[med-svn] [Git][med-team/pbseqlib][master] 5 commits: Fix build against recent Hdf5 lib
Andreas Tille
gitlab at salsa.debian.org
Mon Jul 2 13:51:02 BST 2018
Andreas Tille pushed to branch master at Debian Med / pbseqlib
Commits:
ad4f5ae2 by Andreas Tille at 2018-07-02T13:49:34+02:00
Fix build against recent Hdf5 lib
- - - - -
cc5d193f by Andreas Tille at 2018-07-02T14:41:34+02:00
check DEB_BUILD_OPTIONS in auto_test override
- - - - -
45b936a6 by Andreas Tille at 2018-07-02T14:41:45+02:00
Remove unused lintian override
- - - - -
df671edd by Andreas Tille at 2018-07-02T14:41:54+02:00
hardening=+all
- - - - -
6d264df0 by Andreas Tille at 2018-07-02T14:48:53+02:00
Upload to unstable
- - - - -
5 changed files:
- debian/changelog
- + debian/patches/hdf5-1.10.0-support.patch
- debian/patches/series
- debian/rules
- − debian/source/lintian-overrides
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,6 @@
-pbseqlib (5.3.1+dfsg-1) UNRELEASED; urgency=medium
+pbseqlib (5.3.1+dfsg-1) unstable; urgency=medium
+ [ Andreas Tille ]
* Team upload.
* d/watch: Upstream has tagged a release so use proper watch file
* Exclude binary tools from upstream tarball
@@ -9,8 +10,14 @@ pbseqlib (5.3.1+dfsg-1) UNRELEASED; urgency=medium
- Standards-Version: 4.1.4
- Sequence of fields
- Formatting
+ * check DEB_BUILD_OPTIONS in auto_test override
+ * Remove unused lintian override
+ * hardening=+all
- -- Andreas Tille <tille at debian.org> Tue, 26 Jun 2018 08:39:02 +0200
+ [ Gilles Filippini ]
+ * Fix build against recent Hdf5 lib
+
+ -- Andreas Tille <tille at debian.org> Mon, 02 Jul 2018 14:42:21 +0200
pbseqlib (0~20161219-2) unstable; urgency=medium
=====================================
debian/patches/hdf5-1.10.0-support.patch
=====================================
--- /dev/null
+++ b/debian/patches/hdf5-1.10.0-support.patch
@@ -0,0 +1,344 @@
+Author: Gilles Filippini <pini at debian.org>
+Last-Update: Sun, 1 Jul 2018 21:33:39 +0200
+Description: Fix build against recent Hdf5 lib
+
+--- a/hdf/BufferedHDF2DArray.cpp
++++ b/hdf/BufferedHDF2DArray.cpp
+@@ -29,7 +29,7 @@
+
+ */
+
+-DSLength GetDatasetNDim(H5::Group &parentGroup, std::string datasetName)
++DSLength GetDatasetNDim(H5::CommonFG &parentGroup, std::string datasetName)
+ {
+ HDFData tmpDataset;
+ tmpDataset.InitializeDataset(parentGroup, datasetName);
+--- a/hdf/BufferedHDF2DArray.hpp
++++ b/hdf/BufferedHDF2DArray.hpp
+@@ -53,7 +53,7 @@ private:
+ DSLength rowLength, colLength;
+
+ public:
+- BufferedHDF2DArray(H5::Group *_container, std::string _datasetName);
++ BufferedHDF2DArray(H5::CommonFG *_container, std::string _datasetName);
+
+ BufferedHDF2DArray();
+
+@@ -93,7 +93,7 @@ public:
+ void Read(DSLength startX, DSLength endX, DSLength startY, DSLength endY, H5::DataType typeID,
+ T *dest);
+
+- void Create(H5::Group *_container, std::string _datasetName, DSLength _rowLength);
++ void Create(H5::CommonFG *_container, std::string _datasetName, DSLength _rowLength);
+
+ void TypedCreate(H5::DataSpace &fileSpace, H5::DSetCreatPropList &cparms);
+
+@@ -113,7 +113,7 @@ public:
+ void Flush(DSLength destRow = static_cast<DSLength>(-1));
+ };
+
+-DSLength GetDatasetNDim(H5::Group &parentGroup, std::string datasetName);
++DSLength GetDatasetNDim(H5::CommonFG &parentGroup, std::string datasetName);
+
+ #define DECLARE_TYPED_WRITE_ROW(T, Pred) \
+ template <> \
+--- a/hdf/BufferedHDF2DArrayImpl.hpp
++++ b/hdf/BufferedHDF2DArrayImpl.hpp
+@@ -7,7 +7,7 @@
+ #include <pbdata/utils.hpp>
+
+ template <typename T>
+-BufferedHDF2DArray<T>::BufferedHDF2DArray(H5::Group *_container, std::string _datasetName)
++BufferedHDF2DArray<T>::BufferedHDF2DArray(H5::CommonFG *_container, std::string _datasetName)
+ : HDFData(_container, _datasetName)
+ {
+ }
+@@ -191,7 +191,7 @@ void BufferedHDF2DArray<T>::Read(DSLengt
+ }
+
+ template <typename T>
+-void BufferedHDF2DArray<T>::Create(H5::Group *_container, std::string _datasetName,
++void BufferedHDF2DArray<T>::Create(H5::CommonFG *_container, std::string _datasetName,
+ DSLength _rowLength)
+ {
+ container = _container;
+--- a/hdf/BufferedHDFArray.hpp
++++ b/hdf/BufferedHDFArray.hpp
+@@ -52,7 +52,7 @@ public:
+ */
+ BufferedHDFArray(int pBufferSize = 32768);
+
+- BufferedHDFArray(H5::Group *_container, std::string _datasetName);
++ BufferedHDFArray(H5::CommonFG *_container, std::string _datasetName);
+
+ ~BufferedHDFArray();
+
+@@ -72,7 +72,7 @@ public:
+
+ void Create(HDFGroup &parentGroup, std::string _datasetName);
+
+- void Create(H5::Group *_container, std::string _datasetName);
++ void Create(H5::CommonFG *_container, std::string _datasetName);
+
+ /*
+ * Initialize for reading.
+--- a/hdf/BufferedHDFArrayImpl.hpp
++++ b/hdf/BufferedHDFArrayImpl.hpp
+@@ -20,7 +20,7 @@ BufferedHDFArray<T>::BufferedHDFArray(in
+ }
+
+ template <typename T>
+-BufferedHDFArray<T>::BufferedHDFArray(H5::Group *_container, std::string _datasetName)
++BufferedHDFArray<T>::BufferedHDFArray(H5::CommonFG *_container, std::string _datasetName)
+ : HDFData(_container, _datasetName)
+ {
+ // no-op
+@@ -190,7 +190,7 @@ void BufferedHDFArray<T>::Create(HDFGrou
+ }
+
+ template <typename T>
+-void BufferedHDFArray<T>::Create(H5::Group *_container, std::string _datasetName)
++void BufferedHDFArray<T>::Create(H5::CommonFG *_container, std::string _datasetName)
+ {
+ //
+ // Initialize where the dataset will go.
