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build_failure.linux-64.yaml
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build_failure.linux-64.yaml
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recipe_sha: 9dd147853f61d5e67e767ed724974f0baf58c1fffa7e30799c31880431f172b7 # 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: |-
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o tigrOperon.o -c tigrOperon.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o tilingPath.o -c tilingPath.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o traceInfo.o -c traceInfo.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o trackDb.o -c trackDb.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o trackDbCustom.o -c trackDbCustom.c
trackDbCustom.c: In function 'trackDbInclude':
trackDbCustom.c:294:5: warning: 'splitPath' accessing 512 bytes in a region of size 256 [-Wstringop-overflow=]
294 | splitPath(raFile, incFile, NULL, NULL);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
trackDbCustom.c:294:5: note: referencing argument 2 of type 'char[512]'
trackDbCustom.c:294:5: note: referencing argument 3 of type 'char[128]'
trackDbCustom.c:294:5: note: referencing argument 4 of type 'char[64]'
In file included from trackDbCustom.c:8:
../../inc/common.h:1104:6: note: in a call to function 'splitPath'
1104 | void splitPath(char *path, char dir[PATH_LEN], char name[FILENAME_LEN],
| ^~~~~~~~~
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$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o variantProjector.o -c variantProjector.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o vcfUi.o -c vcfUi.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o vegaInfo.o -c vegaInfo.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o vegaInfoZfish.o -c vegaInfoZfish.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o visiGene.o -c visiGene.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o vntr.o -c vntr.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wabAli.o -c wabAli.c
sed -e 's/\\/\\\\/g; s/"/\\"/g; s/^/"/; s/$/\\n"/;' jWestHeader.html > jWestHeader.h
sed -e 's/\\/\\\\/g; s/"/\\"/g; s/^/"/; s/$/\\n"/;' jWestBanner.html > jWestBanner.h
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o web.o -c web.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o ncRna.o -c ncRna.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wgRna.o -c wgRna.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wigAsciiToBinary.o -c wigAsciiToBinary.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wigDataStream.o -c wigDataStream.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wiggle.o -c wiggle.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wiggleCart.o -c wiggleCart.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wiggleUtils.o -c wiggleUtils.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wikiLink.o -c wikiLink.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o wikiTrack.o -c wikiTrack.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o yaleGencodeAssoc.o -c yaleGencodeAssoc.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o zdobnovSynt.o -c zdobnovSynt.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o oreganno.o -c oreganno.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o oregannoUi.o -c oregannoUi.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o gvUi.o -c gvUi.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o gv.o -c gv.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o omicia.o -c omicia.