookupFileName + ". Trying default location " + tryPath); m->mothurOutEndLine();
- 					ifstream in2;
--					ableToOpen = m->openInputFile(tryPath, in2, "noerror");
-+					ableToOpen = m->openInputFile(tryPath +  m->getSimpleName(lookupFileName), in2, "noerror");
- 					in2.close();
- 					lookupFileName = tryPath;
- 				}
-@@ -335,10 +335,10 @@ ShhherCommand::ShhherCommand(string option) {
- 				for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
- 				exepath = exepath.substr(0, (tempPath.find_last_of('m')));
- 					
--				string tryPath = m->getFullPathName(exepath) + m->getSimpleName(lookupFileName);
--				m->mothurOut("Unable to open " + lookupFileName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine();
-+				string tryPath = "/usr/share/mothur/";
-+				m->mothurOut("Unable to open " + lookupFileName + ". Trying default location " + tryPath); m->mothurOutEndLine();
- 				ifstream in2;
--				int ableToOpen = m->openInputFile(tryPath, in2, "noerror");
-+				int ableToOpen = m->openInputFile(tryPath + m->getSimpleName(lookupFileName), in2, "noerror");
- 				in2.close();
- 				lookupFileName = tryPath;
- 				
diff --git a/debian/patches/series b/debian/patches/series
index 4489857..f6ceefa 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -4,7 +4,6 @@
 0004-Fix-for-FTBFS-cc1plus-error-unrecognized-command-lin.patch
 0005-Don-t-redirect-anything-to-dev-tty.patch
 0006-Turn-off-unportable-optimizations-in-makefile.patch
-0007-Fix-file-searching-logic.patch
 0008-Fix-catchall-command.patch
 0009-Fix-boost_iostreams-flags.patch
 0010-Pass-hardening-flags-to-uchime-build.patch

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