+--- a/hdf/HDFAtom.cpp
++++ b/hdf/HDFAtom.cpp
+@@ -1,7 +1,7 @@
+ #include <hdf/HDFAtom.hpp>
+
+ template <>
+-void HDFAtom<std::string>::Create(H5::H5Object &object, const std::string &atomName)
++void HDFAtom<std::string>::Create(H5::H5Location &object, const std::string &atomName)
+ {
+ H5::StrType strType(0, H5T_VARIABLE);
+ hsize_t defaultDims[] = {1};
+@@ -11,7 +11,7 @@ void HDFAtom<std::string>::Create(H5::H5
+
+ #define DEFINE_TYPED_CREATE_ATOM(T, predtype) \
+ template <> \
+- void HDFAtom<T>::TypedCreate(H5::H5Object &object, const std::string &atomName, \
++ void HDFAtom<T>::TypedCreate(H5::H5Location &object, const std::string &atomName, \
+ H5::DataSpace &defaultDataSpace) \
+ { \
+ attribute = object.createAttribute(atomName.c_str(), (predtype), defaultDataSpace); \
+--- a/hdf/HDFAtom.hpp
++++ b/hdf/HDFAtom.hpp
+@@ -26,9 +26,9 @@ public:
+ }
+ }
+
+- H5::H5Object *GetObject() { return NULL; }
++ H5::H5Location *GetObject() { return NULL; }
+
+- int Initialize(H5::H5Object &object, const std::string &attributeName)
++ int Initialize(H5::H5Location &object, const std::string &attributeName)
+ {
+ attribute = object.openAttribute(attributeName.c_str());
+ isInitialized = true;
+@@ -45,7 +45,7 @@ public:
+ return Initialize(data.dataset, attributeName);
+ }
+
+- int Initialize(H5::Group &object, const std::string &attributeName)
++ int Initialize(H5::H5File &object, const std::string &attributeName)
+ {
+ try {
+ attribute = object.openAttribute(attributeName.c_str());
+@@ -71,14 +71,14 @@ public:
+ // This handles creation of all non-std::string types. A specialization
+ // for std::strings is provided below.
+ //
+- void Create(H5::H5Object &object, const std::string &atomName)
++ void Create(H5::H5Location &object, const std::string &atomName)
+ {
+ hsize_t defaultDims[] = {1};
+ H5::DataSpace defaultDataSpace(1, defaultDims);
+ TypedCreate(object, atomName, defaultDataSpace);
+ }
+
+- void Create(H5::H5Object &object, const std::string &name, const std::string &value)
++ void Create(H5::H5Location &object, const std::string &name, const std::string &value)
+ {
+ H5::StrType strType(0, value.size());
+ attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0, NULL));
+@@ -86,7 +86,7 @@ public:
+ attribute.write(strType, value.c_str());
+ }
+
+- void Create(H5::H5Object &object, const std::string &name, std::vector<int> &vect)
++ void Create(H5::H5Location &object, const std::string &name, std::vector<int> &vect)
+ {
+ hsize_t length = vect.size();
+ H5::ArrayType arrayDataType(H5::PredType::NATIVE_INT, 1, &length);
+@@ -95,7 +95,7 @@ public:
+ attribute.write(H5::PredType::NATIVE_INT, &((vect)[0]));
+ }
+
+- void Create(H5::H5Object &object, const std::string &name, const std::vector<std::string> &vect)
++ void Create(H5::H5Location &object, const std::string &name, const std::vector<std::string> &vect)
+ {
+ hsize_t length = vect.size();
+ H5::StrType strType(0, H5T_VARIABLE);
+@@ -104,7 +104,7 @@ public:
+ attribute.write(strType, &((vect)[0]));
+ }
+
+- void TypedCreate(H5::H5Object &object, const std::string &atomName, H5::DataSpace &dataSpace)
++ void TypedCreate(H5::H5Location &object, const std::string &atomName, H5::DataSpace &dataSpace)
+ {
+ (void)(object);
+ (void)(atomName);
+@@ -132,11 +132,11 @@ public:
+ //
+
+ template <>