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o protVar.o -c protVar.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o pgSnp.o -c pgSnp.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o alignInfo.o -c alignInfo.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o cddInfo.o -c cddInfo.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o loweutils.o -c loweutils.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o cddDesc.o -c cddDesc.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o arCOGs.o -c arCOGs.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o arcogdesc.o -c arcogdesc.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o geneTree.o -c geneTree.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o megablastInfo.o -c megablastInfo.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o pgPhenoAssoc.o -c pgPhenoAssoc.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o pgSiftPred.o -c pgSiftPred.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o pgPolyphenPred.o -c pgPolyphenPred.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o userRegions.o -c userRegions.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -I$PREFIX/include -o variome.o -c variome.c
ar rcus ../../lib/x86_64/jkhgap.a acemblyClass.o adjacency.o affyAllExonProbe.o affyAtlas.o affy10KDetails.o affy120KDetails.o affyOffset.o affyPairs.o agp.o agpFrag.o agpGap.o alignSeqSizes.o altGraph.o altGraphX.o ancientRref.o annoFormatVep.o annoGratorGpVar.o annoGrateWigDb.o annoStreamDb.o annoStreamDbFactorSource.o annoStreamDbPslPlus.o annoStreamWig.o api.o atomDb.o autoUpgrade.o axtInfo.o axtLib.o bactigPos.o hgBam.o barChartBed.o barChartCategory.o barChartUi.o barChartData.o barChartSample.o baseMaskCommon.o bdgpExprLink.o bdgpGeneInfo.o bed.o bed5FloatScore.o bed5Pval.o bed6FloatScore.o bed8Attrs.o bed12Source.o bed12wSeq.o bedCart.o bgiGeneInfo.o bgiGeneSnp.o bgiSnp.o bigBedFind.o bigBedLabel.o bigGenePred.o bigPsl.o bigTransMap.o bioImage.o blastTab.o blastzNet.o blatServers.o borf.o borkPseudoHom.o botDelay.o cart.o cartDb.o cartJson.o cartTrackDb.o cdsEvidence.o cdsOrtho.o cdsPick.o cdsSpec.o ccdsInfo.o ccdsNotes.o ccdsGeneMap.o celeraCoverage.o celeraDupPositive.o cgapSage/cgapSage.o cgapSage/cgapSageLib.o cgh.o chainCart.o chainDb.o chainLink.o chainNet.o chainNetDbLoad.o chicken13kInfo.o chromBins.o chromAlias.o chr18deletions.o chromGraph.o chromGraphFactory.o chromInfo.o chromInserts.o chromKeeper.o clonePos.o codeBlast.o codeBlastScore.o cogs.o cogsxra.o columnInfo.o contigAcc.o coordConv.o cnpIafrate.o cnpIafrate2.o cnpLocke.o cnpRedon.o cnpSebat.o cnpSebat2.o cnpSharp2.o cnpSharpCutoff.o cnpSharpSample.o cnpSharp.o cpgIsland.o cpgIslandExt.o ctgPos.o ctgPos2.o customComposite.o bedDetail.o cgiApoptosis.o customAdjacency.o customFactory.o customPp.o customTrack.o cutter.o cv.o cytoBand.o dbDb.o dbRIP.o dbSnpRs.o defaultDb.o delConrad2.o delHinds2.o dgv.o dgvPlus.o dless.o dnaMotifSql.o dnaMarkovSql.o dnaProbe.o dv.o dvBed.o dvXref2.o easyGene.o ec.o ecCode.o ecAttribute.o ecAttributeCode.o encode/encodeErge.o encode/encodeErgeHssCellLines.o encode/encodeHapMapAlleleFreq.o encode/encodeIndels.o encode/encodePeak.o encode/encodeRegionInfo.o encode/encodeRegionInfoCustom.o encode/encodeRna.o encode/encodeStanfordPromoters.o encode/encodeStanfordPromotersAverage.o encode/pairedTagAlign.o encode/peptideMapping.o encode/tagAlign.o encode/wgEncodeGencodeAttrs.o encode/wgEncodeGencodeExonSupport.o encode/wgEncodeGencodeEntrezGene.o encode/wgEncodeGencodeTag.o encode/wgEncodeGencodeGeneSymbol.o