Bulk

build-fail-blacklist

@@ -94,6 +94,26 @@ recipes/stringtie/1.2.2
 recipes/stringtie/1.2.4
 recipes/stringtie/1.3.0
 recipes/stringtie/1.3.3
+recipes/art/3.11.14
+recipes/bcbiogff/0.6.2
+recipes/biopet/0.8.0
+recipes/metfrag/2.3.1
+recipes/metfrag/2.4.2
+recipes/varscan/2.4.2
+recipes/bbmap/37.10
+recipes/bbmap/37.17
+recipes/bbmap/37.52
+recipes/bbmap/37.99
+recipes/gatk4/4.0.3.0
+recipes/mira/3.4.1.1
+recipes/mira/4.9.5
+recipes/mira/4.9.6
+recipes/ngmlr/0.2.3
+recipes/ngmlr/0.2.4
+recipes/rnastructure/5.7
+recipes/rnastructure/6.0
+recipes/snpeff/4.1l
+recipes/snpeff/4.2
 
 # stl_algobase.h:548:18: error: cannot bind non-const lvalue reference of type 'HitSink::batch&' to an rvalue of type 'std::remove_reference<HitSink::batch&>::type {aka HitSink::batch}'
 recipes/bowtie
@@ -116,6 +136,10 @@ recipes/smina
 recipes/cmv
 recipes/fwdpp
 recipes/parafly
+recipes/rdflib-jsonld
+recipes/smashbenchmarking
+recipes/saffrontree
+recipes/slclust
 
 # tracking master branch
 recipes/frc
@@ -253,6 +277,15 @@ recipes/tablet
 
 # RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml  url=https://pypi.org/simple/funcsigs/
 recipes/pytest-marks
+recipes/hivtrace
+recipes/imfusion/0.3.0
+recipes/imfusion/0.3.2
+recipes/poretools/0.5.1
+recipes/hubward
+recipes/pasta/1.7.8
+recipes/pasta/0.2
+recipes/nucleoatac/0.3.1
+recipes/phylotoast
 
 # git checkout problem
 recipes/pbdagcon
@@ -265,9 +298,6 @@ recipes/ms
 # GL missing, needs the extended base image
 recipes/emperor
 
-# RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml  url=https://pypi.org/simple/HyPhy/
-recipes/hivtrace
-
 # sed: can't read /opt/conda/conda-bld/idba_1530055808563/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin/aclocal: No such file or directory
 recipes/idba
 
@@ -292,30 +322,12 @@ recipes/metavelvet-sl-pipeline
 # CMake Error: CMAKE_C_COMPILER not set, after EnableLanguage
 recipes/openbabel/2.3.2
 
-# RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml  url=https://files.pythonhosted.org/packages/source/c/certifi/certifi-2016.9.26.tar.gz#md5=baa81e951a29958563689d868ef1064d
-recipes/imfusion/0.3.0
-recipes/imfusion/0.3.2
-recipes/poretools/0.5.1
-
-# RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml  url=https://pypi.org/simple/pyaml/#
-recipes/hubward
-
-# RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml  url=https://files.pythonhosted.org/packages/source/c/certifi/certifi-2016.9.26.tar.gz#md5=baa81e951a29958563689d868ef1064d
-recipes/pasta/1.7.8
-recipes/pasta/0.2
-
 # Conflicting numpy and qiime
 recipes/koeken
 
-# RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml  url=https://files.pythonhosted.org/packages/source/c/certifi/certifi-2016.9.26.tar.gz#md5=baa81e951a29958563689d868ef1064d
-recipes/nucleoatac/0.3.1
-
 # no clue currently
 recipes/hap.py
 
-# RuntimeError: Setuptools downloading is disabled in conda build. Be sure to add all dependencies in the meta.yaml  url=https://pypi.org/simple/click/
-recipes/phylotoast
-
 # takes hours to build
 recipes/plastid
 
@@ -331,6 +343,10 @@ recipes/intemap
 # zlib missing
 recipes/polymutt
 recipes/prophyle/0.2.1
+recipes/trimmomatic/0.35
+recipes/megahit
+recipes/dsk
+recipes/lofreq
 
