[med-svn] [bamtools] 01/01: Spring cleaning
Michael Crusoe
misterc-guest at moszumanska.debian.org
Mon Mar 7 06:53:25 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to tag debian/2.4.0+dfsg-4
in repository bamtools.
commit 35ac2060e9d33f4a3137126c281f3b055de08d6b
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date: Sat Mar 5 05:56:22 2016 -0800
Spring cleaning
priority->extra; standards version bump
Update my email address & tweak Vcs-Git URL
split out dev -doc, fix typo, forwad patches
quiet some doxygen warnings, add gcc-6 compat, include
$devlibs, fixed spelling error in our changelog
---
debian/changelog | 19 ++++++-
debian/clean | 2 +-
debian/control | 26 +++++++--
debian/libbamtools-dev.install | 1 -
...tools-dev.doc-base => libbamtools-doc.doc-base} | 0
...amtools-dev.install => libbamtools-doc.install} | 1 -
debian/libbamtools2.4.0.lintian-overrides | 1 +
.../patches/0002-support-out-of-source-build.patch | 2 +-
...bamtools-to-lib.-Installing-libraries-to-.patch | 2 +-
.../0006-Fix-Doxyfile-input-source-path.patch | 2 +-
debian/patches/0007-Big_Endian.patch | 4 +-
debian/patches/doxygen-tweak | 66 ++++++++++++++++++++++
debian/patches/gcc-6_compat | 20 +++++++
.../patches/non-deprecated-jsoncpp-function-names | 15 +++++
debian/patches/series | 4 ++
debian/patches/spelling | 15 +++++
debian/rules | 21 ++++---
17 files changed, 181 insertions(+), 20 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 41c1cc4..343c1a5 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,23 @@
+bamtools (2.4.0+dfsg-4) UNRELEASED; urgency=medium
+
+ * Lower priority to 'extra' due to dependency on libjsoncpp1
+ * Split out -doc package for library documentation & enable standalone -arch
+ and -indep building
+ * Fix spelling error from upstream
+ * Update Standards-Version
+ * Update my email address
+ * Fix Vcs-Git URL
+ * Quiet some Doxygen warnings
+ * Add gcc-6 compat
+ * Include ${devlibs} for -dev package
+ * Forwarded many patches upstream
+ * Remove the html docs directory during d/rules clean
+
+ -- Michael R. Crusoe <crusoe at ucdavis.edu> Sat, 05 Mar 2016 05:54:38 -0800
+
bamtools (2.4.0+dfsg-3) unstable; urgency=medium
- * allow to read bam files on big endian systems (Closes: #807979)
+ * allows one to read bam files on big endian systems (Closes: #807979)
* added sam_spec_example.sam and sam_spec_example.bam files
* activated cmake testing framework abd added simple tests
diff --git a/debian/clean b/debian/clean
index 3675a60..991c2c6 100644
--- a/debian/clean
+++ b/debian/clean
@@ -2,4 +2,4 @@ bin/*
lib/*
include/*
src/toolkit/bamtools_version.h
-
+html/
diff --git a/debian/control b/debian/control
index 5d51cb8..226bb57 100644
--- a/debian/control
+++ b/debian/control
@@ -1,11 +1,11 @@
Source: bamtools
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Michael R. Crusoe <michael.crusoe at gmail.com>,
+Uploaders: Michael R. Crusoe <crusoe at ucdavis.edu>,
Andreas Tille <tille at debian.org>,
Kevin Murray <spam at kdmurray.id.au>,
Dominique Belhachemi <domibel at debian.org>
Section: science
-Priority: optional
+Priority: extra
Build-Depends: debhelper (>= 9.0.0),
d-shlibs (>= 0.56),
cmake,
@@ -13,9 +13,9 @@ Build-Depends: debhelper (>= 9.0.0),
libjsoncpp-dev,
help2man,
doxygen
-Standards-Version: 3.9.6
+Standards-Version: 3.9.7
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bamtools.git
-Vcs-Git: https://anonscm.debian.org/cgit/debian-med/bamtools.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/bamtools.git
Homepage: https://github.com/pezmaster31/bamtools/wiki
Package: bamtools
@@ -55,7 +55,9 @@ Package: libbamtools-dev
Architecture: any
Section: libdevel
Depends: libbamtools2.4.0 (= ${binary:Version}),
+ ${devlibs:Depends},
${misc:Depends}
+Suggests: libbamtools-doc (= ${binary:Version})
Description: C++ API for manipulating BAM (genome alignment) files
BamTools facilitates research analysis and data management using BAM
files. It copes with the enormous amount of data produced by current
@@ -84,3 +86,19 @@ Description: dynamic library for manipulating BAM (genome alignment) files
command-line toolkit.