encode/wgEncodeGencodePdb.o encode/wgEncodeGencodePubMed.o encode/wgEncodeGencodeRefSeq.o encode/wgEncodeGencodeGeneSource.o encode/wgEncodeGencodeTranscriptSource.o encode/wgEncodeGencodeTranscriptSupport.o encode/wgEncodeGencodeTranscriptionSupportLevel.o encode/wgEncodeGencodeUniProt.o encode/wgEncodeGencodePolyAFeature.o encode/wgEncodeGencodeAnnotationRemark.o encode/wgEncodeCell.o encode/encodeExp.o encode3/encode2Manifest.o encode3/encode3Valid.o ensFace.o ensInfo.o ensPhusionBlast.o ensXRefZfish.o est3.o estOrientInfo.o estPair.o exoFish.o expData.o expRecord.o exprBed.o facetField.o factorSource.o fbTables.o featureBits.o fileUi.o findKGAlias.o findKGProtAlias.o fishClones.o flyBase2004Xref.o flyBaseSwissProt.o flyreg.o flyreg2.o gbExtFile.o gbWarn.o gbMiscDiff.o gbProtAnn.o gcPercent.o gbSeq.o genbank.o genbankBlackList.o gencodeGeneClass.o gencodeIntron.o genMapDb.o geneBands.o geneCheck.o geneCheckDetails.o geneCheckWidget.o geneGraph.o genePred.o genePredReader.o geneSimilarities.o genoLay.o genomeRangeTreeFile.o genomicDups.o genomicSuperDups.o geoMirror.o ggCluster.o ggDbIo.o ggDump.o ggGraph.o ggMrnaAli.o ggTypes.o glDbRep.o goa.o goaPart.o googleAnalytics.o gpFx.o growthCondition.o grp.o gtexAse.o gtexBoxplot.o gtexEqtlCluster.o gtexInfo.o gtexDonor.o gtexGeneBed.o gtexSample.o gtexSampleData.o gtexTissue.o gtexTissueData.o gtexTissueMedian.o gtexUi.o gwasCatalog.o hAnno.o haplotypes.o hapmapAllelesOrtho.o hapmapAllelesSummary.o hapmapPhaseIIISummary.o hapmapSnps.o hapmapSnpsCombined.o hashJoin.o hCommon.o hCytoBand.o hdb.o hgColors.o hgConfig.o hgExp.o hgFind.o hgFindSpec.o hgFindSpecCustom.o hgHgvs.o hgHgvsParse.o hgGene.o hgMaf.o hgRelate.o hgSeq.o hgdpGeo.o hPrint.o hVarSubst.o hvGfx.o HInv.o hubConnect.o hubSearchText.o hui.o humanParalog.o imageClone.o indelShift.o interact.o interactUi.o isochores.o ispyTables.o itemAttr.o itemConf.o itemDetailsHtml.o jalview.o jaxOrtholog.o jaxQTL.o jaxQTL3.o jksql.o joiner.o jsHelper.o kg1ToKg2.o jgiGene.o joinMixer.o kgAlias.o kgColor.o kgProtAlias.o kgXref.o knownInfo.o knownMore.o knownToSuper.o lav.o ld.o ld2.o lfs.o liftOver.o liftOverChain.o liftUp.o llaInfo.o longRange.o lrg.o lsSnpPdb.o lsSnpPdbChimera.o mafFrames.o mafGene.o mafSummary.o makeItemsItem.o mammalPsg.o mapSts.o mathWig.o mcnBreakpoints.o mdb.o metaChromGraph.o microarray.o minChromSize.o minGeneInfo.o mrnaMisMatch.o mouseOrtho.o mouseSyn.o mouseSynWhd.o mysqlTableStatus.o ncbiRefLink.o ncbiRefSeqLink.o netAlign.o netCart.o nonCodingUi.o omimTitle.o ooUtils.o orthoAlleles.o pal.o pbStamp.o pcrResult.o pepPred.o peptideAtlasPeptide.o plasEndPairs.o polyGenotype.o protFeat.o pscreen.o pseudoGeneLink.o pslReader.o pslWScore.o putaInfo.o qaSeq.o rangeTreeFile.o rankProp.o recombRate.o recombRateRat.o recombRateMouse.o refLink.o refSeqStatus.o rgdQtl.o riken.o rhMapZfishInfo.o rikenBest.o rikenCluster.o rmskOut.o rmskAlign.o rmskJoined.o rmskOut2.o rnaFold.o rnaGene.o rnaGroup.o rnaHybridization.o rnaPLFold.o tRNAs.o gbRNAs.o snoRNAs.o lowelabPfamHit.o lowelabArkinOperonScore.o lowelabTIGROperonScore.o rnaSecStr.o tfbsConsFactors.o roughAli.o transMapStuff.o transMapInfo.o transMapGene.o transMapSrc.o sage.o sageCounts.o sageExp.o samAlignment.o sample.o sanger22extra.o sangerGene.o sangerGeneToWBGeneID.o sargassoSeaXra.o scopDes.o scoredRef.o search.o seqWindow.o sessionThumbnail.o sgdAbundance.o sgdClone.o sgdDescription.o sgdOther.o simpleNucDiff.o simpleRepeat.o snakeUi.o snp.o snp125.o snp125CodingCoordless.o snp132Ext.o snpExceptions.o