Pierre Gruet pushed to branch master at Debian Med / ugene
Commits: 5407e187 by Pierre Gruet at 2024-10-04T15:36:28+02:00 Patching out _neon methods to avoid build failure on arm64 - - - - - 6f9d2f47 by Pierre Gruet at 2024-10-04T15:38:25+02:00 Using signed char to allow one to have negative char variables on arm architectures - - - - - c2d2fea0 by Pierre Gruet at 2024-10-04T15:42:27+02:00 Upload to unstable - - - - - 4 changed files: - debian/changelog - debian/patches/series - + debian/patches/signed_char_neighbour_table.patch - + debian/patches/undefined_references.patch Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,11 @@ +ugene (51.0+dfsg-2) unstable; urgency=medium + + * Patching out _neon methods to avoid build failure on arm64 + * Using signed char to allow one to have negative char variables on arm + architectures + + -- Pierre Gruet <[email protected]> Fri, 04 Oct 2024 15:38:37 +0200 + ugene (51.0+dfsg-1) unstable; urgency=medium * New upstream version 51.0+dfsg ===================================== debian/patches/series ===================================== @@ -5,3 +5,5 @@ use_debian_sqlite.patch python_interpreter.patch set_rpath.patch plugins_directory.patch +undefined_references.patch +signed_char_neighbour_table.patch ===================================== debian/patches/signed_char_neighbour_table.patch ===================================== @@ -0,0 +1,28 @@ +Description: indicating we use signed char, so that we don't depend on the + default choice of the implementation +Author: Pierre Gruet <[email protected]> +Forwarded: https://github.com/ugeneunipro/ugene/issues/1682 +Last-Update: 2024-10-04 + +--- a/src/plugins_3rdparty/ball/src/include/BALL/DATATYPE/hashGrid.h ++++ b/src/plugins_3rdparty/ball/src/include/BALL/DATATYPE/hashGrid.h +@@ -37,7 +37,7 @@ + { + namespace __private + { +- extern const char BALL_EXPORT neighbour_table_[27][3]; ++ extern const signed char BALL_EXPORT neighbour_table_[27][3]; + } + + template <typename Item> class HashGrid3; +--- a/src/plugins_3rdparty/ball/src/source/DATATYPE/hashGrid.cpp ++++ b/src/plugins_3rdparty/ball/src/source/DATATYPE/hashGrid.cpp +@@ -9,7 +9,7 @@ + { + namespace __private + { +- const char neighbour_table_[27][3] = ++ const signed char neighbour_table_[27][3] = + { + { 0, 0, 0 }, { 0, 0, -1 }, { 0, 0, 1 }, + { 0, -1, -1 }, { 0, -1, 0 }, { 0, -1, 1 }, ===================================== debian/patches/undefined_references.patch ===================================== @@ -0,0 +1,62 @@ +Description: removing _neon signatures to avoid build failure on aarch64 +Author: Pierre Gruet <[email protected]> +Forwarded: https://github.com/ugeneunipro/ugene/issues/1681 +Last-Update: 2024-10-04 + +--- a/src/libs_3rdparty/samtools/src/samtools_core/htslib/htscodecs/htscodecs/rANS_static32x16pr.h ++++ b/src/libs_3rdparty/samtools/src/samtools_core/htslib/htscodecs/htscodecs/rANS_static32x16pr.h +@@ -145,28 +145,6 @@ + #endif // HAVE_AVX512 + + //---------------------------------------------------------------------- +-// Arm Neon implementation +-#if defined(__ARM_NEON) && defined(__aarch64__) +-unsigned char *rans_compress_O0_32x16_neon(unsigned char *in, +- unsigned int in_size, +- unsigned char *out, +- unsigned int *out_size); +- +-unsigned char *rans_uncompress_O0_32x16_neon(unsigned char *in, +- unsigned int in_size, +- unsigned char *out, +- unsigned int out_sz); +- +-unsigned char *rans_compress_O1_32x16_neon(unsigned char *in, +- unsigned int in_size, +- unsigned char *out, +- unsigned int *out_size); +- +-unsigned char *rans_uncompress_O1_32x16_neon(unsigned char *in, +- unsigned int in_size, +- unsigned char *out, +- unsigned int out_sz); +-#endif // ARM_NEON + + #ifdef __cplusplus + } +--- a/src/libs_3rdparty/samtools/src/samtools_core/htslib/htscodecs/htscodecs/rANS_static4x16pr.c ++++ b/src/libs_3rdparty/samtools/src/samtools_core/htslib/htscodecs/htscodecs/rANS_static4x16pr.c +@@ -1066,11 +1066,6 @@ + unsigned int *out_size) { + + if (do_simd) { +- if ((rans_cpu & RANS_CPU_ENC_NEON) && have_neon()) +- return order & 1 +- ? rans_compress_O1_32x16_neon +- : rans_compress_O0_32x16_neon; +- else + return order & 1 + ? rans_compress_O1_32x16 + : rans_compress_O0_32x16; +@@ -1089,11 +1084,6 @@ + unsigned int out_size) { + + if (do_simd) { +- if ((rans_cpu & RANS_CPU_DEC_NEON) && have_neon()) +- return order & 1 +- ? rans_uncompress_O1_32x16_neon +- : rans_uncompress_O0_32x16_neon; +- else + return order & 1 + ? rans_uncompress_O1_32x16 + : rans_uncompress_O0_32x16; View it on GitLab: https://salsa.debian.org/med-team/ugene/-/compare/f204bf5e682d9ffaaef5adf0f96cc418d63c56e4...c2d2fea03c8a4225aaa9f700d7f149ce5351458b -- View it on GitLab: https://salsa.debian.org/med-team/ugene/-/compare/f204bf5e682d9ffaaef5adf0f96cc418d63c56e4...c2d2fea03c8a4225aaa9f700d7f149ce5351458b You're receiving this email because of your account on salsa.debian.org.
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