.
This is the runtime library.
+
+Package: libbamtools-doc
+Architecture: all
+Section: doc
+Depends: ${misc:Depends}
+Description: docs for dynamic library for manipulating BAM (genome alignment) files
+ BamTools facilitates research analysis and data management using BAM
+ files. It copes with the enormous amount of data produced by current
+ sequencing technologies that is typically stored in compressed, binary
+ formats that are not easily handled by the text-based parsers commonly
+ used in bioinformatics research.
+ .
+ BamTools provides both a C++ API for BAM file support as well as a
+ command-line toolkit.
+ .
+ This is the documentation for the library.
diff --git a/debian/libbamtools-dev.install b/debian/libbamtools-dev.install
index 5f4df6f..7687141 100644
--- a/debian/libbamtools-dev.install
+++ b/debian/libbamtools-dev.install
@@ -1,2 +1 @@
debian/cmake usr/share
-html usr/share/doc/libbamtools-dev
diff --git a/debian/libbamtools-dev.doc-base b/debian/libbamtools-doc.doc-base
similarity index 100%
rename from debian/libbamtools-dev.doc-base
rename to debian/libbamtools-doc.doc-base
diff --git a/debian/libbamtools-dev.install b/debian/libbamtools-doc.install
similarity index 61%
copy from debian/libbamtools-dev.install
copy to debian/libbamtools-doc.install
index 5f4df6f..c49fe91 100644
--- a/debian/libbamtools-dev.install
+++ b/debian/libbamtools-doc.install
@@ -1,2 +1 @@
-debian/cmake usr/share
html usr/share/doc/libbamtools-dev
diff --git a/debian/libbamtools2.4.0.lintian-overrides b/debian/libbamtools2.4.0.lintian-overrides
index a91ee70..536b82d 100644
--- a/debian/libbamtools2.4.0.lintian-overrides
+++ b/debian/libbamtools2.4.0.lintian-overrides
@@ -1 +1,2 @@
libbamtools2.4.0: spelling-error-in-binary usr/lib/x86_64-linux-gnu/libbamtools.so.2.4.0 ment meant
+libbamtools2.4.0: spelling-error-in-binary usr/lib/x86_64-linux-gnu/libbamtools.so.2.4.0 unknow unknown
diff --git a/debian/patches/0002-support-out-of-source-build.patch b/debian/patches/0002-support-out-of-source-build.patch
index e5d1eb0..ae8f236 100644
--- a/debian/patches/0002-support-out-of-source-build.patch
+++ b/debian/patches/0002-support-out-of-source-build.patch
@@ -1,7 +1,7 @@
From: Dominique Belhachemi <domibel at debian.org>
Date: Fri, 21 Sep 2012 11:16:28 -0400
Subject: support out-of-source build
-
+Forwarded: https://github.com/pezmaster31/bamtools/pull/117
---
CMakeLists.txt | 5 +++--
src/ExportHeader.cmake | 2 +-
diff --git a/debian/patches/0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch b/debian/patches/0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch
index 1a35403..ddd0575 100644
--- a/debian/patches/0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch
+++ b/debian/patches/0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch
@@ -3,7 +3,7 @@ Date: Wed, 7 Nov 2012 19:11:51 -0700
Subject: Install libbamtools to /usr/lib. Installing libraries to
/usr/lib/bamtools requires setting LD_LIBRARY_PATH or the executable's
rpath. Installing libraries to /usr/lib is cleaner.
