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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
MIT License
1.65k stars 3.29k forks source link

bootstrap & circleci not working (macOS/docker) #12773

Open hepcat72 opened 5 years ago

hepcat72 commented 5 years ago

I don't know if this is just me and others on mac can do this successfully, or if no one is trying this on macOS and it's just broken, but while conda build recipes/anise_basil and the remote circleci builds for linux and macOS all work, I cannot get circleci build or the bootstrap method to work locally.

The bootstrap method issues the following error (everything up to the error looks correct/normal).

12:59:17 BIOCONDA ERROR BUILD FAILED: the built package /tmp/miniconda/miniconda/conda-bld/osx-64/anise_basil-1.2.0-py27h38e7a2c_0.tar.bz2 cannot be found
12:59:18 BIOCONDA ERROR BUILD SUMMARY: of 1 recipes, 1 failed and 0 were skipped. Details of recipes and environments follow.
12:59:18 BIOCONDA ERROR BUILD SUMMARY: FAILED recipe recipes/anise_basil

The circleci build shows:

Docker image digest: sha256:7b3f88035e74739f72373aff135919f3a42cf59006b2832ec6293afdf727c5c1
====>> Spin up Environment
Build-agent version 0.1.1250-22bf9f5d (2018-12-12T11:32:15+0000)
Starting container bioconda/bioconda-utils-build-env
  using image bioconda/bioconda-utils-build-env@sha256:fdcde89ed9712456a7d23de8ef4282d74b47bde72ce3eb255d09994e8fa98721

Using build environment variables:
  BASH_ENV=/tmp/.bash_env-localbuild-1545324987
  CI=true
  CIRCLECI=true
  CIRCLE_BRANCH=basil
  CIRCLE_BUILD_NUM=
  CIRCLE_JOB=build
  CIRCLE_NODE_INDEX=0
  CIRCLE_NODE_TOTAL=1
  CIRCLE_REPOSITORY_URL=https://github.com/hepcat72/bioconda-recipes.git
  CIRCLE_SHA1=8a87ff3aba9e340a46f19bda9a97c402daf63b53
  CIRCLE_SHELL_ENV=/tmp/.bash_env-localbuild-1545324987
  CIRCLE_WORKING_DIRECTORY=~/project

====>> Checkout code
  #!/bin/bash -eo pipefail
mkdir -p /root/project && cp -r /tmp/_circleci_local_build_repo/. /root/project
====>> Setup ssh
  #!/bin/bash -eo pipefail
mkdir -p ~/.ssh
ssh-keyscan -H github.com >> ~/.ssh/known_hosts

# github.com SSH-2.0-babeld-f43b814b
====>> echo ". /opt/conda/etc/profile.d/conda.sh" >> $BASH_ENV
  #!/bin/bash -eo pipefail
echo ". /opt/conda/etc/profile.d/conda.sh" >> $BASH_ENV
====>> echo "conda activate" >> $BASH_ENV
  #!/bin/bash -eo pipefail
echo "conda activate" >> $BASH_ENV
====>> Download common definitions
  #!/bin/bash -eo pipefail
curl -s https://raw.githubusercontent.com/bioconda/bioconda-common/master/common.sh > .circleci/common.sh

====>> Setup bioconda-utils
  #!/bin/bash -eo pipefail
.circleci/setup.sh
remote: Enumerating objects: 118, done.        
remote: Counting objects: 100% (118/118), done.        
remote: Compressing objects: 100% (14/14), done.        
remote: Total 193 (delta 105), reused 112 (delta 103), pack-reused 75        
Receiving objects: 100% (193/193), 566.09 KiB | 14.15 MiB/s, done.
Resolving deltas: 100% (107/107), completed with 36 local objects.
From https://github.com/bioconda/bioconda-recipes
 * [new branch]          master     -> __upstream__d3SW0W1GU9/master
bioconda-utils is /opt/conda/bin/bioconda-utils
====>> Linting
  #!/bin/bash -eo pipefail
bioconda-utils lint recipes config.yml \
--loglevel debug --full-report \
--git-range master HEAD

