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build_failure.osx-64.yaml
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recipe_sha: b2d5e4755a159055f9b727e022dfec5dd0019e3404a04a019e679afc9fca3cd4 # 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: |-
make[3]: Entering directory '$SRC_DIR/src/gmap/src'
../config/install-sh -c -d '$SRC_DIR/src/../inst/usr/bin'
/bin/sh ../libtool --mode=install /usr/bin/install -c gmap gmapl get-genome gmapindex iit_store iit_get iit_dump gsnap gsnapl uniqscan uniqscanl snpindex cmetindex atoiindex '$SRC_DIR/src/../inst/usr/bin'
libtool: install: /usr/bin/install -c gmap $SRC_DIR/src/../inst/usr/bin/gmap
libtool: install: /usr/bin/install -c gmapl $SRC_DIR/src/../inst/usr/bin/gmapl
libtool: install: /usr/bin/install -c get-genome $SRC_DIR/src/../inst/usr/bin/get-genome
libtool: install: /usr/bin/install -c gmapindex $SRC_DIR/src/../inst/usr/bin/gmapindex
libtool: install: /usr/bin/install -c iit_store $SRC_DIR/src/../inst/usr/bin/iit_store
sys.exit(execute())
libtool: install: /usr/bin/install -c iit_get $SRC_DIR/src/../inst/usr/bin/iit_get
libtool: install: /usr/bin/install -c iit_dump $SRC_DIR/src/../inst/usr/bin/iit_dump
libtool: install: /usr/bin/install -c gsnap $SRC_DIR/src/../inst/usr/bin/gsnap
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute
libtool: install: /usr/bin/install -c gsnapl $SRC_DIR/src/../inst/usr/bin/gsnapl
libtool: install: /usr/bin/install -c uniqscan $SRC_DIR/src/../inst/usr/bin/uniqscan
libtool: install: /usr/bin/install -c uniqscanl $SRC_DIR/src/../inst/usr/bin/uniqscanl
libtool: install: /usr/bin/install -c snpindex $SRC_DIR/src/../inst/usr/bin/snpindex
api.build(
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build
libtool: install: /usr/bin/install -c cmetindex $SRC_DIR/src/../inst/usr/bin/cmetindex
return build_tree(
libtool: install: /usr/bin/install -c atoiindex $SRC_DIR/src/../inst/usr/bin/atoiindex
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '$SRC_DIR/src/gmap/src'
make[2]: Leaving directory '$SRC_DIR/src/gmap/src'
Making install in util
make[2]: Entering directory '$SRC_DIR/src/gmap/util'
cp gmap_compress.pl gmap_compress
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree
packages_from_this = build(
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build
chmod x gmap_compress
cp gmap_uncompress.pl gmap_uncompress
chmod x gmap_uncompress
cp gmap_process.pl gmap_process
chmod x gmap_process
raise BuildScriptException(str(exc), caused_by=exc) from exc
conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bioconductor-gmapr_1735858995018/work/conda_build.sh']' returned non-zero exit status 1.
cp gmap_setup.pl gmap_setup
chmod x gmap_setup
cp gmap_build.pl gmap_build
chmod x gmap_build
cp gmap_reassemble.pl gmap_reassemble
chmod x gmap_reassemble
cp md_coords.pl md_coords
chmod x md_coords
cp fa_coords.pl fa_coords
chmod x fa_coords
cp psl_splicesites.pl psl_splicesites
chmod x psl_splicesites
cp psl_introns.pl psl_introns
chmod x psl_introns
cp psl_genes.pl psl_genes
chmod x psl_genes
cp gtf_splicesites.pl gtf_splicesites
chmod x gtf_splicesites
cp gtf_introns.pl gtf_introns
chmod x gtf_introns
cp gtf_genes.pl gtf_genes
chmod x gtf_genes
cp gff3_splicesites.pl gff3_splicesites
chmod x gff3_splicesites
cp gff3_introns.pl gff3_introns
chmod x gff3_introns
cp gff3_genes.pl gff3_genes
chmod x gff3_genes
cp dbsnp_iit.pl dbsnp_iit
chmod x dbsnp_iit
cp gvf_iit.pl gvf_iit
chmod x gvf_iit
cp vcf_iit.pl vcf_iit
chmod x vcf_iit
make[3]: Entering directory '$SRC_DIR/src/gmap/util'
../config/install-sh -c -d '$SRC_DIR/src/../inst/usr/bin'
/usr/bin/install -c gmap_compress gmap_uncompress gmap_process gmap_setup gmap_build gmap_reassemble md_coords fa_coords psl_splicesites psl_introns psl_genes gtf_splicesites gtf_introns gtf_genes gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '$SRC_DIR/src/../inst/usr/bin'
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '$SRC_DIR/src/gmap/util'
make[2]: Leaving directory '$SRC_DIR/src/gmap/util'
Making install in tests
make[2]: Entering directory '$SRC_DIR/src/gmap/tests'
make[3]: Entering directory '$SRC_DIR/src/gmap/tests'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '$SRC_DIR/src/gmap/tests'
make[2]: Leaving directory '$SRC_DIR/src/gmap/tests'
make[2]: Entering directory '$SRC_DIR/src/gmap'
make[3]: Entering directory '$SRC_DIR/src/gmap'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '$SRC_DIR/src/gmap'
make[2]: Leaving directory '$SRC_DIR/src/gmap'
make[1]: Leaving directory '$SRC_DIR/src/gmap'
Creating a generic function from function directory in package gmapR
Creating a generic function for bamPaths from package Rsamtools in package gmapR
Note: ... may be used in an incorrect context
Error: package or namespace load failed for gmapR in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '$PREFIX/lib/R/library/00LOCK-work/00new/gmapR/libs/gmapR.so':
dlopen($PREFIX/lib/R/library/00LOCK-work/00new/gmapR/libs/gmapR.so, 0x0006): symbol not found in flat namespace '_bam_aux2A'
Error: loading failed
Execution halted
# Last 100 lines of the build log.
category: |-
test failure