Sascha Steinbiss pushed to branch master at Debian Med / nanopolish
Commits: df0f8daa by Sascha Steinbiss at 2021-02-20T15:48:49+01:00 patch code to not define PR_R7 and PT_R9 - - - - - 0d4caf1e by Sascha Steinbiss at 2021-02-20T15:49:09+01:00 add patch - - - - - 3 changed files: - debian/changelog - + debian/patches/rename_enum.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,12 @@ +nanopolish (0.13.2-2) unstable; urgency=medium + + * Team upload. + * Patch code to not define PR_R7 and PT_R9 to avoid FTBFS on + some archs (Closes: #960634) + Thanks to Barry Arndt for the hint. + + -- Sascha Steinbiss <[email protected]> Sat, 20 Feb 2021 15:06:55 +0100 + nanopolish (0.13.2-1) unstable; urgency=medium [ Michael R. Crusoe ] ===================================== debian/patches/rename_enum.patch ===================================== @@ -0,0 +1,109 @@ +Description: do not define PT_R{7,9} + Defining these enum values will cause a FTBFS on some architectures + due to them already existing in some architecture-dependent headers. + We rename them to avoid clashes. Thanks to Barry Arndt fot the hint. +Author: Sascha Steinbiss <[email protected]> +Forwarded: https://github.com/jts/nanopolish/issues/883 +Last-Update: 2021-02-20 +--- a/src/hmm/nanopolish_profile_hmm.cpp ++++ b/src/hmm/nanopolish_profile_hmm.cpp +@@ -22,7 +22,7 @@ + + float profile_hmm_score(const HMMInputSequence& sequence, const HMMInputData& data, const uint32_t flags) + { +- if(data.read->pore_type == PT_R9) { ++ if(data.read->pore_type == PORETYPE_R9) { + return profile_hmm_score_r9(sequence, data, flags); + } else { + return profile_hmm_score_r7(sequence, data, flags); +@@ -57,7 +57,7 @@ + + std::vector<HMMAlignmentState> profile_hmm_align(const HMMInputSequence& sequence, const HMMInputData& data, const uint32_t flags) + { +- if(data.read->pore_type == PT_R9) { ++ if(data.read->pore_type == PORETYPE_R9) { + return profile_hmm_align_r9(sequence, data, flags); + } else { + return profile_hmm_align_r7(sequence, data, flags); +--- a/src/nanopolish_call_variants.cpp ++++ b/src/nanopolish_call_variants.cpp +@@ -673,7 +673,7 @@ + + double num_kmers = variant_offset_end - variant_offset_start; + double log_gamma = sum_duration > MIN_DURATION ? DurationModel::log_gamma_sum(sum_duration, params, num_kmers) : 0.0f; +- if(read->pore_type == PT_R9) { ++ if(read->pore_type == PORETYPE_R9) { + duration_likelihoods[var_sequence_length] += log_gamma; + } + if(opt::verbose > 3) { +--- a/src/nanopolish_squiggle_read.cpp ++++ b/src/nanopolish_squiggle_read.cpp +@@ -106,7 +106,7 @@ + void SquiggleRead::init(const std::string& read_sequence, const Fast5Data& data, const uint32_t flags) + { + this->nucleotide_type = SRNT_DNA; +- this->pore_type = PT_UNKNOWN; ++ this->pore_type = PORETYPE_UNKNOWN; + this->f_p = nullptr; + + this->events_per_base[0] = events_per_base[1] = 0.0f; +@@ -219,7 +219,7 @@ + // in this case, we have to set this strand to be invalid + if(!event_maps_1d[si].empty()) { + // run version-specific load +- if(pore_type == PT_R7) { ++ if(pore_type == PORETYPE_R7) { + _load_R7(si); + } else { + _load_R9(si, read_sequences_1d[si], event_maps_1d[si], p_model_states, flags); +@@ -231,10 +231,10 @@ + + // Build the map from k-mers of the read sequence to events + if(read_type == SRT_2D) { +- if(pore_type == PT_R9) { ++ if(pore_type == PORETYPE_R9) { + build_event_map_2d_r9(); + } else { +- assert(pore_type == PT_R7); ++ assert(pore_type == PORETYPE_R7); + build_event_map_2d_r7(); + } + } else { +@@ -298,7 +298,7 @@ + } + + this->read_type = SRT_TEMPLATE; +- this->pore_type = PT_R9; ++ this->pore_type = PORETYPE_R9; + + // Set the base model for this read to either the nucleotide or U->T RNA model + this->base_model[strand_idx] = PoreModelSet::get_model(kit, alphabet, strand_str, k); +@@ -1122,11 +1122,11 @@ + assert(f_p and f_p->is_open()); + if (f_p->have_basecall_model(0)) + { +- pore_type = PT_R7; ++ pore_type = PORETYPE_R7; + } + else + { +- pore_type = PT_R9; ++ pore_type = PORETYPE_R9; + } + } + +--- a/src/nanopolish_squiggle_read.h ++++ b/src/nanopolish_squiggle_read.h +@@ -21,9 +21,9 @@ + + enum PoreType + { +- PT_UNKNOWN = 0, +- PT_R7, +- PT_R9, ++ PORETYPE_UNKNOWN = 0, ++ PORETYPE_R7, ++ PORETYPE_R9, + }; + + // the type of the read ===================================== debian/patches/series ===================================== @@ -2,3 +2,4 @@ add-shebang-to-script.patch reproducible.patch fix_remaining_python_interpreters.patch staticMinimap2Library.patch +rename_enum.patch View it on GitLab: https://salsa.debian.org/med-team/nanopolish/-/compare/6fa303abb77cb1bc622aef3c3e45f4c9b48b5bd7...0d4caf1e51a7040872879917e8290cfbcfed73fe -- View it on GitLab: https://salsa.debian.org/med-team/nanopolish/-/compare/6fa303abb77cb1bc622aef3c3e45f4c9b48b5bd7...0d4caf1e51a7040872879917e8290cfbcfed73fe You're receiving this email because of your account on salsa.debian.org.
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