 # /opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-redhat-linux/4.8.2/ld: cannot find -lc
 recipes/piler
@@ -356,17 +372,9 @@ recipes/pizzly
 # compiles its own zlib
 recipes/plink2
 
-# Unknown problems
-recipes/rdflib-jsonld
-recipes/smashbenchmarking
-
 # natsort conflicts with python
 recipes/qcumber
 
-# Unknown issues
-recipes/saffrontree
-recipes/slclust
-
 # ModuleNotFoundError: No module named 'fasta', note that the project is deprecated in favor of pyfaidx
 recipes/pyfasta
 
@@ -376,9 +384,6 @@ recipes/spanki
 # perl issues
 recipes/vcftools/0.1.11
 
-# zlib
-recipes/trimmomatic/0.35
-
 # broken pipe
 recipes/antarna
 
@@ -397,9 +402,6 @@ recipes/ngseqbasic
 recipes/footprint
 recipes/mirdeep2/2.0.0.8
 
-# zlib
-recipes/megahit
-
 # missing bioc package
 recipes/customprodb
 
@@ -450,9 +452,6 @@ recipes/bumbershoot
 # /opt/conda/conda-bld/phipack_1530829563675/work/conda_build.sh: line 139: cd: src/: No such file or directory
 recipes/phipack
 
-# zlib
-recipes/dsk
-
 # perl
 recipes/vcftools/0.1.10
 
@@ -462,9 +461,6 @@ recipes/prinseq
 # checking whether the C compiler works... no
 recipes/fastme
 
-# but ['zlib'] not in reqs/run, i.e. it is overlinked (likely) or a missing dependency (less likely)
-recipes/lofreq
-
 # perl script could not be found
 recipes/rnaclust
 
@@ -764,30 +760,8 @@ recipes/bioconductor-subcellbarcode
 recipes/bioconductor-gladiatox
 recipes/bioconductor-biocgenerics
 
-# Build and rendering failures that are breaking bulk and the nightly uploads
-recipes/sqt
-recipes/tepid
-recipes/aragorn/1.2.38
-recipes/art/3.11.14
-recipes/autodock-vina
-recipes/bcbiogff/0.6.2
-recipes/bcbiogff
-recipes/biopet/0.8.0
-recipes/biopet
-recipes/blockbuster
-recipes/metfrag
-recipes/metfrag/2.3.1
-recipes/metfrag/2.4.2
-recipes/varscan/2.4.2
+# Source seems to have moved
 recipes/discovar
-recipes/ccat/3.0
-recipes/transabyss
-recipes/soapdenovo2-prepare
-recipes/damidseq_pipeline
-recipes/repeatmodeler
-recipes/detonate
-recipes/pal_finder
-recipes/dfam
 
 # ld: unknown option: -T
 recipes/bioconductor-lpsymphony
@@ -846,90 +820,8 @@ recipes/bioconductor-nanotubes
 recipes/bioconductor-msqc1
 recipes/bioconductor-clumsiddata
 
