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chapmanb / cloudbiolinux

CloudBioLinux: configure virtual (or real) machines with tools for biological analyses
http://cloudbiolinux.org
MIT License
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AWS ubuntu13.04: install fails on seal #117

Closed andersje closed 11 years ago

andersje commented 11 years ago

running fab -f ./fabfile.py -H localhost install_custom:seal generates a failure:

make: Leaving directory `/tmp/pip_build_ubuntu/seal/bl/lib/seq/aligner/bwa/libbwa'

Buildfile: /tmp/pip_build_ubuntu/seal/build.xml

 [echo] debug.build: false

version_check:

find_hadoop:

BUILD FAILED

/tmp/pip_build_ubuntu/seal/build.xml:71: exec returned: 1

Total time: 1 second

error: Could not build Java components

Cleaning up... Command /usr/local/anaconda/bin/python -c "import setuptools;file='/tmp/pip_build_ubuntu/seal/setup.py';exec(compile(open(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /tmp/pip-GxgqL9-record/install-record.txt --single-version-externally-managed failed with error code 1 in /tmp/pip_build_ubuntu/seal Traceback (most recent call last): File "/usr/local/anaconda/bin/pip", line 6, in sys.exit(main()) File "/usr/local/anaconda/lib/python2.7/site-packages/pip/init.py", line 161, in main return command.main(args[1:], options) File "/usr/local/anaconda/lib/python2.7/site-packages/pip/basecommand.py", line 169, in main text = '\n'.join(complete_log) UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 25: ordinal not in range(128)

Fatal error: local() encountered an error (return code 1) while executing 'export JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64 && /usr/local/anaconda/bin/pip install --pre seal'

Aborting.

chapmanb commented 11 years ago

Jeremy; Thanks for the problem report. This is working cleanly on my 13.04 test machine, so I'm not sure right now how to replicate. Unfortunately the error message isn't very enlightening.

Is hadoop installed on that machine? It fails during the hadoop check before it gets to the compile. I'm using the hadoop-0.20 package from apt:

https://github.com/chapmanb/cloudbiolinux/blob/master/config/packages.yaml#L199

andersje commented 11 years ago

Here is the dump of the failure...

INFO: This is a Base Flavor - no overrides INFO: Reading default fabricrc.txt DBG [config.py]: Using config file /home/ubuntu/sandbox/cloudbiolinux/cloudbio/../config/fabricrc.txt DBG [init.py]: BioLinux base Edition 1.7.0 INFO: This is a biolinux INFO: Distribution auto INFO: Get local environment INFO: Ubuntu setup DBG [distribution.py]: Debian-shared setup DBG [distribution.py]: Source=raring DBG [distribution.py]: NixPkgs: Ignored INFO: Now, testing connection to host... INFO: Connection to host appears to work! DBG [utils.py]: Expand paths DBG [config.py]: Using config file /home/ubuntu/sandbox/cloudbiolinux/cloudbio/../config/custom.yaml INFO: Reading /home/ubuntu/sandbox/cloudbiolinux/cloudbio/../config/custom.yaml DBG [shared.py]: Packages to install: anaconda,emboss,pgdspider,bowtie,bowtie2,bwa,gmap,lastz,mosaik,snap,star,bfast,novoalign,novosort,plink_seq,ucsc_tools,delly,freec,hydra,lumpy,cufflinks,picard,sambamba,samtools,shrec,tophat,bamtools,bedtools,cram,dwgsim,fastq_screen,fastqc,fastx_toolkit,ogap,rnaseqc,varianttools,vcftools,bcbio_variation,crisp,freebayes,gatk_protected,gemini,grabix,mutect,snpeff,stacks,tabix,tassel,varscan,vcflib,macs,abyss,cortex_var,ray,transabyss,trinity,velvet,directag,idpqonvert,myrimatch,mzmine,omssa,pepitome,percolator,tagrecon,transproteomic_pipeline,morpheus,proteomics_wine_env,proteowizard,nginx,novnc,proftpd,sge,gnu_parallel,pydoop,seal,galaxy_webapp,cbl_galaxy_tools,galaxy_protk,protvis,leiningen,beast,tracer,bx-python,netsa-python,rpy,homebrew,s3fs,viralassembly,viralassembly_cleanall,viralvigor,viralvigor_cleanall,viralvigor_test,viralvigor_validate INFO: Custom install for 'seal' start time: 2013-09-12 14:18:53.866169 DBG [fabfile.py]: Importing module cloudbio.custom.distributed DBG [fabfile.py]: Looking for custom install function cloudbio.custom.distributed.install_seal Traceback (most recent call last): File "", line 1, in ImportError: No module named bl.mr.seq.seqal