16:57:10 BIOCONDA INFO Recipes newly unblacklisted:

16:57:10 BIOCONDA INFO Recipes to consider according to git: 
recipes/anise_basil
 recipes/anise_basil
16:57:10 BIOCONDA DEBUG get_recipes(recipes, package='['*']'): *
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16:57:10 BIOCONDA DEBUG blacklisted: recipes/flexbar/3.3.0
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16:57:10 BIOCONDA INFO Recipes to lint:
recipes/anise_basil
Setting build platform. This is only useful when pretending to be on another platform, such as for rendering necessary dependencies on a non-native platform. I trust that you know what you're doing.
No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.11
Adding in variants from internal_defaults
Adding in variants from /opt/conda/conda_build_config.yaml
Adding in variants from /opt/conda/lib/python3.6/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml
16:57:10 BIOCONDA DEBUG lint recipes/anise_basil
Downloading: 100% 9/9 [00:04<00:00,  2.24files/s]
Downloading: 100% 9/9 [00:03<00:00,  1.74files/s]
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====>> Testingh: 443kB [00:00, 688MB/s]s]s]
  #!/bin/bash -eo pipefail0:01, 5.59MB/s]/s]
bioconda-utils build recipes config.yml \s]
--git-range master HEAD0:00, 29.8MB/s]/s]/s]
conda-forge/osx: 5.05MB [00:00, 24.0MB/s]
16:57:28 BIOCONDA INFO Recipes newly unblacklisted:

16:57:28 BIOCONDA INFO Recipes modified according to git: anise_basil
16:57:28 BIOCONDA INFO blacklist: abyss/1.5.2, abyss/1.9.0, aenum, amos, amptk, ant, antarna, antismash, arvados-cli, azure-cli, bcbio-rnaseq, bellmans-gapc, bio-vcf, bioconductor-atlasrdf, bioconductor-camera, bioconductor-cosmiq, bioconductor-edger/3.12.1, bioconductor-faahko, bioconductor-flagme, bioconductor-ggbio/1.22.0, bioconductor-ipo, bioconductor-jaspar2018, bioconductor-jmosaics, bioconductor-lobstahs, bioconductor-masigpro/1.49.4, bioconductor-meshsim, bioconductor-metab, bioconductor-metams, bioconductor-mmdiff, bioconductor-mmnet, bioconductor-msmseda, bioconductor-msnbase, bioconductor-msnid, bioconductor-mspurity, bioconductor-mvgst, bioconductor-mzr, bioconductor-org.dm.eg.db/3.3.0, bioconductor-pbase, bioconductor-profia, bioconductor-proloc, bioconductor-prolocgui, bioconductor-proteomicsannotationhubdata, bioconductor-rcytoscape, bioconductor-risa, bioconductor-simat, bioconductor-synapter, bioconductor-xcms, bioconductor-yamss, biomaj, blast-legacy/2.2.22, blast/2.2.21, bowtie/1.0.0, bpipe, brass, bucketcache, bumbershoot, bwa/0.6.2, c-ares, cansnper, canvas, cap-mirseq, carna, cas-offinder, cassiopee, cgat-scripts, check-sort-order, circos-tools, cmfinder, cmfinder/0.2, cmv, cortex_con, cosi2, cufflinks, customprodb, denovogear, desman, dialign-tx, dimspy, dimspy/1.0.0, dimspy/1.1.0, dimspy/1.2.0, disco/1.2, discovar-denovo, domclust, dreamtools, dsk, e-pcr, edlib, effectivet3, emperor, erds, esimsa, expansionhunter, export2graphlan, fastme, fastspar, fastuniq, fermikit, fgap, fiji/20151222, flexbar/3.3.0, flock, footprint, frc, frogs, fseq, funcannot, fwdpp, fwdpp/0.5.3, fwdpp/0.5.4, fwdpy11, gap2seq, garnet, gclib, genblasta, genepender, genepop, genomebaser, genometester4, genometools, genometools-genometools/1.5.10-nocairo, gffcompare, gfinisher, gfold, ghc/6.8.3, ghmm, ghostx, ghostz, gnu-getopt, guidescan, hap.py, hivtrace, hubward, hurry.filesize, icqsol, idba, ig-checkfcs, igblast/1.4.0, igvtools, illuminate, imfusion/0.3.0, 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osra/2.1.0, panoct, pantools, parafly, pash, pbdagcon, percolator, perl-bio-db-sam, perl-biox-workflow-command, perl-btlib/0.19, perl-dbm-deep, perl-estscan1/1.3, perl-estscan2/2.1, perl-file-homedir, perl-hpc-runner-command-plugin-logger-sqlite/0.0.3, perl-hpc-runner-command/3.2.13, perl-locale-maketext-simple/0.21, perl-mixin-linewise, perl-mldbm-sync, perl-module-fromperlver/0.008002, perl-moosex-app/1.39, perl-pcap, perl-pod-checker/1.60, perl-pod-coverage-trustpod/0.100003, perl-pod-elemental, perl-set-intervaltree, perl-sql-statement, perl-statistics-ttest, perl-symbol-util/0.0203, perl-text-ansitable/0.48, phipack, phylotoast, picard/1.97, piler, pizzly, pkiss, plastid, plink2, polymutt, popt, poretools/0.5.1, portcullis/1.1.0, portcullis/1.1.1, pout2mzid, primerprospector, prinseq, proot, prophyle/0.2.1, prosic, pycoqc, pyfasta, pygresql, pysftp, pytest-marks, pytest-timeout, python-levenshtein, pyvcf, pyvcf/0.6.7, qcumber, qiime/1.9.1, r-DGEclustering, r-ampvis, r-annotables, r-argumentcheck, r-asics, r-basejump, r-bcbiobase, r-bcbiornaseq, r-bio3d, r-biodb, r-biom, r-biomark, r-boutroslabplottinggeneral, r-chbutils, r-cimpl, r-cnogpro, r-data.table/1.10.4, r-dbchip, r-deoptimr, r-diptest, r-diptest/0.75_7, r-dpeak, r-drc, r-dynamictreecut, r-gam, r-gbm, r-genabel, r-genabel.data, r-genenet, r-genometricorr, r-george, r-giant, r-gprofiler, r-gpseq, r-grimport, r-gsalib, r-gsmoothr, r-haplo.stats, r-histonehmm, r-ic10trainingdata, r-ichorcna, r-icluster, r-idr, r-inlinedocs, r-intego, r-km.ci, r-kmsurv, r-kriging, r-lme4qtl, r-lsd, r-maldiquant, r-matrixeqtl, r-metarnaseq, r-microseq, r-mixomics, r-mlgt, r-mmgenome, r-mqtl, r-msqrob, r-nastiseq, r-ncbit, r-ngsplot, r-ngsplot-hg19, r-ngsplot-hg38, r-ngsplot-mm10, r-pamr, r-patpro, r-peer, r-phangorn, r-phewas, r-pinfsc50, r-plasmidprofiler, r-pore, r-precrec, r-prestor, r-probmetab, r-propcis, r-pscbs/0.61.0, r-purbayes, r-qiimer, r-qorts, r-qtl, r-quorts, r-rBLAST, r-raceid3, r-rcircos, r-readbrukerflexdata, r-readmzxmldata, r-rematch2, r-rentrez, r-robustrankaggreg, r-rphylip, r-rubic, r-scimpute, r-seqinr, r-smvar, r-snpassoc, r-soap-nmr, r-solarius, r-spieceasi, r-tfmpvalue, r-wasabi, r-workflowscriptscommon, r-xmlrpc, r-xnomial, r-zerone, ra-integrate, rdflib-jsonld, rdkit/2015.09.2, rdkit/2016.03.3, rdock, reago, real, regex, relocate2, relocate2/2.0.1, remurna, rmap, rnabob, rnaclust, rnashapes/3.3.0, saffrontree, sam, samtools/0.1.19, samtools/1.1, scikit-bio, searchgui/3.2.20, secimtools, semeta, sff2fastq, shiver, shorah, short-read-connector, sistr_cmd, slclust, sloika, smalt, smashbenchmarking, smina, smoove, snap, snippy/3.0, snpomatic, snvphyl-tools, soapaligner, soapcoverage, soapdenovo2, soapdenovo2-gapcloser, somatic-sniper, spanki, spectral_hk, spingo, sprai, sprinkles, sqlitebrowser, swiftlink, tablet, talloc, tedna, tpp, transcomb, transtermhp, trimmomatic/0.35, vcftools/0.1.10, vcftools/0.1.11, visceral-evaluatesegmentation, vnl, wgs-assembler, xcftools, xdg
16:57:28 BIOCONDA INFO Generating DAG
16:57:28 BIOCONDA INFO Inspected 0 of 1 recipes
16:57:28 BIOCONDA INFO Building and testing 1 recipes in total
16:57:28 BIOCONDA INFO Recipes to build: 
anise_basil
16:57:28 BIOCONDA INFO Building and testing subdag 1 of 1 (1 recipes)
16:57:28 BIOCONDA INFO Determining expected packages
Setting build platform. This is only useful when pretending to be on another platform, such as for rendering necessary dependencies on a non-native platform. I trust that you know what you're doing.
No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.11
Adding in variants from internal_defaults
Adding in variants from /opt/conda/conda_build_config.yaml
Adding in variants from /opt/conda/lib/python3.6/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml
Downloading: 100% 9/9 [00:03<00:00,  2.25files/s]
Attempting to finalize metadata for anise_basil
Solving environment: ...working... doneB/s]
Solving environment: ...working... done]/s]]
Solving environment: ...working... done]/s]
Solving environment: ...working... done]/s]
Solving environment: ...working... done
Downloading: 100% 9/9 [00:04<00:00,  1.61files/s]
16:58:24 BIOCONDA INFO BUILD START recipes/anise_basil
.17:00:07 BIOCONDA ERROR COMMAND FAILED: /opt/conda/bin/conda build --no-anaconda-upload --channel conda-forge --channel bioconda --channel defaults -e /opt/conda/conda_build_config.yaml -m /opt/conda/lib/python3.6/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml recipes/anise_basil/meta.yaml
17:00:07 BIOCONDA ERROR STDOUT+STDERR:s]/s]
No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.11
WARNING:conda_build.metadata:No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.11
Adding in variants from internal_defaults
INFO:conda_build.variants:Adding in variants from internal_defaults
Adding in variants from /opt/conda/conda_build_config.yaml
INFO:conda_build.variants:Adding in variants from /opt/conda/conda_build_config.yaml
Adding in variants from /opt/conda/lib/python3.6/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml
INFO:conda_build.variants:Adding in variants from /opt/conda/lib/python3.6/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml
Attempting to finalize metadata for anise_basil
INFO:conda_build.metadata:Attempting to finalize metadata for anise_basil
Solving environment: ...working... done
Solving environment: ...working... done
Solving environment: ...working... done
BUILD START: ['anise_basil-1.2.0-py36h38e7a2c_0.tar.bz2']
Solving environment: ...working... done

