Debian Patches

Status for genomicsdb/1.4.4-3

Patch Description Author Forwarded Bugs Origin Last update
string_view_needs_cxx17.patch string_view requires C++-17 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
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
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
ignoring_sdk_to_download.patch removing references to unpackaged SDK in the code 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
missing_links_in_libs.patch the links to fmt are missing, adding them Pierre Gruet <pgt@debian.org> yes 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
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
JsonFormat_methods.patch a few changes to calls to JsonFormat methods have to be changed when building against protobuf-java-format 1.3 instead of 1.2 Pierre Gruet <pgt@debian.org> yes 2022-07-26
tests_in_all_target.patch stopping excluding tests from the all target so tha they are built during the Debian build Pierre Gruet <pgt@debian.org> not-needed 2022-07-26
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
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
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
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_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
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
spelling.patch fixing a tiny spelling error Pierre Gruet <pgt@debian.org> yes 2022-07-26
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
int_type_initialization.patch initializing with 0 instead of "" in order to avoid error: cast from const char* to mup::int_type {aka int} loses precision Pierre Gruet <pgt@debian.org> yes 2022-09-11
missing_inclusion_tiledb_constants.patch including tiledb_constants.h is necessary so that TILEDB_IO_* definitions are found Pierre Gruet <pgt@debian.org> yes 2022-09-11
using_debian_packaged_catch2.patch catch2 is Debian-packaged, the embedded copy in the source of genomicsdb-tiledb is too old, things have improved in lattest versions. Pierre Gruet <pgt@debian.org> yes 2022-09-11

All known versions for source package 'genomicsdb'

Links