debian/changelog

-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@debian.org>  Tue, 26 Jun 2018 08:39:02 +0200
+  [ Gilles Filippini ]
+  * Fix build against recent Hdf5 lib
+
+ -- Andreas Tille <tille@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

+Author: Gilles Filippini <pini@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

 hdf5-1.10.1-support.patch
+hdf5-1.10.0-support.patch

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

-# 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