## Package Plan ##

  environment location: /opt/conda/conda-bld/anise_basil_1545325104934/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p

The following NEW packages will be INSTALLED:

    blas:            1.0-mkl               conda-forge
    boost:           1.68.0-py36h3e44d54_1 conda-forge
    boost-cpp:       1.68.0-h3a22d5f_0     conda-forge
    bzip2:           1.0.6-h470a237_2      conda-forge
    ca-certificates: 2018.11.29-ha4d7672_0 conda-forge
    certifi:         2018.11.29-py36_1000  conda-forge
    icu:             58.2-hfc679d8_0       conda-forge
    intel-openmp:    2019.1-144            defaults   
    libffi:          3.2.1-hfc679d8_5      conda-forge
    libgcc-ng:       7.2.0-hdf63c60_3      conda-forge
    libgfortran-ng:  7.2.0-hdf63c60_3      conda-forge
    libstdcxx-ng:    7.2.0-hdf63c60_3      conda-forge
    mkl:             2018.0.3-1            defaults   
    mkl_fft:         1.0.10-py36_0         conda-forge
    mkl_random:      1.0.2-py36_0          conda-forge
    ncurses:         6.1-hfc679d8_2        conda-forge
    numpy:           1.15.0-py36h1b885b7_0 defaults   
    numpy-base:      1.15.0-py36h3dfced4_0 defaults   
    openssl:         1.0.2p-h470a237_1     conda-forge
    pip:             18.1-py36_1000        conda-forge
    python:          3.6.7-h5001a0f_1      conda-forge
    readline:        7.0-haf1bffa_1        conda-forge
    setuptools:      40.6.3-py36_0         conda-forge
    sqlite:          3.26.0-hb1c47c0_0     conda-forge
    tk:              8.6.9-ha92aebf_0      conda-forge
    wheel:           0.32.3-py36_0         conda-forge
    xz:              5.2.4-h470a237_1      conda-forge
    zlib:            1.2.11-h470a237_3     conda-forge

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Solving environment: ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /opt/conda/conda-bld/anise_basil_1545325104934/_build_env

The following NEW packages will be INSTALLED:

    bzip2:                  1.0.6-h470a237_2        conda-forge
    ca-certificates:        2018.11.29-ha4d7672_0   conda-forge
    cmake:                  3.13.1-h011004d_0       conda-forge
    curl:                   7.63.0-h74213dd_0       conda-forge
    expat:                  2.2.5-hfc679d8_2        conda-forge
    krb5:                   1.16.2-hbb41f41_0       conda-forge
    libcurl:                7.63.0-hbdb9355_0       conda-forge
    libedit:                3.1.20170329-haf1bffa_1 conda-forge
    libgcc-ng:              7.2.0-hdf63c60_3        conda-forge
    libssh2:                1.8.0-h5b517e9_3        conda-forge
    libstdcxx-ng:           7.2.0-hdf63c60_3        conda-forge
    libuv:                  1.24.1-h470a237_0       conda-forge
    make:                   4.2.1-h470a237_1002     conda-forge
    ncurses:                6.1-hfc679d8_2          conda-forge
    openssl:                1.0.2p-h470a237_1       conda-forge
    rhash:                  1.3.6-h470a237_1        conda-forge
    tk:                     8.6.9-ha92aebf_0        conda-forge
    toolchain:              2.3.0-0                 conda-forge
    toolchain_c_linux-64:   2.3.0-0                 conda-forge
    toolchain_cxx_linux-64: 2.3.0-0                 conda-forge
    xz:                     5.2.4-h470a237_1        conda-forge
    zlib:                   1.2.11-h470a237_3       conda-forge

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
CMake Error at /opt/conda/conda-bld/anise_basil_1545325104934/_build_env/share/cmake-3.13/Modules/CMakeDetermineCCompiler.cmake:48 (message):
  Could not find compiler set in environment variable CC:

  gcc.
Call Stack (most recent call first):
  CMakeLists.txt:2 (project)