+-void HDFAtom<std::string>::Create(H5::H5Object &object, const std::string &atomName);
++void HDFAtom<std::string>::Create(H5::H5Location &object, const std::string &atomName);
+
+ #define DECLARE_TYPED_CREATE_ATOM(T, predtype) \
+ template <> \
+- void HDFAtom<T>::TypedCreate(H5::H5Object &object, const std::string &atomName, \
++ void HDFAtom<T>::TypedCreate(H5::H5Location &object, const std::string &atomName, \
+ H5::DataSpace &defaultDataSpace);
+
+ DECLARE_TYPED_CREATE_ATOM(int, H5::PredType::NATIVE_INT)
+--- a/hdf/HDFAttributable.cpp
++++ b/hdf/HDFAttributable.cpp
+@@ -12,7 +12,7 @@ using namespace H5;
+ //
+ // whereas HDF5 1.10 has for attr_operator_t
+ //
+-// typedef void(* H5::attr_operator_t)(H5Object &loc, const H5std_string attr_name, void *operator_data)
++// typedef void(* H5::attr_operator_t)(H5Location &loc, const H5std_string attr_name, void *operator_data)
+
+ template <typename T>
+ void CallStoreAttributeName(T &obj, std::string attrName, void *attrList)
+@@ -21,7 +21,7 @@ void CallStoreAttributeName(T &obj, std:
+ ((std::vector<std::string> *)attrList)->push_back(std::string(attrName));
+ }
+
+-void HDFAttributable::StoreAttributeNames(H5Object &thisobject,
++void HDFAttributable::StoreAttributeNames(H5Location &thisobject,
+ const std::vector<std::string> &attributeNames)
+ {
+ int nAttr = thisobject.getNumAttrs();
+@@ -32,14 +32,14 @@ void HDFAttributable::StoreAttributeName
+ thisobject.iterateAttrs(&CallStoreAttributeName, bounds, (void *)&attributeNames);
+ }
+
+-H5Object *HDFAttributable::GetObject() { return NULL; }
++H5Location *HDFAttributable::GetObject() { return NULL; }
+
+ int HDFAttributable::ContainsAttribute(const std::string &attributeName)
+ {
+ size_t i;
+ std::vector<std::string> tmpAttributeNames;
+ try {
+- H5Object *obj = GetObject();
++ H5Location *obj = GetObject();
+ assert(obj != NULL);
+ StoreAttributeNames(*obj, tmpAttributeNames);
+ for (i = 0; i < tmpAttributeNames.size(); i++) {
+--- a/hdf/HDFAttributable.hpp
++++ b/hdf/HDFAttributable.hpp
+@@ -12,10 +12,10 @@ class HDFAttributable
+ public:
+ std::vector<std::string> attributeNameList;
+
+- void StoreAttributeNames(H5::H5Object &thisobject,
++ void StoreAttributeNames(H5::H5Location &thisobject,
+ const std::vector<std::string> &attributeNames);
+
+- virtual H5::H5Object *GetObject();
++ virtual H5::H5Location *GetObject();
+
+ int ContainsAttribute(const std::string &attributeName);
+ };
+--- a/hdf/HDFData.cpp
++++ b/hdf/HDFData.cpp
+@@ -2,9 +2,9 @@
+
+ using namespace H5;
+
+-H5Object *HDFData::GetObject() { return &dataset; }
++H5Location *HDFData::GetObject() { return &dataset; }
+
+-HDFData::HDFData(Group *_container, const std::string &_datasetName)
++HDFData::HDFData(CommonFG *_container, const std::string &_datasetName)
+ {
+ container = _container;
+ datasetName = _datasetName;
+@@ -32,7 +32,7 @@ int HDFData::Initialize(HDFGroup &parent
+ std::exit(EXIT_FAILURE);
+ }
+
+-int HDFData::BaseInitializeDataset(Group &hdfFile, const std::string &_datasetName)
++int HDFData::BaseInitializeDataset(CommonFG &hdfFile, const std::string &_datasetName)
+ {
+ dataset = hdfFile.openDataSet(_datasetName.c_str());
+ isInitialized = true;
+@@ -45,7 +45,7 @@ int HDFData::InitializeDataset(HDFGroup
+ return InitializeDataset(group.group, _datasetName);
+ }
+
+-int HDFData::InitializeDataset(Group &hdfFile, const std::string &_datasetName)