Warning: local() encountered an error (return code 1) while executing '/usr/local/anaconda/bin/python -c 'import bl.mr.seq.seqal''

Downloading/unpacking seal Running setup.py egg_info for package seal

Installing collected packages: seal Running setup.py install for seal changing mode of build/scripts-2.7/find_fq_format from 664 to 775 changing mode of build/scripts-2.7/demux from 664 to 775 changing mode of build/scripts-2.7/prq_to_fastq from 664 to 775 changing mode of build/scripts-2.7/seal_path.py from 664 to 775 changing mode of build/scripts-2.7/bwa_index_to_mmap from 664 to 775 changing mode of build/scripts-2.7/read_sort from 664 to 775 changing mode of build/scripts-2.7/tsvsort from 664 to 775 changing mode of build/scripts-2.7/distcp_files from 664 to 775 changing mode of build/scripts-2.7/version from 664 to 775 changing mode of build/scripts-2.7/prq_local from 664 to 775 changing mode of build/scripts-2.7/merge_alignments from 664 to 775 changing mode of build/scripts-2.7/recab_table_fetch from 664 to 775 changing mode of build/scripts-2.7/align_script from 664 to 775 changing mode of build/scripts-2.7/recab_table from 664 to 775 changing mode of build/scripts-2.7/seqal from 664 to 775 changing mode of build/scripts-2.7/digest_fasta from 664 to 775 changing mode of build/scripts-2.7/realign_snp from 664 to 775 changing mode of build/scripts-2.7/prq from 664 to 775 make: Entering directory /tmp/pip_build_ubuntu/seal/bl/lib/seq/aligner/bwa/libbwa' gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS bwtaln.c -o bwtaln.ol gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS bwtgap.c -o bwtgap.ol gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS bwt.c -o bwt.ol gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS bwape.c -o bwape.ol bwape.c: In function ‘infer_isize’: bwape.c:122:27: warning: variable ‘p50’ set but not used [-Wunused-but-set-variable] bwape.c: In function ‘bwa_sai2sam_pe_core’: bwape.c:708:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwape.c:711:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwape.c:724:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwape.c: In function ‘bwa_paired_sw’: bwape.c:552:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwape.c: In function ‘bwa_cal_pac_pos_pe’: bwape.c:344:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwape.c:348:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS bwase.c -o bwase.ol bwase.c: In function ‘bwa_aln2seq_core’: bwase.c:111:15: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] bwase.c: In function ‘bwa_print_sam1’: bwase.c:508:17: warning: variable ‘m_is_N’ set but not used [-Wunused-but-set-variable] bwase.c: In function ‘bwa_sai2sam_se_core’: bwase.c:668:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwase.c:684:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwase.c:689:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwase.c: In function ‘bwa_refine_gapped’: bwase.c:358:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwase.c:364:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS stdaln.c -o stdaln.ol stdaln.c: In function ‘aln_local_core’: stdaln.c:545:25: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] stdaln.c: In function ‘aln_extend_core’: stdaln.c:865:16: warning: variable ‘tmp_len’ set but not used [-Wunused-but-set-variable] gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS bwtio.c -o bwtio.ol bwtio.c: In function ‘bwt_restore_bwt’: bwtio.c:95:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwtio.c:96:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwtio.c:97:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwtio.c: In function ‘bwt_restore_sa’: bwtio.c:69:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwtio.c:71:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwtio.c:72:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwtio.c:73:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwtio.c:80:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS bwaseqio.c -o bwaseqio.ol gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS bntseq.c -o bntseq.ol bntseq.c: In function ‘bns_restore_core’: bntseq.c:103:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] bntseq.c:111:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] bntseq.c:119:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] bntseq.c:128:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] bntseq.c:134:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS cs2nt.c -o cs2nt.ol gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS kstring.c -o kstring.ol gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS utils.c -o utils.ol gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS bamlite.c -o bamlite.ol gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS bwamisc.c -o bwamisc.ol gcc -shared bwtaln.ol bwtgap.ol bwt.ol bwape.ol bwase.ol stdaln.ol bwtio.ol bwaseqio.ol bntseq.ol cs2nt.ol kstring.ol utils.ol bamlite.ol bwamisc.ol -lz -o /tmp/pip_build_ubuntu/seal/build/lib/bl/lib/seq/aligner/bwa/libbwa.so make: Leaving directory/tmp/pip_build_ubuntu/seal/bl/lib/seq/aligner/bwa/libbwa' Buildfile: /tmp/pip_build_ubuntu/seal/build.xml [echo] debug.build: false

version_check:

find_hadoop:

BUILD FAILED
/tmp/pip_build_ubuntu/seal/build.xml:71: exec returned: 1

Total time: 1 second
error: Could not build Java components
Complete output from command /usr/local/anaconda/bin/python -c "import setuptools;__file__='/tmp/pip_build_ubuntu/seal/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-cT_e4o-record/install-record.txt --single-version-externally-managed:
running install

running build

running build_py

creating build

creating build/lib

creating build/lib/bl

copying bl/init.py -> build/lib/bl

creating build/lib/bl/lib

copying bl/lib/version.py -> build/lib/bl/lib

copying bl/lib/init.py -> build/lib/bl/lib

creating build/lib/bl/lib/tools

copying bl/lib/tools/seal_config_file.py -> build/lib/bl/lib/tools

copying bl/lib/tools/init.py -> build/lib/bl/lib/tools

copying bl/lib/tools/hadut.py -> build/lib/bl/lib/tools

copying bl/lib/tools/standard_monitor.py -> build/lib/bl/lib/tools

copying bl/lib/tools/event_monitor.py -> build/lib/bl/lib/tools

copying bl/lib/tools/deprecation_utils.py -> build/lib/bl/lib/tools

creating build/lib/bl/lib/seq

copying bl/lib/seq/init.py -> build/lib/bl/lib/seq

creating build/lib/bl/lib/seq/aligner

copying bl/lib/seq/aligner/mapping.py -> build/lib/bl/lib/seq/aligner

copying bl/lib/seq/aligner/init.py -> build/lib/bl/lib/seq/aligner

copying bl/lib/seq/aligner/sam_flags.py -> build/lib/bl/lib/seq/aligner

copying bl/lib/seq/aligner/sam_mapping.py -> build/lib/bl/lib/seq/aligner

creating build/lib/bl/lib/seq/aligner/bwa

copying bl/lib/seq/aligner/bwa/bwa_core.py -> build/lib/bl/lib/seq/aligner/bwa

copying bl/lib/seq/aligner/bwa/bwa_iterator.py -> build/lib/bl/lib/seq/aligner/bwa

copying bl/lib/seq/aligner/bwa/init.py -> build/lib/bl/lib/seq/aligner/bwa

copying bl/lib/seq/aligner/bwa/constants.py -> build/lib/bl/lib/seq/aligner/bwa

copying bl/lib/seq/aligner/bwa/bwa_mapping.py -> build/lib/bl/lib/seq/aligner/bwa

copying bl/lib/seq/aligner/bwa/bwa_aligner.py -> build/lib/bl/lib/seq/aligner/bwa

creating build/lib/bl/lib/seq/aligner/io

copying bl/lib/seq/aligner/io/init.py -> build/lib/bl/lib/seq/aligner/io

copying bl/lib/seq/aligner/io/protobuf_mapping.py -> build/lib/bl/lib/seq/aligner/io

copying bl/lib/seq/aligner/io/sam_formatter.py -> build/lib/bl/lib/seq/aligner/io