CMake Error: CMAKE_C_COMPILER not set, after EnableLanguage
CMake Error: CMAKE_CXX_COMPILER not set, after EnableLanguage
-- Configuring incomplete, errors occurred!
See also "/opt/conda/conda-bld/anise_basil_1545325104934/work/build/CMakeFiles/CMakeOutput.log".
Source cache directory is: /opt/conda/conda-bld/src_cache
Downloading source to cache: 8785a8ccaca992fa9b3baf21e837e888d696a219_bb1606b652.tar.gz
Downloading https://github.com/holtgrewe/lemon-mirror/archive/8785a8ccaca992fa9b3baf21e837e888d696a219.tar.gz
Success
Extracting download
Source cache directory is: /opt/conda/conda-bld/src_cache
Downloading source to cache: seqan-v2.0.1_b0eb92aee2.tar.gz
Downloading https://github.com/seqan/seqan/archive/seqan-v2.0.1.tar.gz
Success
Extracting download
Source cache directory is: /opt/conda/conda-bld/src_cache
Downloading source to cache: v1.2.0_05e727da4b.tar.gz
Downloading https://github.com/seqan/anise_basil/archive/v1.2.0.tar.gz
Success
Extracting download
source tree in: /opt/conda/conda-bld/anise_basil_1545325104934/work
Traceback (most recent call last):
  File "/opt/conda/bin/conda-build", line 11, in <module>
    sys.exit(main())
  File "/opt/conda/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 438, in main
    execute(sys.argv[1:])
  File "/opt/conda/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 429, in execute
    verify=args.verify)
  File "/opt/conda/lib/python3.6/site-packages/conda_build/api.py", line 201, in build
    notest=notest, need_source_download=need_source_download, variants=variants)
  File "/opt/conda/lib/python3.6/site-packages/conda_build/build.py", line 2204, in build_tree
    notest=notest,
  File "/opt/conda/lib/python3.6/site-packages/conda_build/build.py", line 1445, in build
    utils.check_call_env(cmd, env=env, cwd=src_dir, stats=build_stats)
  File "/opt/conda/lib/python3.6/site-packages/conda_build/utils.py", line 313, in check_call_env
    return _func_defaulting_env_to_os_environ('call', *popenargs, **kwargs)
  File "/opt/conda/lib/python3.6/site-packages/conda_build/utils.py", line 293, in _func_defaulting_env_to_os_environ
    raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-e', '/opt/conda/conda-bld/anise_basil_1545325104934/work/conda_build.sh']' returned non-zero exit status 1.

17:00:07 BIOCONDA ERROR BUILD FAILED recipes/anise_basil
17:00:09 BIOCONDA ERROR BUILD SUMMARY: of 1 recipes, 1 failed and 0 were skipped. Details of recipes and environments follow.
17:00:09 BIOCONDA ERROR BUILD SUMMARY: FAILED recipe recipes/anise_basil
Error: Exited with code 1
Step failed
Error: runner failed
{"Runner":true,"level":"error","msg":"runner failed","task-id":"localbuild-1545324987","time":"2018-12-20T17:00:10Z"}
Task failed
Error: job failed

I've tried a number of things, including...

docker pull bioconda/bioconda-utils-build-env circleci update check - already up to date conda update conda-build

I've also been contemplating a macOS update to mojave. Currently on 10.13.6. Is anyone else having this problem?

bgruening commented 5 years ago

ping @bioconda/osx

gkarthik commented 5 years ago

Based on the log I think this is a duplicate of #12755. Could you try adding conda_build_config.yaml? More details in #12755.

CMake Error at /opt/conda/conda-bld/anise_basil_1545325104934/_build_env/share/cmake-3.13/Modules/CMakeDetermineCCompiler.cmake:48 (message):
  Could not find compiler set in environment variable CC:
hepcat72 commented 5 years ago

OK. I'm a noob. Where do I get that file (conda_build_config.yaml) from and where do I add (/put) it? (or can you point me to documentation that answers those questions?)

hepcat72 commented 5 years ago

Based on reading about conda_build_config.yaml here:

by installing their conda-forge-pinning conda package in our build environment [...] that package unpacks the config YAML into our conda environment so that it can be used for building all recipes.