-
+Forwarded: https://github.com/pezmaster31/bamtools/pull/82
---
src/api/CMakeLists.txt | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/debian/patches/0006-Fix-Doxyfile-input-source-path.patch b/debian/patches/0006-Fix-Doxyfile-input-source-path.patch
index b4cc12d..43ebfbd 100644
--- a/debian/patches/0006-Fix-Doxyfile-input-source-path.patch
+++ b/debian/patches/0006-Fix-Doxyfile-input-source-path.patch
@@ -1,7 +1,7 @@
From: Kevin Murray <spam at kdmurray.id.au>
Date: Thu, 24 Sep 2015 18:04:10 +1000
Subject: Fix Doxyfile input source path
-
+Forwarded: https://github.com/pezmaster31/bamtools/pull/118
---
docs/Doxyfile | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/debian/patches/0007-Big_Endian.patch b/debian/patches/0007-Big_Endian.patch
index e9235d4..efc75ad 100644
--- a/debian/patches/0007-Big_Endian.patch
+++ b/debian/patches/0007-Big_Endian.patch
@@ -1,7 +1,7 @@
-Description: read bam files on big endian systems
+Subject: read bam files on big endian systems
Author: Dominique Belhachemi <domibel at debian.org>
Bug-Debian: https://bugs.debian.org/807979
-Forwarded: https://github.com/pezmaster31/bamtools/issues/113
+Forwarded: https://github.com/pezmaster31/bamtools/pull/119
Index: bamtools/src/api/BamAux.h
===================================================================
diff --git a/debian/patches/doxygen-tweak b/debian/patches/doxygen-tweak
new file mode 100644
index 0000000..400ab28
--- /dev/null
+++ b/debian/patches/doxygen-tweak
@@ -0,0 +1,66 @@
+From: Michael R. Crusoe <crusoe at ucdavis.edu>
+Subject: fixes a couple Doxygen warnings
+Forwarded: https://github.com/pezmaster31/bamtools/pull/120
+
+--- bamtools.orig/src/api/BamMultiReader.cpp
++++ bamtools/src/api/BamMultiReader.cpp
+@@ -361,10 +361,10 @@
+ method can be useful when you know, for example, that your BAM files are sorted
+ by coordinate but upstream processes did not set the header tag properly.
+
+- \note This method should \bold not be called while reading alignments via
++ \note This method should \b not be called while reading alignments via
+ GetNextAlignment() or GetNextAlignmentCore(). For proper results, you should
+ call this method before (or immediately after) opening files, rewinding,
+- jumping, etc. but \bold not once alignment fetching has started. There is
++ jumping, etc. but \b not once alignment fetching has started. There is
+ nothing in the API to prevent you from doing so, but the results may be
+ unexpected.
+
+--- bamtools.orig/docs/Doxyfile
++++ bamtools/docs/Doxyfile
+@@ -1454,7 +1454,7 @@
+ # DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory
+ # containing the font.
+
+-DOT_FONTNAME = FreeSans
++# DOT_FONTNAME = FreeSans
+
+ # The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
+ # The default size is 10pt.
+--- bamtools.orig/src/api/BamAlignment.h
++++ bamtools/src/api/BamAlignment.h
+@@ -143,12 +143,13 @@
+ bool SkipToNextTag(const char storageType,
+ char*& pTagData,
+ unsigned int& numBytesParsed) const;
+-
++ //! \internal
+ // internal data
+ private:
+
+ struct BamAlignmentSupportData {
+-
++
++ //! \internal
+ // data members
+ std::string AllCharData;
+ uint32_t BlockLength;
+@@ -156,7 +157,8 @@
+ uint32_t QueryNameLength;
+ uint32_t QuerySequenceLength;
+ bool HasCoreOnly;
+-
++
++ //! \internal
+ // constructor
+ BamAlignmentSupportData(void)
+ : BlockLength(0)
+@@ -171,7 +173,6 @@
+ friend class Internal::BamWriterPrivate;
+
+ mutable std::string ErrorString; // mutable to allow updates even in logically const methods
+- //! \endinternal
+ };
+
+ // ---------------------------------------------------------
diff --git a/debian/patches/gcc-6_compat b/debian/patches/gcc-6_compat
new file mode 100644
index 0000000..f1a168d
--- /dev/null
+++ b/debian/patches/gcc-6_compat
@@ -0,0 +1,20 @@
+From d5c951f45ed768570df65e29ba9ab9eef2369f37 Mon Sep 17 00:00:00 2001
+From: Matei David <matei at cs.toronto.edu>
+Date: Wed, 3 Feb 2016 23:50:26 -0500
+Subject: [PATCH] add c++98 compile and link flag
+Forwarded: https://github.com/pezmaster31/bamtools/pull/116
+
+---
+ CMakeLists.txt | 1 +
