Source: ivar Version: 1.4.2+dfsg-1 Severity: serious Tags: patch Control: block 1037700 by -1
https://ci.debian.net/data/autopkgtest/testing/i386/i/ivar/36393644/log.gz ... 29s 132,133c132,133 29s < Consensus_ZI-27_threshold_0_quality_20 130 N G 0 0 0 7 6 37 1 7 0.000582751 TRUE NA NA NA NA NA NA 29s < Consensus_ZI-27_threshold_0_quality_20 131 N A 0 0 0 7 6 37 1 7 0.000582751 TRUE NA NA NA NA NA NA 29s --- 29s > Consensus_ZI-27_threshold_0_quality_20 130 N G 0 0 0 7 6 38 1 7 0.000582751 TRUE NA NA NA NA NA NA 29s > Consensus_ZI-27_threshold_0_quality_20 131 N A 0 0 0 7 6 38 1 7 0.000582751 TRUE NA NA NA NA NA NA 29s 169c169 29s < Consensus_ZI-27_threshold_0_quality_20 165 N T 0 0 0 7 6 37 1 7 0.000582751 TRUE NA NA NA NA NA NA 29s --- 29s > Consensus_ZI-27_threshold_0_quality_20 165 N T 0 0 0 7 6 38 1 7 0.000582751 TRUE NA NA NA NA NA NA 29s 174c174 29s < Consensus_ZI-27_threshold_0_quality_20 170 N G 0 0 0 7 6 37 1 7 0.000582751 TRUE NA NA NA NA NA NA 29s --- 29s > Consensus_ZI-27_threshold_0_quality_20 170 N G 0 0 0 7 6 38 1 7 0.000582751 TRUE NA NA NA NA NA NA 29s 205c205 29s < Consensus_ZI-27_threshold_0_quality_20 201 N A 0 0 0 7 6 37 1 7 0.000582751 TRUE NA NA NA NA NA NA 29s --- 29s > Consensus_ZI-27_threshold_0_quality_20 201 N A 0 0 0 7 6 38 1 7 0.000582751 TRUE NA NA NA NA NA NA 29s 4376c4376 29s < Consensus_ZI-27_threshold_0_quality_20 7015 N G 0 0 0 8 1 37 1 8 0.0001554 TRUE NA NA NA NA NA NA 29s --- 29s > Consensus_ZI-27_threshold_0_quality_20 7015 N G 0 0 0 8 1 38 1 8 0.0001554 TRUE NA NA NA NA NA NA 29s 4379c4379 29s < Consensus_ZI-27_threshold_0_quality_20 7018 N G 0 0 0 8 1 36 1 8 0.0001554 TRUE NA NA NA NA NA NA 29s --- 29s > Consensus_ZI-27_threshold_0_quality_20 7018 N G 0 0 0 8 1 37 1 8 0.0001554 TRUE NA NA NA NA NA NA 29s 4405c4405 29s < Consensus_ZI-27_threshold_0_quality_20 7044 N A 0 0 0 8 1 37 1 8 0.0001554 TRUE NA NA NA NA NA NA 29s --- 29s > Consensus_ZI-27_threshold_0_quality_20 7044 N A 0 0 0 8 1 38 1 8 0.0001554 TRUE NA NA NA NA NA NA 29s 4447c4447 29s < Consensus_ZI-27_threshold_0_quality_20 7086 N A 0 0 0 8 2 35 1 8 0.0001554 TRUE NA NA NA NA NA NA 29s --- 29s > Consensus_ZI-27_threshold_0_quality_20 7086 N A 0 0 0 8 2 36 1 8 0.0001554 TRUE NA NA NA NA NA NA 29s autopkgtest [15:35:51]: test run-unit-test: -----------------------] 29s run-unit-test FAIL non-zero exit status 1 The fix is attached. For background see the first bullet point in the C++ section of https://gcc.gnu.org/gcc-13/changes.html
Description: Remove -std=c++11 to fix autopkgtest failure with gcc 13 --- ivar-1.4.2+dfsg.orig/src/Makefile.am +++ ivar-1.4.2+dfsg/src/Makefile.am @@ -1,6 +1,6 @@ LIBS = -lhts -lz -lpthread -CXXFLAGS += -v -g -std=c++11 -Wall -Wextra -Werror +CXXFLAGS += -v -g -Wall -Wextra -Werror # this lists the binaries to produce, the (non-PHONY, binary) targets in # the previous manual Makefile --- ivar-1.4.2+dfsg.orig/tests/Makefile.am +++ ivar-1.4.2+dfsg/tests/Makefile.am @@ -1,6 +1,6 @@ LIBS = -lhts -lz -lpthread -CXXFLAGS += -g -std=c++11 -Wall -Wextra -Werror +CXXFLAGS += -g -Wall -Wextra -Werror TESTS = check_primer_trim check_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases check_isize_trim check_interval_tree check_amplicon_search check_consensus_min_insert_threshold check_PROGRAMS = check_primer_trim check_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases check_isize_trim check_interval_tree check_amplicon_search check_consensus_min_insert_threshold