creating build/lib/bl/mr

copying bl/mr/test_utils.py -> build/lib/bl/mr

copying bl/mr/init.py -> build/lib/bl/mr

creating build/lib/bl/mr/lib

copying bl/mr/lib/init.py -> build/lib/bl/mr/lib

copying bl/mr/lib/hit_processor_chain_link.py -> build/lib/bl/mr/lib

copying bl/mr/lib/hadoop_event_monitor.py -> build/lib/bl/mr/lib

copying bl/mr/lib/emit_sam_link.py -> build/lib/bl/mr/lib

copying bl/mr/lib/jc_wrapper.py -> build/lib/bl/mr/lib

copying bl/mr/lib/filter_link.py -> build/lib/bl/mr/lib

creating build/lib/bl/mr/seq

copying bl/mr/seq/init.py -> build/lib/bl/mr/seq

copying bl/mr/seq/utils.py -> build/lib/bl/mr/seq

creating build/lib/bl/mr/seq/seqal

copying bl/mr/seq/seqal/mapper.py -> build/lib/bl/mr/seq/seqal

copying bl/mr/seq/seqal/reducer.py -> build/lib/bl/mr/seq/seqal

copying bl/mr/seq/seqal/seqal_run.py -> build/lib/bl/mr/seq/seqal

copying bl/mr/seq/seqal/init.py -> build/lib/bl/mr/seq/seqal

copying bl/mr/seq/seqal/seqal_config.py -> build/lib/bl/mr/seq/seqal

copying bl/mr/seq/seqal/seqal_app.py -> build/lib/bl/mr/seq/seqal

running build_scripts

creating build/scripts-2.7

copying and adjusting bin/find_fq_format -> build/scripts-2.7

copying and adjusting bin/demux -> build/scripts-2.7

copying bin/prq_to_fastq -> build/scripts-2.7

copying bin/seal_path.py -> build/scripts-2.7

copying and adjusting bin/bwa_index_to_mmap -> build/scripts-2.7

copying and adjusting bin/read_sort -> build/scripts-2.7

copying and adjusting bin/tsvsort -> build/scripts-2.7

copying and adjusting bin/distcp_files -> build/scripts-2.7

copying and adjusting bin/version -> build/scripts-2.7

copying and adjusting bin/prq_local -> build/scripts-2.7

copying and adjusting bin/merge_alignments -> build/scripts-2.7

copying and adjusting bin/recab_table_fetch -> build/scripts-2.7

copying and adjusting bin/align_script -> build/scripts-2.7

copying and adjusting bin/recab_table -> build/scripts-2.7

copying and adjusting bin/seqal -> build/scripts-2.7

copying and adjusting bin/digest_fasta -> build/scripts-2.7

copying and adjusting bin/realign_snp -> build/scripts-2.7

copying and adjusting bin/prq -> build/scripts-2.7

changing mode of build/scripts-2.7/find_fq_format from 664 to 775

changing mode of build/scripts-2.7/demux from 664 to 775

changing mode of build/scripts-2.7/prq_to_fastq from 664 to 775

changing mode of build/scripts-2.7/seal_path.py from 664 to 775

changing mode of build/scripts-2.7/bwa_index_to_mmap from 664 to 775

changing mode of build/scripts-2.7/read_sort from 664 to 775

changing mode of build/scripts-2.7/tsvsort from 664 to 775

changing mode of build/scripts-2.7/distcp_files from 664 to 775

changing mode of build/scripts-2.7/version from 664 to 775

changing mode of build/scripts-2.7/prq_local from 664 to 775

changing mode of build/scripts-2.7/merge_alignments from 664 to 775

changing mode of build/scripts-2.7/recab_table_fetch from 664 to 775

changing mode of build/scripts-2.7/align_script from 664 to 775

changing mode of build/scripts-2.7/recab_table from 664 to 775

changing mode of build/scripts-2.7/seqal from 664 to 775

changing mode of build/scripts-2.7/digest_fasta from 664 to 775

changing mode of build/scripts-2.7/realign_snp from 664 to 775

changing mode of build/scripts-2.7/prq from 664 to 775

make: Entering directory `/tmp/pip_build_ubuntu/seal/bl/lib/seq/aligner/bwa/libbwa'

gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS bwtaln.c -o bwtaln.ol

gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS bwtgap.c -o bwtgap.ol

gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS bwt.c -o bwt.ol

gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS bwape.c -o bwape.ol

bwape.c: In function ‘infer_isize’:

bwape.c:122:27: warning: variable ‘p50’ set but not used [-Wunused-but-set-variable]

bwape.c: In function ‘bwa_sai2sam_pe_core’:

bwape.c:708:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]

bwape.c:711:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]

bwape.c:724:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]

bwape.c: In function ‘bwa_paired_sw’:

bwape.c:552:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]

bwape.c: In function ‘bwa_cal_pac_pos_pe’:

bwape.c:344:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]

bwape.c:348:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]

gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS bwase.c -o bwase.ol

bwase.c: In function ‘bwa_aln2seq_core’:

bwase.c:111:15: warning: variable ‘k’ set but not used [-Wunused-but-set-variable]

bwase.c: In function ‘bwa_print_sam1’:

bwase.c:508:17: warning: variable ‘m_is_N’ set but not used [-Wunused-but-set-variable]

bwase.c: In function ‘bwa_sai2sam_se_core’:

bwase.c:668:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]

bwase.c:684:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]

bwase.c:689:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]

bwase.c: In function ‘bwa_refine_gapped’:

bwase.c:358:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]

bwase.c:364:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]

gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS stdaln.c -o stdaln.ol

stdaln.c: In function ‘aln_local_core’:

stdaln.c:545:25: warning: variable ‘b’ set but not used [-Wunused-but-set-variable]

stdaln.c: In function ‘aln_extend_core’:

stdaln.c:865:16: warning: variable ‘tmp_len’ set but not used [-Wunused-but-set-variable]

gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS bwtio.c -o bwtio.ol

bwtio.c: In function ‘bwt_restore_bwt’:

bwtio.c:95:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]

bwtio.c:96:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]

bwtio.c:97:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]

bwtio.c: In function ‘bwt_restore_sa’:

bwtio.c:69:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]

bwtio.c:71:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]

bwtio.c:72:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]

bwtio.c:73:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]

bwtio.c:80:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]

gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS bwaseqio.c -o bwaseqio.ol

gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS bntseq.c -o bntseq.ol

bntseq.c: In function ‘bns_restore_core’:

bntseq.c:103:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]

bntseq.c:111:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]

bntseq.c:119:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]

bntseq.c:128:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]

bntseq.c:134:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]

gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS cs2nt.c -o cs2nt.ol

gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS kstring.c -o kstring.ol

gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS utils.c -o utils.ol

gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS bamlite.c -o bamlite.ol

gcc -c -fPIC -Wall -O3 -m64 -DHAVE_PTHREAD -DBWT_ENABLE_MMAP -DBWT_EXPORT_LIBRARY_FUNCTIONS bwamisc.c -o bwamisc.ol

gcc -shared bwtaln.ol bwtgap.ol bwt.ol bwape.ol bwase.ol stdaln.ol bwtio.ol bwaseqio.ol bntseq.ol cs2nt.ol kstring.ol utils.ol bamlite.ol bwamisc.ol -lz -o /tmp/pip_build_ubuntu/seal/build/lib/bl/lib/seq/aligner/bwa/libbwa.so

make: Leaving directory `/tmp/pip_build_ubuntu/seal/bl/lib/seq/aligner/bwa/libbwa'

Buildfile: /tmp/pip_build_ubuntu/seal/build.xml

 [echo] debug.build: false

version_check:

find_hadoop:

BUILD FAILED

/tmp/pip_build_ubuntu/seal/build.xml:71: exec returned: 1

Total time: 1 second

error: Could not build Java components

Cleaning up... Command /usr/local/anaconda/bin/python -c "import setuptools;file='/tmp/pip_build_ubuntu/seal/setup.py';exec(compile(open(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /tmp/pip-cT_e4o-record/install-record.txt --single-version-externally-managed failed with error code 1 in /tmp/pip_build_ubuntu/seal Traceback (most recent call last): File "/usr/local/anaconda/bin/pip", line 6, in sys.exit(main()) File "/usr/local/anaconda/lib/python2.7/site-packages/pip/init.py", line 161, in main return command.main(args[1:], options) File "/usr/local/anaconda/lib/python2.7/site-packages/pip/basecommand.py", line 169, in main text = '\n'.join(complete_log) UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 25: ordinal not in range(128)

Fatal error: local() encountered an error (return code 1) while executing 'export JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64 && /usr/local/anaconda/bin/pip install --pre seal'

Aborting. [localhost] Executing task 'install_custom' [localhost] local: cat /etc/*release | grep DISTRIB_CODENAME | cut -f 2 -d = [localhost] local: echo $HOME [localhost] local: uname -m [localhost] local: /usr/local/anaconda/bin/python -c 'import bl.mr.seq.seqal' [localhost] local: /usr/local/anaconda/bin/python -c 'import pydoop' [localhost] local: export JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64 && /usr/local/anaconda/bin/pip install --pre seal

ii hadoop-0.20 0.20.2+923.479-1~maverick-cdh3 all A software platform for processing vast amounts of data ii hadoop-0.20-pipes 0.20.2+923.479-1~maverick-cdh3 amd64 Interface to author Hadoop MapReduce jobs in C++ ii hadoop-0.20-source 0.20.2+923.479-1~maverick-cdh3 all Source code for Hadoop ii hadoop-hive 0.7.1+42.61-2~maverick-cdh3 all A data warehouse infrastructure built on top of Hadoop ii hadoop-pig 0.8.1+28.47-1~maverick-cdh3 all A platform for analyzing large data sets using Hadoop ii libhdfs0 0.20.2+923.479-1~maverick-cdh3 amd64 JNI Bindings to access Hadoop HDFS from C

andersje commented 11 years ago

If it helps, I can get you an account on this particular machine, and you can try building it there yourself...just email me your public key :)

chapmanb commented 11 years ago

Resolved (well, sort of) offline. It turns out to have something to do with caching on environmental variables dealing with Hadoop. We could not identify the exact problem but decided it was suitably niche.

brainstorm commented 11 years ago

@ilveroluca @crs4 might be interested in this bug report...