+ 1 file changed, 1 insertion(+)
+
+--- bamtools.orig/CMakeLists.txt
++++ bamtools/CMakeLists.txt
+@@ -42,6 +42,7 @@
+
+ # define compiler flags for all code
+ set( CMAKE_BUILD_TYPE Release )
++set( CMAKE_CXX_FLAGS_RELEASE "-std=c++98 ${CMAKE_CXX_FLAGS_RELEASE}" )
+ add_definitions( -Wall -D_FILE_OFFSET_BITS=64 )
+
+ # -----------------------------------------------
diff --git a/debian/patches/non-deprecated-jsoncpp-function-names b/debian/patches/non-deprecated-jsoncpp-function-names
new file mode 100644
index 0000000..7b9b73f
--- /dev/null
+++ b/debian/patches/non-deprecated-jsoncpp-function-names
@@ -0,0 +1,15 @@
+From: Michael R. Crusoe <crusoe at ucdavis.edu>
+Subject: Use the non-deprecated function name
+Forwarded: https://github.com/pezmaster31/bamtools/pull/121
+
+--- bamtools.orig/src/toolkit/bamtools_filter.cpp
++++ bamtools/src/toolkit/bamtools_filter.cpp
+@@ -647,7 +647,7 @@
+ if ( !reader.parse(document, root) ) {
+ // use built-in error reporting mechanism to alert user what was wrong with the script
+ cerr << "bamtools filter ERROR: failed to parse script - see error message(s) below" << endl
+- << reader.getFormatedErrorMessages();
++ << reader.getFormattedErrorMessages();
+ return false;
+ }
+
diff --git a/debian/patches/series b/debian/patches/series
index 8e3563c..d399e0c 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,6 @@
+doxygen-tweak
0001-ignore-thirdparty-and-fix-jsoncpp.patch
+non-deprecated-jsoncpp-function-names
0002-support-out-of-source-build.patch
0003-remove-custom-ExportHeader-function-use-install-inst.patch
0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch
@@ -6,3 +8,5 @@
0006-Fix-Doxyfile-input-source-path.patch
0007-Big_Endian.patch
0008_Cmake_Test.patch
+spelling
+gcc-6_compat
diff --git a/debian/patches/spelling b/debian/patches/spelling
new file mode 100644
index 0000000..a77f66a
--- /dev/null
+++ b/debian/patches/spelling
@@ -0,0 +1,15 @@
+From: Michael R. Crusoe <crusoe at ucdavis.edu>
+Subject: Fix typo
+Forwarded: https://github.com/pezmaster31/bamtools/pull/122
+
+--- bamtools.orig/src/toolkit/bamtools_split.cpp
++++ bamtools/src/toolkit/bamtools_split.cpp
+@@ -199,7 +199,7 @@
+
+ // if we get here, no property was specified
+ cerr << "bamtools split ERROR: no property given to split on... " << endl
+- << "Please use -mapped, -paired, -reference, or -tag TAG to specifiy desired split behavior." << endl;
++ << "Please use -mapped, -paired, -reference, or -tag TAG to specify desired split behavior." << endl;
+ return false;
+ }
+
diff --git a/debian/rules b/debian/rules
index 5216d3d..bf8fdfa 100755
--- a/debian/rules
+++ b/debian/rules
@@ -9,24 +9,31 @@ DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
%:
dh $@ --parallel
-override_dh_auto_build:
- dh_auto_build
+override_dh_auto_configure-indep:
+
+override_dh_auto_test-indep:
+
+override_dh_auto_build-indep:
+ doxygen -u docs/Doxyfile
doxygen docs/Doxyfile
+ mv docs/Doxyfile.bak docs/Doxyfile
-override_dh_install:
+override_dh_install-indep:
+ dh_install --indep
+ rm -f debian/libbamtools-doc/usr/share/doc/libbamtools-dev/html/jquery.js
+ ln -s /usr/share/javascript/jquery/jquery.js debian/libbamtools-doc/usr/share/doc/libbamtools-dev/html/jquery.js
+
+override_dh_install-arch:
d-shlibmove --commit \
--multiarch \
--devunversioned \
--exclude-la \
--movedev debian/tmp/usr/include/* usr/include \
debian/tmp/usr/lib/lib*.so
- dh_install
+ dh_install --arch
# no need to install different versions of bamtools
rm -rf debian/$(DEBPKGNAME)/usr/bin/$(DEBPKGNAME)
mv debian/$(DEBPKGNAME)/usr/bin/$(DEBPKGNAME)-[0-9]* debian/$(DEBPKGNAME)/usr/bin/$(DEBPKGNAME)
- rm -f debian/libbamtools-dev/usr/share/doc/libbamtools-dev/html/jquery.js
- ln -s /usr/share/javascript/jquery/jquery.js debian/libbamtools-dev/usr/share/doc/libbamtools-dev/html/jquery.js
-
#override_dh_installman:
# LD_LIBRARY_PATH=debian/tmp/usr/lib:${LD_LIBRARY_PATH} help2man --name "a command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files" --no-info --no-discard-stderr debian/tmp/usr/bin/bamtools > debian/bamtools.1
--
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