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build_failure.osx-64.yaml
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recipe_sha: c777d5ab57b801fb6169fcedc71981d53a534a3812a453cf49ff028b0c60b10d # The hash of the recipe's meta.yaml at which this recipe failed to build.
skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
log: |-
about:
home: https://github.com/BGI-Qingdao/TGS-GapCloser
license: GPL-3.0-only
File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in <module>
sys.exit(execute())
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute
api.build(
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build
license_file: LICENSE
summary: A gap-closing software tool that uses error-prone long reads generated
return build_tree(
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree
packages_from_this = build(
by third-generation-sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled
contigs to fill N-gap in the genome assembly.
extra:
copy_test_source_files: true
final: true
recipe-maintainers:
- cchd0001
source tree in: /opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1734796763069/work
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build
raise BuildScriptException(str(exc), caused_by=exc) from exc
conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1734796763069/work/conda_build.sh']' returned non-zero exit status 2.
export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1734796763069/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p
export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1734796763069/_build_env
export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/tgsgapcloser_1734796763069/work
INFO: activate_clang_osx-64.sh made the following environmental changes:
AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar
AS=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-as
CC=x86_64-apple-darwin13.4.0-clang
CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
CHECKSYMS=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-checksyms
CLANG=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
CMAKE_PREFIX_PATH=:$PREFIX
CPPFLAGS=-D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem $PREFIX/include
DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
HOST=x86_64-apple-darwin13.4.0
INDR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-indr
INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool
LD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld
LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib
LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib
LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool
LIPO=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-lipo
NM=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-nm
NMEDIT=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-nmedit
OTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-otool
PAGESTUFF=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-pagestuff
RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib
REDO_PREBINDING=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-redo_prebinding
SEGEDIT=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-segedit
SEG_ADDR_TABLE=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-seg_addr_table
SEG_HACK=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-seg_hack
SIZE=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-size
STRINGS=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strings
STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip
_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0
INFO: activate_clangxx_osx-64.sh made the following environmental changes:
CLANGXX=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
CXX=x86_64-apple-darwin13.4.0-clang
CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -std=c14 -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -std=c14 -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
cd minimap2 && make
make[1]: Entering directory '$SRC_DIR/minimap2'
x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC main.c -o main.o
x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC kthread.c -o kthread.o
x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC kalloc.c -o kalloc.o
x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC misc.c -o misc.o
x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC bseq.c -o bseq.o
x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC sketch.c -o sketch.o
x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC sdust.c -o sdust.o
x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC options.c -o options.o
x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC index.c -o index.o
x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC chain.c -o chain.o
x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC align.c -o align.o
x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC hit.c -o hit.o
x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC map.c -o map.o
x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC format.c -o format.o
x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC pe.c -o pe.o
x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC esterr.c -o esterr.o
x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -DHAVE_KALLOC splitidx.c -o splitidx.o
x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -msse2 -DHAVE_KALLOC ksw2_ll_sse.c -o ksw2_ll_sse.o
x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_extz2_sse.c -o ksw2_extz2_sse41.o
x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_extd2_sse.c -o ksw2_extd2_sse41.o
x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_exts2_sse.c -o ksw2_exts2_sse41.o
x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extz2_sse.c -o ksw2_extz2_sse2.o
x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_extd2_sse.c -o ksw2_extd2_sse2.o
x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY ksw2_exts2_sse.c -o ksw2_exts2_sse2.o
x86_64-apple-darwin13.4.0-clang -c -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH ksw2_dispatch.c -o ksw2_dispatch.o
$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -csru libminimap2.a kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o
x86_64-apple-darwin13.4.0-clang -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -Wall -O2 -Wc-compat main.o -o minimap2 -L. -lminimap2 -lm -lz -lpthread
make[1]: Leaving directory '$SRC_DIR/minimap2'
cd main_src_ont && make CC=x86_64-apple-darwin13.4.0-clang CXX=x86_64-apple-darwin13.4.0-clang
make[1]: Entering directory '$SRC_DIR/main_src_ont'
rm -rf tgsgapcloser.o tgsgapcandidate.o tgsseqsplit.o tgsseqgen.o tgsgapcloser tgsgapcandidate tgsseqsplit tgsseqgen ../common/files/file_reader.o ../biocommon/sam_bam/sam_parser.o ../biocommon/pair/pair_sam_parser.o ../biocommon/fasta/fasta.o ../biocommon/fastq/fastq.o ../biocommon/seq/seq.o ../biocommon/paf/PAF.o ../biocommon/align_common/align_result.o ../common/files/file_writer.o ../common/files/gzstream.o ../common/log/log.o ../common/log/logfilter.o ../common/time/timetools.o ../common/string/stringtools.o ../appcommon/contigPairInfo.o ../appcommon/ScaffInfo.o ../appcommon/ONT2Gap.o ../common/args/argsparser.o
x86_64-apple-darwin13.4.0-clang -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -std=c14 -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tgsgapcloser-1.2.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c11 -I../ -g -c tgsgapcloser.cpp -o tgsgapcloser.o
make[1]: Leaving directory '$SRC_DIR/main_src_ont'
# Last 100 lines of the build log.
category: |-
compiler error