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build_failure.osx-64.yaml
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build_failure.osx-64.yaml
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recipe_sha: 68289bc6e777b3809eb35883aa841d04653b86d7d5ae8ed9d545b7883991fcfc # 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: |2-
for(uint32_t j = idx 1; ((j < junctions.size()) && (junctions[j].refidx == junctions[idx].refidx) && (std::abs(junctions[j].refpos - junctions[idx].refpos) < 2 * c.delta)); j) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~
src/telomere.h:277:5: note: in instantiation of function template specialization 'lorax::outputTelomereSVs<lorax::TelomereConfig, std::map<unsigned long, lorax::TelomereRecord>>' requested here
outputTelomereSVs(c, junctions, telreads);
^
src/telomere.h:342:12: note: in instantiation of function template specialization 'lorax::runTelomere<lorax::TelomereConfig>' requested here
return runTelomere(c);
^
src/telomere.h:176:133: warning: comparison of integers of different signs: 'int' and 'const uint32_t' (aka 'const unsigned int') [-Wsign-compare]
if ((junctions[i].refidx == junctions[jctidx[compId]].refidx) && (std::abs(junctions[i].refpos - junctions[jctidx[compId]].refpos) < c.delta)) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~
src/telomere.h:208:135: warning: comparison of integers of different signs: 'int' and 'const uint32_t' (aka 'const unsigned int') [-Wsign-compare]
if ((junctions[i].refidx == junctions[jctidx[compId]].refidx) && (std::abs(junctions[i].refpos - junctions[jctidx[compId]].refpos) < c.delta)) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~
In file included from src/lorax.cpp:16:
src/amplicon.h:234:70: warning: comparison of integers of different signs: 'int' and 'const uint32_t' (aka 'const unsigned int') [-Wsign-compare]
if (std::abs(gp - (int32_t) scanRegions[refIndex][ri].start) < c.bpuncertain) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~
src/amplicon.h:458:24: note: in instantiation of function template specialization 'lorax::selectReads<lorax::AmpliconConfig, std::vector<std::vector<lorax::BedEntry>>, std::map<unsigned long, std::set<unsigned int>>>' requested here
int32_t candsize = selectReads(c, scanRegions, candidates, readAmp);
^
src/amplicon.h:593:12: note: in instantiation of function template specialization 'lorax::runAmplicon<lorax::AmpliconConfig>' requested here
return runAmplicon(c);
^
src/amplicon.h:240:68: warning: comparison of integers of different signs: 'int' and 'const uint32_t' (aka 'const unsigned int') [-Wsign-compare]
if (std::abs(gp - (int32_t) scanRegions[refIndex][ri].end) < c.bpuncertain) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~
13 warnings and 17 errors generated.
make: *** [Makefile:53: src/lorax] Error 1
Extracting download
Traceback (most recent call last):
File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in <module>
sys.exit(execute())
source tree in: /opt/mambaforge/envs/bioconda/conda-bld/lorax_1717638680548/work
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute
export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/lorax_1717638680548/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol
export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/lorax_1717638680548/_build_env
export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/lorax_1717638680548/work
INFO: activate_clang_osx-64.sh made the following environmental changes:
AR=x86_64-apple-darwin13.4.0-ar
AS=x86_64-apple-darwin13.4.0-as
CC=x86_64-apple-darwin13.4.0-clang
CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
api.build(
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build
return build_tree(
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree
packages_from_this = build(
CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/lorax-0.3.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms
CLANG=x86_64-apple-darwin13.4.0-clang
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build
utils.check_call_env(
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env
return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs)
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ
raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/lorax_1717638680548/work/conda_build.sh']' returned non-zero exit status 2.
CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin
CMAKE_PREFIX_PATH=:$PREFIX
CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0
CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0
CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9
DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/lorax-0.3.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
HOST=x86_64-apple-darwin13.4.0
INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool
LD=x86_64-apple-darwin13.4.0-ld
LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib
LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib
LIBTOOL=x86_64-apple-darwin13.4.0-libtool
LIPO=x86_64-apple-darwin13.4.0-lipo
MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib
NM=x86_64-apple-darwin13.4.0-nm
NMEDIT=x86_64-apple-darwin13.4.0-nmedit
OBJC=x86_64-apple-darwin13.4.0-clang
OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
OTOOL=x86_64-apple-darwin13.4.0-otool
PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff
RANLIB=x86_64-apple-darwin13.4.0-ranlib
REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding
SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk
SEGEDIT=x86_64-apple-darwin13.4.0-segedit
SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table
SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack
SIZE=x86_64-apple-darwin13.4.0-size
STRINGS=x86_64-apple-darwin13.4.0-strings
STRIP=x86_64-apple-darwin13.4.0-strip
_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0
ac_cv_func_malloc_0_nonnull=yes
ac_cv_func_realloc_0_nonnull=yes
build_alias=x86_64-apple-darwin13.4.0
host_alias=x86_64-apple-darwin13.4.0
INFO: activate_clangxx_osx-64.sh made the following environmental changes:
CLANGXX=x86_64-apple-darwin13.4.0-clang
CXX=x86_64-apple-darwin13.4.0-clang
CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/lorax-0.3.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/lorax-0.3.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
if [ -r src/htslib/Makefile ]; then cd src/htslib && autoreconf -i && ./configure --disable-s3 --disable-gcs --disable-libcurl --disable-plugins && make && make lib-static && cd ../../ && touch .htslib; fi
x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/lorax-0.3.9 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D__STDC_FORMAT_MACROS -std=c11 -isystem $SRC_DIR/src/htslib/ -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing -fpermissive -O3 -fno-tree-vectorize -DNDEBUG src/lorax.cpp -o src/lorax -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -L$SRC_DIR/src/htslib/ -L$SRC_DIR/src/htslib//lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time -lhts -lz -llzma -lbz2 -Wl,-rpath,$SRC_DIR/src/htslib/
# Last 100 lines of the build log.