snpFasta.o snpMap.o snpTmp.o snpUi.o snp125Exceptions.o snp125Ui.o softPromoter.o softberryHom.o soTerm.o spDb.o splignAlign.o sqlSanity.o stanMad.o stsAlias.o stsInfo.o stsInfo2.o stsInfoMouse.o stsInfoMouseNew.o stsInfoRat.o stsMap.o stsMapMouse.o stsMapMouseNew.o stsMapRat.o stsMarker.o suggest.o switchDbTss.o synMap.o synteny100000.o syntenyBerk.o syntenySanger.o sqlProg.o tfbsCons.o tfbsConsSites.o tablesTables.o tableDescriptions.o tableStatus.o targetDb.o tfbsConsMap.o tagRepo.o taxonDivision.o taxonGeneticCode.o taxonName.o taxonNode.o taxonXref.o tigrCmrGene.o tigrOperon.o tilingPath.o traceInfo.o trackDb.o trackDbCustom.o trackHub.o trackLayout.o trackTable.o trackVersion.o trashDir.o transRegCode.o transRegCodeCondition.o transRegCodeProbe.o txAliDiff.o txCluster.o txCommon.o txEdgeBed.o txEdgeOrtho.o txGraph.o txInfo.o txRnaAccs.o ucscRetroInfo.o ucscRetroOrtho.o validateGisaid.o variant.o variantProjector.o vcfUi.o vegaInfo.o vegaInfoZfish.o visiGene.o vntr.o wabAli.o web.o ncRna.o wgRna.o wigAsciiToBinary.o wigDataStream.o wiggle.o wiggleCart.o wiggleUtils.o wikiLink.o wikiTrack.o yaleGencodeAssoc.o zdobnovSynt.o oreganno.o oregannoUi.o gvUi.o gv.o omicia.o protVar.o pgSnp.o alignInfo.o cddInfo.o loweutils.o cddDesc.o arCOGs.o arcogdesc.o geneTree.o megablastInfo.o pgPhenoAssoc.o pgSiftPred.o pgPolyphenPred.o userRegions.o variome.o
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ucsc-endsinlf-377 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I $PREFIX/include -I/include -I$PREFIX/include/libpng16 -o endsInLf.o -c endsInLf.c
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -O -g -o $SRC_DIR/bin/endsInLf endsInLf.o ../../lib/x86_64/jkweb.a -L$PREFIX/lib -lmysqlclient -lstdc -lrt -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -lpthread -lssl -lcrypto ../../htslib/libhts.a -L$PREFIX/lib -lpng16 -lm -lz -lm
/opt/conda/conda-bld/ucsc-endsinlf_1724783725175/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../lib/x86_64/jkweb.a(htmshell.o):/usr/local/src/conda/ucsc-endsinlf-377/kent/src/lib/../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../lib/x86_64/jkweb.a(cheapcgi.o):/usr/local/src/conda/ucsc-endsinlf-377/kent/src/lib/../inc/htmshell.h:163: first defined here
/opt/conda/conda-bld/ucsc-endsinlf_1724783725175/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/12.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: ../../lib/x86_64/jkweb.a(portimpl.o):/usr/local/src/conda/ucsc-endsinlf-377/kent/src/lib/../inc/htmshell.h:163: multiple definition of htmlRecover'; ../../lib/x86_64/jkweb.a(cheapcgi.o):/usr/local/src/conda/ucsc-endsinlf-377/kent/src/lib/../inc/htmshell.h:163: first defined here
collect2: error: ld returned 1 exit status
make: *** [../../inc/userApp.mk:31: /opt/conda/conda-bld/ucsc-endsinlf_1724783725175/work/bin/endsInLf] Error 1
Traceback (most recent call last):
File "/opt/conda/bin/conda-build", line 11, in <module>
sys.exit(execute())
File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute
api.build(
File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build
return build_tree(
File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree
packages_from_this = build(
File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build
utils.check_call_env(
File "/opt/conda/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/conda/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/conda/conda-bld/ucsc-endsinlf_1724783725175/work/conda_build.sh']' returned non-zero exit status 1.
# Last 100 lines of the build log.