Without the change the build on `master` fails as
https://hydra.nixos.org/build/249070958:
In file included from /build/source/src/sortmerna/kseq_load.cpp:38:
/build/source/include/kseq_load.hpp:61:12: error: 'uint64_t' has not been declared
61 | uint64_t number_total_read,
| ^~~~~~~~
Without the change the build on `master` fails as
https://hydra.nixos.org/build/249090788:
/build/source/src/config/option_collation.cpp: In function 'auto octopus::options::make_variant_generator_builder(const OptionMap&, boost::optional<const octopus::ReadSetProfile&>)':
/build/source/src/config/option_collation.cpp:1298: error: redundant move in initialization [-Werror=redundant-move]
1298 | throw ConflictingSourceVariantFile {std::move(source_path), *output_path};
|
Blanket `-Werror` frequently causes build failures unless upstream is
quick at addressing build failures.
Without the change build fails on `master` as
https://hydra.nixos.org/build/249164637:
In file included from Histogram.cpp:1:
Histogram.h:104:61: error: 'uint32_t' does not name a type
104 | Histogram(const int32_t& start, const int32_t& end, const uint32_t& width);
| ^~~~~~~~
Without the change build fails on `master` against `gcc-13` as
https://hydra.nixos.org/build/247673319:
In file included from /build/source/src/main_local_assemble.cpp:27:
/build/source/src/localasm/local_assemble.h:31:3: error: 'uint32_t' does not name a type
31 | uint32_t kmin{11};
| ^~~~~~~~
/build/source/src/localasm/local_assemble.h:1:1: note: 'uint32_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
+++ |+#include <cstdint>
The build of `hh-suite` stopped working with GCC 13 because
GCC stopped transitively including a couple of headers like
`cstdint` in various scenarios.
There already is an upstream PR proposed that fixes this issue [1]
but hasn't been merged yet. This change pulls in this correction
using `fetchpatch`, fixing the build for now.
[1]: https://github.com/soedinglab/hh-suite/pull/357
Without the change build fails on `master` against `gcc-13` as
https://hydra.nixos.org/build/246505636:
mapper/../common/defs.h:53:9: error: 'uint32_t' does not name a type
53 | typedef uint32_t ref_pos_t;
| ^~~~~~~~
mapper/../common/defs.h:35:1: note: 'uint32_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
34 | #include <string>
+++ |+#include <cstdint>