-# Rendering errors that are breaking bulk and the nightly upload
-recipes/adam
-recipes/albatradis
-recipes/anise_basil
-recipes/bamclipper
-recipes/bbmap/37.10
-recipes/bbmap/37.17
-recipes/bbmap/37.52
-recipes/bbmap/37.62
-recipes/bbmap/37.99
-recipes/bcftools-snvphyl-plugin
-recipes/biotradis
-recipes/bsmap
-recipes/cannoli
-recipes/cgview
-recipes/crisper_recognition_tool
-recipes/Drop-seq_tools
-recipes/dsh-bio
-recipes/dwgsim
-recipes/dxua
-recipes/fastindep
-recipes/fgbio
-recipes/gatk4/4.0.3.0
-recipes/gatk-framework
-recipes/gb_taxonomy_tools
-recipes/genblastg
-recipes/gromacs/2018
-recipes/hr2
-recipes/indelfixer
-recipes/je-suite
-recipes/mdust
-recipes/metacherchant
-recipes/mgltools
-recipes/mira
-recipes/mira/3.4.1.1
-recipes/mira/4.9.5
-recipes/mira/4.9.6
-recipes/mobster
-recipes/mummer4
-recipes/mvicuna
-recipes/netreg
-recipes/ngmlr/0.2.3
-recipes/ngmlr/0.2.4
-recipes/npinv
-recipes/opsin/1.4.0
-recipes/opsin/2.1.0
-recipes/opsin/2.4.0
-recipes/pathwaymatcher
-recipes/pauda
-recipes/pepnovo
-recipes/pyteomics
-recipes/qorts
-recipes/rabix-bunny
-recipes/ragout
-recipes/rawtools
-recipes/rdp_classifier/2.2
+# Source no longer exists at the URL
 recipes/recon
-recipes/regtools
-recipes/repeatscout
-recipes/rnacode/0.3
-recipes/rna-seqc
-recipes/rnastructure
-recipes/rnastructure/5.7
-recipes/rnastructure/6.0
-recipes/seqbuster
-recipes/seqcluster
-recipes/shorah/1.1.3
-recipes/snpeff/4.1l
-recipes/snpeff/4.2
-recipes/snver
-recipes/soapdenovo2-errorcorrection
-recipes/soapec
-recipes/socru
-recipes/ssake
-recipes/subread
-recipes/tantan
-recipes/tophat-recondition
-recipes/tracer
-recipes/vcfsamplecompare
-recipes/watchdog-wms
-recipes/wdltool
-recipes/womtool
-recipes/xtandem
-recipes/yaha
 
 # Depends on bioconductor-biocgenerics, which can't be built until after R 3.6.1 is released and conda-forge moves its pinnings
 recipes/bioconductor-a4

recipes/Drop-seq_tools/meta.yaml

@@ -2,23 +2,17 @@
 {% set version = "2.0.0" %}
 {% set versiongrep = "2.0.0(1ef3a59_1539205128)" %}
 
-about:
-  home: http://mccarrolllab.com/dropseq/
-  license: MIT License
-  license_family: MIT
-  summary: |
-    Package for the analysis of Drop-seq data developed by Jim Nemesh in the McCarroll Lab
 package:
   name: dropseq_tools
   version: {{ version }}
 
-build:
-  number: 0
-
 source:
   url: https://github.com/broadinstitute/Drop-seq/releases/download/v{{ version }}/{{ name }}-{{ version }}.zip
   md5: 3032444ec1c747181c6e9394d1e2a914
 
+build:
+  number: 0
+
 requirements:
   run:
     - openjdk >=8
@@ -55,6 +49,13 @@ test:
     - 'TrimStartingSequence -- --help 2>&1 | grep "{{ versiongrep }}"'
     - 'ValidateReference -- --help 2>&1 | grep "{{ versiongrep }}"'
 
+about:
+  home: http://mccarrolllab.com/dropseq/
+  license: MIT License
+  license_family: MIT
+  summary: |
+    Package for the analysis of Drop-seq data developed by Jim Nemesh in the McCarroll Lab
+
 extra:
   notes: |
     Drop-seq_tools utilities are wrapper shell scripts. To get help on individual tool, use e.g. `PolyATrimmer -- --help`

recipes/adam/meta.yaml

@@ -1,25 +1,20 @@
 {% set version="0.26.0" %}
 
-about:
-  home: https://github.com/bigdatagenomics/adam
-  license: Apache 2
-  summary: Genomics analysis platform built on Apache Avro, Apache Spark and Parquet
-
 package:
   name: adam
   version: {{ version }}
 
-build:
-  number: 1
-  noarch: generic
-
 source:
   url: https://search.maven.org/remotecontent?filepath=org/bdgenomics/adam/adam-distribution-spark2_2.11/{{ version }}/adam-distribution-spark2_2.11-{{ version }}-bin.tar.gz
   sha256: 17a8a5021ef23db9beea9047d4dba8351bfe9d51f9b332708654fa647a60e64d
   patches:
     - adam-shell.patch
     - adam-submit.patch
 
+build:
+  number: 1
+  noarch: generic
+
 requirements:
   build:
   run:
@@ -30,3 +25,8 @@ test:
   commands:
     - adam-submit --help
     - adam-submit transform --help
+
+about:
+  home: https://github.com/bigdatagenomics/adam
+  license: Apache 2
+  summary: Genomics analysis platform built on Apache Avro, Apache Spark and Parquet