[med-svn] [salmon] 01/04: add debian-med standard gbp.conf

[Michael Crusoe]

This is an automated email from the git hooks/post-receive script.

misterc-guest pushed a commit to branch master
in repository salmon.

commit eb10dee7980f044860e45b696b42e0a8a01f8fb8
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Fri Jan 29 23:36:40 2016 -0800

    add debian-med standard gbp.conf
    
    and fix some typos
---
 debian/control                  |  2 +-
 debian/copyright                |  2 ++
 debian/gbp.conf                 | 12 +++++++++++
 debian/patches/cmake-typo-fixes | 44 +++++++++++++++++++++++++++++++++++++++++
 debian/patches/series           |  2 ++
 debian/patches/spelling-fixes   | 11 +++++++++++
 6 files changed, 72 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index 5f7fcf4..0871a2a 100644
--- a/debian/control
+++ b/debian/control
@@ -29,7 +29,7 @@ Build-Depends: debhelper (>= 9),
                python-sphinx | python3-sphinx,
                zlib1g-dev
 Standards-Version: 3.9.6
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/<pkg>/trunk/
+Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/<pkg>/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/<pkg>/trunk/
 Homepage: https://github.com/COMBINE-lab/salmon
 
diff --git a/debian/copyright b/debian/copyright
index c467015..f8f41e8 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -2,6 +2,8 @@ Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: salmon
 Source: https://github.com/COMBINE-lab/salmon/
 Files-Excluded: doc/build/*
+ include/CollapsedIterativeOptimizer.hpp.bak
+ src/SalmonQuantify.cpp.bak
 
 Files: *
 Copyright: © 2015 The Salmon Authors
diff --git a/debian/gbp.conf b/debian/gbp.conf
new file mode 100644
index 0000000..32012ce
--- /dev/null
+++ b/debian/gbp.conf
@@ -0,0 +1,12 @@
+[DEFAULT]
+# The default name for the upstream branch is "upstream".
+# Change it if the name is different (for instance, "master").
+upstream-branch = upstream
+# The default name for the Debian branch is "master".
+# Change it if the name is different (for instance, "debian/unstable").
+debian-branch = master
+# gbp import-orig uses the following names for the upstream tags.
+# Change the value if you are not using gbp import-orig
+upstream-tag = upstream/%(version)s
+# Always use pristine-tar.
+pristine-tar = True
diff --git a/debian/patches/cmake-typo-fixes b/debian/patches/cmake-typo-fixes
new file mode 100644
index 0000000..f63204f
--- /dev/null
+++ b/debian/patches/cmake-typo-fixes
@@ -0,0 +1,44 @@
+--- salmon.orig/CMakeLists.txt
++++ salmon/CMakeLists.txt
+@@ -6,8 +6,8 @@
+ 
+ set(CPACK_PACKAGE_VERSION "0.4.2")
+ set(CPACK_PACKAGE_VERSION_MAJOR "0")
+-set(CPACK_PACKAGE_VERSION_MINOR 4")
+-set(CPACK_PACKAGE_VERSION_PATCH 2")
++set(CPACK_PACKAGE_VERSION_MINOR "4")
++set(CPACK_PACKAGE_VERSION_PATCH "2")
+ set(CPACK_GENERATOR "TGZ")
+ set(CPACK_SOURCE_GENERATOR "TGZ")
+ set(CPACK_PACKAGE_VENDOR Stony Brook University")
+--- salmon.orig/include/tensemble/GBMRegressor.h
++++ salmon/include/tensemble/GBMRegressor.h
+@@ -63,7 +63,7 @@
+     if (loss_function==SQUARE_LOSS) {
+         loss=new SquareLoss();
+     }else {
+-        fprintf(stderr, "Error: Unknow loss function\n");
++        fprintf(stderr, "Error: Unknown loss function\n");
+         return ENSEMBLE_FAIL;
+     }
+     //allocate memory for prior and trees
+--- salmon.orig/include/tensemble/cmdline.h
++++ salmon/include/tensemble/cmdline.h
+@@ -91,7 +91,7 @@
+                 value[s] = "";
+             }
+         } else {
+-            fprintf(stderr, "Error: Unknow parameter %s.\n",s.c_str());
++            fprintf(stderr, "Error: Unknown parameter %s.\n",s.c_str());
+             print_help();
+             return false;
+         }
+@@ -135,7 +135,7 @@
+             }
+         }
+         if (i==len) {
+-            fprintf(stderr, "Error: Unknow parameter %s.\n",iter->first.c_str());
++            fprintf(stderr, "Error: Unknown parameter %s.\n",iter->first.c_str());
+ //            print_help();
+             return false;
+         }
diff --git a/debian/patches/series b/debian/patches/series
index d3140e5..7417274 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,3 +2,5 @@ dependency-fix
 jellyfish-update
 cmake-adj
 drop-mathjax
+cmake-typo-fixes
+spelling-fixes
diff --git a/debian/patches/spelling-fixes b/debian/patches/spelling-fixes
new file mode 100644
index 0000000..2a78659
--- /dev/null
+++ b/debian/patches/spelling-fixes
@@ -0,0 +1,11 @@
+--- salmon.orig/src/SalmonQuantify.cpp
++++ salmon/src/SalmonQuantify.cpp
+@@ -2928,7 +2928,7 @@
+                                         "many reads, then just keep the data in memory for subsequent rounds of inference. Obviously, this value should "
+                                         "not be too large if you wish to keep a low memory usage, but setting it large enough can substantially speed up "
+                                         "inference on \"small\" files that contain only a few million reads.")
+-    ("maxOcc,m", po::value<int>(&(memOptions->max_occ))->default_value(200), "(S)MEMs occuring more than this many times won't be considered.")
++    ("maxOcc,m", po::value<int>(&(memOptions->max_occ))->default_value(200), "(S)MEMs occurring more than this many times won't be considered.")
+     ("maxReadOcc,w", po::value<uint32_t>(&(sopt.maxReadOccs))->default_value(100), "Reads \"mapping\" to more than this many places won't be considered.")
+     ("noEffectiveLengthCorrection", po::bool_switch(&(sopt.noEffectiveLengthCorrection))->default_value(false), "Disables "
+                         "effective length correction when computing the probability that a fragment was generated "

-- 
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