++int HDFData::InitializeDataset(CommonFG &hdfFile, const std::string &_datasetName)
+ {
+ try {
+ datasetName = _datasetName;
+--- a/hdf/HDFData.hpp
++++ b/hdf/HDFData.hpp
+@@ -17,13 +17,13 @@ public:
+ H5::DataSpace sourceSpace, destSpace;
+ H5::DataSpace fullSourceSpace;
+ bool fileDataSpaceInitialized;
+- H5::Group *container;
++ H5::CommonFG *container;
+ std::string datasetName;
+ bool isInitialized;
+
+- H5::H5Object *GetObject();
++ H5::H5Location *GetObject();
+
+- HDFData(H5::Group *_container, const std::string &_datasetName);
++ HDFData(H5::CommonFG *_container, const std::string &_datasetName);
+
+ HDFData();
+
+@@ -43,11 +43,11 @@ public:
+ //
+ virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName);
+
+- int BaseInitializeDataset(H5::Group &hdfFile, const std::string &_datasetName);
++ int BaseInitializeDataset(H5::CommonFG &hdfFile, const std::string &_datasetName);
+
+ int InitializeDataset(HDFGroup &group, const std::string &_datasetName);
+
+- int InitializeDataset(H5::Group &hdfFile, const std::string &_datasetName);
++ int InitializeDataset(H5::CommonFG &hdfFile, const std::string &_datasetName);
+
+ void Close();
+ };
+--- a/hdf/HDFGroup.cpp
++++ b/hdf/HDFGroup.cpp
+@@ -12,7 +12,7 @@ void HDFGroup::AddGroup(std::string grou
+
+ H5Object *HDFGroup::GetObject() { return &group; }
+
+-int HDFGroup::Initialize(Group &fg, std::string groupName)
++int HDFGroup::Initialize(CommonFG &fg, std::string groupName)
+ {
+ try {
+ group = fg.openGroup(groupName.c_str());
+--- a/hdf/HDFGroup.hpp
++++ b/hdf/HDFGroup.hpp
+@@ -25,7 +25,7 @@ public:
+
+ H5::H5Object* GetObject();
+
+- int Initialize(H5::Group& fg, std::string groupName);
++ int Initialize(H5::CommonFG& fg, std::string groupName);
+
+ int Initialize(HDFGroup& parentGroup, std::string groupName);
+
=====================================
debian/patches/series
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
hdf5-1.10.1-support.patch
+hdf5-1.10.0-support.patch
=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -19,6 +19,8 @@ ifeq (yes,$(shell dpkg --compare-versions $(HDF5_VERSION) '>=' 1.10.1 && echo ye
export DEB_CPPFLAGS_MAINT_APPEND=-DHAVE_HDF5_1_10_1
endif
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
%:
dh $@
@@ -29,9 +31,11 @@ override_dh_auto_build:
dh_auto_build -- PREFIX_INC=..
override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
# Ignore the return code because some tests
# require data that is not available in the source distribution.
-$(MAKE) -k gtest
+endif
override_dh_auto_install:
mkdir -p debian/libpbdata-dev/usr/include/pbseq
=====================================
debian/source/lintian-overrides deleted
=====================================
--- a/debian/source/lintian-overrides
+++ /dev/null
@@ -1,3 +0,0 @@
-# This is a build artifact that should not have been distributed,
-# but the source for it is indeed present.
-source-is-missing hdf/HDFAlnInfoGroup.o.tmp.rm.login14-biofx01.11097
View it on GitLab: https://salsa.debian.org/med-team/pbseqlib/compare/ead5c6f0d465a2fff39f11145386a262da309e34...6d264df05b17c493576a5ac5008a8a0f4fc6dc63
--
View it on GitLab: https://salsa.debian.org/med-team/pbseqlib/compare/ead5c6f0d465a2fff39f11145386a262da309e34...6d264df05b17c493576a5ac5008a8a0f4fc6dc63
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