I tried:

conda install conda-forge-pinning

I then edited meta.yaml to increment the build number and ran circleci build.

Same result:

CMake Error at /opt/conda/conda-bld/anise_basil_1546897584819/_build_env/share/cmake-3.13/Modules/CMakeDetermineCCompiler.cmake:48 (message):
  Could not find compiler set in environment variable CC:

  gcc.
Call Stack (most recent call first):
  CMakeLists.txt:2 (project)

CMake Error: CMAKE_C_COMPILER not set, after EnableLanguage
CMake Error: CMAKE_CXX_COMPILER not set, after EnableLanguage
-- Configuring incomplete, errors occurred!
See also "/opt/conda/conda-bld/anise_basil_1546897584819/work/build/CMakeFiles/CMakeOutput.log".
Source cache directory is: /opt/conda/conda-bld/src_cache
Downloading source to cache: 8785a8ccaca992fa9b3baf21e837e888d696a219_bb1606b652.tar.gz
Downloading https://github.com/holtgrewe/lemon-mirror/archive/8785a8ccaca992fa9b3baf21e837e888d696a219.tar.gz
Success
Extracting download
Source cache directory is: /opt/conda/conda-bld/src_cache
Downloading source to cache: seqan-v2.0.1_b0eb92aee2.tar.gz
Downloading https://github.com/seqan/seqan/archive/seqan-v2.0.1.tar.gz
Success
Extracting download
Source cache directory is: /opt/conda/conda-bld/src_cache
Downloading source to cache: v1.2.0_05e727da4b.tar.gz
Downloading https://github.com/seqan/anise_basil/archive/v1.2.0.tar.gz
Success
Extracting download
source tree in: /opt/conda/conda-bld/anise_basil_1546897584819/work
Traceback (most recent call last):
  File "/opt/conda/bin/conda-build", line 11, in <module>
    sys.exit(main())
  File "/opt/conda/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 438, in main
    execute(sys.argv[1:])
  File "/opt/conda/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 429, in execute
    verify=args.verify)
  File "/opt/conda/lib/python3.6/site-packages/conda_build/api.py", line 201, in build
    notest=notest, need_source_download=need_source_download, variants=variants)
  File "/opt/conda/lib/python3.6/site-packages/conda_build/build.py", line 2204, in build_tree
    notest=notest,
  File "/opt/conda/lib/python3.6/site-packages/conda_build/build.py", line 1445, in build
    utils.check_call_env(cmd, env=env, cwd=src_dir, stats=build_stats)
  File "/opt/conda/lib/python3.6/site-packages/conda_build/utils.py", line 313, in check_call_env
    return _func_defaulting_env_to_os_environ('call', *popenargs, **kwargs)
  File "/opt/conda/lib/python3.6/site-packages/conda_build/utils.py", line 293, in _func_defaulting_env_to_os_environ
    raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-e', '/opt/conda/conda-bld/anise_basil_1546897584819/work/conda_build.sh']' returned non-zero exit status 1.

21:48:33 BIOCONDA ERROR BUILD FAILED recipes/anise_basil
21:48:36 BIOCONDA ERROR BUILD SUMMARY: of 1 recipes, 1 failed and 0 were skipped. Details of recipes and environments follow.
21:48:36 BIOCONDA ERROR BUILD SUMMARY: FAILED recipe recipes/anise_basil
Error: Exited with code 1
Step failed
Error: runner failed
{"Runner":true,"level":"error","msg":"runner failed","task-id":"localbuild-1546897436","time":"2019-01-07T21:48:37Z"}
Task failed
Error: job failed
hepcat72 commented 5 years ago

I also tried obtaining a copy of this file and putting it in recipes/anise_basil.

Still got the same error.