Debian Patches
Status for genomicsdb/1.5.4-5
| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| build_jni.patch | building the JNI as a shared lib in the CMake process, and loading it from the canonical Debian path from Java code | Pierre Gruet <pgt@debian.org> | not-needed | 2022-07-26 | ||
| catch2_3.patch | adapting CMakeLists.txt files and code to build against catch2 3.x | Pierre Gruet <pgt@debian.org> | not-needed | debian | 2023-11-02 | |
| disabling_mpi_for_tests.patch | skipping MPI tests for tools/test_tools.sh | Pierre Gruet <pgt@debian.org> | no | 2023-06-27 | ||
| fmt10.patch | introducing format_as functions to comply with fmtlib 10 | Pierre Gruet <pgt@debian.org> | yes | debian | 2024-11-30 | |
| gcc-13.patch | adding missing includes of cstdint to build with gcc-13 | Pierre Gruet <pgt@debian.org> | yes | debian | 2023-06-28 | |
| handling_rpaths.patch | setting RPATH to contain the path to private libraries, it will be emptied afterwards for the libs that don't need it. | Pierre Gruet <pgt@debian.org> | not-needed | 2022-07-26 | ||
| htslib_define_PATH_MAX.patch | Define PATH_MAX as it is done in cram/open_trace_file.c if not existent. The definition should be removed from this C file since the header file affects all three C files where this definition is used. |
Andreas Tille <tille@debian.org>, | no | debian | ||
| htslib_fix_float_precision | ppc64el float handling fix I dug a bit further and it looks like that sam_parse1() is actually generating a different value for the floats in question, so when they are loaded back for the comparison they are already screwed up because strtod() is used in float_to_le() and so also in u32_to_le(), which are inlined and float_to_le() takes a float and not a double as the first argument the use strtof() instead of strtod() in there looks the best, avoiding a truncation from double to float, which might cause precision issues, specially between different archs (like casts) plus optimization. So the following change fixed the issue for me. |
Gustavo Romero <gromero@linux.vnet.ibm.com> | no | |||
| htslib_testShebang.patch | Build with -fPIC instead of -fpic It doesn't make a difference on x86, but is required for linking the library on s390x and sparc64. |
Adrian Bunk <bunk@debian.org> | no | |||
| ignoring_sdk_to_download.patch | removing references to unpackaged SDK in the code | Pierre Gruet <pgt@debian.org> | not-needed | 2022-07-26 | ||
| JsonFormat_from_libprotobuf-java.patch | looking for protobuf classes instead of relying on embedding | Pierre Gruet <pgt@debian.org> | not-needed | 2023-06-28 | ||
| library_names_and_install_paths.patch | installing the main lib in /usr/lib/<triplet> and the component libs in /usr/lib/<triplet>/genomicsdb. Also we install the headers of the private libraries in a subfolder in /usr/include/genomicsdb. |
Pierre Gruet <pgt@debian.org> | not-needed | 2022-07-27 | ||
| missing_links_in_libs.patch | the links to fmt are missing, adding them | Pierre Gruet <pgt@debian.org> | yes | 2022-07-26 | ||
| no_download_of_dependencies.patch | not downloading anything, using the Debian packages | Pierre Gruet <pgt@debian.org> | not-needed | 2022-07-26 | ||
| no_spark_in_Java_build.patch | excluding the spark classes from the build, we won't be able to handle them as we don't have spark in Debian. | Pierre Gruet <pgt@debian.org> | not-needed | 2022-07-26 | ||
| pom.patch | adding missing dependencies in the pom, and also tweaking a bit the protobuf lines so that .proto files are effectively treated | Pierre Gruet <pgt@debian.org> | yes | 2022-07-26 | ||
| query_config_serialization.patch | disabling test assertions that fails because of "old" protobuf in Debian. This patch should be deactivated later. | Pierre Gruet <pgt@debian.org> | not-needed | 2024-08-08 | ||
| rapidjson_methods.patch | GetLength() method is not in the Debian-packaged rapidjson, writing a substitute | Pierre Gruet <pgt@debian.org> | not-needed | 2024-07-17 | ||
| run_tests_in_not_yet_installed_dir.patch | at the test step, the package has not been installed, so we look for the binaries in the source tree | Pierre Gruet <pgt@debian.org> | not-needed | 2022-07-26 | ||
| strip_tiledb_CMakeLists.patch | stripping the CMakeLists.txt file of the tiledb component from unneeded git commands, and ignoring unpackaged software. | Pierre Gruet <pgt@debian.org> | not-needed | 2022-07-26 | ||
| tests_in_all_target.patch | stopping excluding tests from the all target so that they are built during the Debian build | Pierre Gruet <pgt@debian.org> | not-needed | 2022-07-26 | ||
| use_shared_protobuf_lib.patch | linking to the shared protobuf library, not to the static one | Pierre Gruet <pgt@debian.org> | not-needed | 2022-07-26 | ||
| using_htslib_from_component.patch | genomicsdb needs a fork of htslib, which is too different from the Debian-packaged one. We provide it as a component. | Pierre Gruet <pgt@debian.org> | not-needed | 2022-07-26 | ||
| using_timedb_from_component.patch | genomicsdb requires a fork of tiledb which is too different from the Debian-packaged one. We provide it as a component. | Pierre Gruet <pgt@debian.org> | not-needed | 2022-07-26 | ||
| variant_array_schema_hidden_if_no_DEBUG.patch | adding preprocessor tests for DEBUG is necessary to avoid /<<PKGBUILDDIR>>/src/main/cpp/src/genomicsdb/variant_storage_manager.cc:154:24: error: ‘m_variant_array_schema’ was not declared in this scope; did you mean ‘VariantArraySchema’? 154 | assert(field_size == m_variant_array_schema->dim_size_in_bytes()); | ^~~~~~~~~~~~~~~~~~~~~~ |
Pierre Gruet <pgt@debian.org> | no | 2024-07-16 |
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