update blacklist from #15196

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,53 @@
+Bioconda Code of Conduct
+========================
+
+- Be respectful
+- Be welcoming
+- Be considerate
+- Focus on what's best for the community
+- Gracefully accept constructive criticism
+- Show courtesy and respect towards other community members
+- Be respectful of different viewpoints and experiences
+- Use welcoming and inclusive language
+
+Reporting an issue
+------------------
+If you see a violation of the code of conduct, please report it to a Bioconda core
+member. You can find core members at
+https://github.com/orgs/bioconda/teams/core/members, and emails on each users'
+GitHub profile page.
+
+Enforcement
+-----------
+Upon receiving a report, the Bioconda core team will meet privately to discuss
+the matter and determine the best course of action.
+
+Possible responses may include:
+
+- taking no further action (if we determine no violation occurred)
+- a private reprimand from the core members to the individual(s) involved. In
+  this case, a core member will deliver that reprimand via email, copying the
+  rest of the core.
+- a public reprimand. In this case a core member will deliver the reprimand via
+  the same channel as the violation occurred (e.g., via comment on PR or issue)
+
+- an imposed vacation (e.g., asking the individual to refrain from participating
+  for a week). A core member will deliver a request for the individual to take
+  such a "vacation" voluntarily, but if they don't disagree then a temporary
+  ban may be imposed.
+
+- a permanent or temporary ban from Bioconda
+
+Once a resolution is agreed upon, but before it is enacted, the core will
+contact the original reporter and discuss the resolution and will note any
+feedback for the record, but is not obligated to act on such feedback.
+
+The core will never publicly discuss the issue; any public statements will be
+made by core members.
+
+If the incident involves a core member, the core member must recuse themselves
+from the response process.
+
+This policy was modified from
+https://www.djangoproject.com/conduct/enforcement-manual, [CCBY
+3.0](https://creativecommons.org/licenses/by/3.0/)

.github/welcome_new_contributor.md

@@ -1,4 +1,4 @@
-Thanks for opening your first pull request! As you're new to bioconda, please read through our [documentation about contributing recipes](https://bioconda.github.io/contributing.html). If you need help, please ping one of the following teams:
+Welcome to Bioconda, @{{user}}! Thank you for opening your first pull request! As you're new to Bioconda, please read through our [documentation about contributing recipes](https://bioconda.github.io/contributing.html). If you need help, please ping one of the following teams:
 
  - `@bioconda/haskel` for Haskell packages
  - `@bioconda/lib` for C/C++ packages
@@ -8,5 +8,9 @@ Thanks for opening your first pull request! As you're new to bioconda, please re
  - `@bioconda/r` for R packages
  - `@bioconda/rust` for Rust packages
  - `@bioconda/core` in other cases
+
+You can also join our [Gitter channel](https://gitter.im/bioconda/Lobby) to find help.
 
-Please ping `@bioconda/core` when your pull request is passing tests and ready to be merged. If you would like to be added to the bioconda team (so you can merge your own pull requests once all tests have passed) please mention that to `@bioconda/core` and they'll happily add you to the bioconda group.
+Please ping `@bioconda/core` when your pull request is passing tests and ready to be merged. 
+
+If you would like to join Bioconda, please mention that to `@bioconda/core` and they will happily send out an invitation link to you!

build-fail-blacklist

@@ -1,3 +1,10 @@
+# ../../utils//fileType/FileRecordTypeChecker.h:120:21: error: 'constexpr' needed for in-class initialization of static data member 'const float FileRecordTypeChecker::PERCENTAGE_PRINTABLE' of non-integral type [-fpermissive]
+recipes/bedtools/2.20.1
+recipes/bedtools/2.19.1
+
+# last-pair-probs.cc:501:10: error: cannot convert 'std::istream {aka std::basic_istream<char>}' to 'bool' in return
+recipes/last/638
+
 # Timeout downloading from sourceforge
 recipes/transcomb
 
@@ -8,7 +15,6 @@ recipes/perl-sub-identify/0.12
 recipes/perl-scalar-list-utils/1.45
 recipes/perl-extutils-constant/0.24
 recipes/seq-seq-pan
-recipes/moods
 recipes/pylibseq
 recipes/metasnv
 recipes/gqt
@@ -159,6 +165,14 @@ recipes/soapaligner
 # missing tarball
 recipes/metagene_annotator
 recipes/sloika
+recipes/genometools
+recipes/nanonet
+recipes/knot
+recipes/moreutils
+recipes/jali
+recipes/intervalstats
+recipes/mrbayes
+recipes/igvtools
 
 # missing dep
 recipes/oligotyping
@@ -200,6 +214,7 @@ recipes/libmuscle
 
 # compilation error
 recipes/osra/2.0.1
+recipes/lightning
 
 # unable to access jarfile
 recipes/effectivet3
@@ -213,9 +228,6 @@ recipes/discovar-denovo
 # seqan errors
 recipes/bowtie/1.0.0
 
-# tarball missing
-recipes/mrbayes
-
 # depends on perl-pcap
 recipes/brass
 
@@ -234,10 +246,6 @@ recipes/qiime/1.9.1
 # requires wgs-assembler, which has a build fail
 recipes/sprai
 
-# missing tarballs
-recipes/genometools
-recipes/nanonet
-
 # missing dependency
 recipes/genomebaser
 recipes/garnet
@@ -320,9 +328,6 @@ recipes/primerprospector
 # missing URL
 recipes/intemap
 
-# compilation error
-recipes/lightning
-
 # zlib missing
 recipes/polymutt
 recipes/prophyle/0.2.1
@@ -495,9 +500,6 @@ recipes/perl-bio-db-sam
 recipes/krona/2.6
 recipes/krona/2.5
 
-# tarball missing
-recipes/igvtools
-
 # /opt/conda/conda-bld/pash_1531691261758/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in `require': cannot load such file -- brl/util/textFileUtil (LoadError)
 recipes/pash
 
@@ -537,26 +539,15 @@ recipes/ghc/6.8.3
 # missing python dep
 recipes/hurry.filesize
 
-# missing tarball
-recipes/knot
-recipes/moreutils
-
 # compilation error, missing boost header
 recipes/k-slam
 
-# missing tarball
-recipes/jali
-recipes/intervalstats
-
 # failing
 recipes/igblast/1.4.0
 
 # missing fortran lib, will fix this upstream
 recipes/ig-checkfcs
 
-# I got far with desmon but not it fails inside Docker with a missing perl module
-recipes/desman
-
 # fortran missing :(
 recipes/fastspar
 
@@ -722,7 +713,6 @@ recipes/bioconductor-org.mm.eg.db/3.3.0
 recipes/bioconductor-qdnaseq.mm10/1.4.0
 recipes/bioconductor-rgraphviz/2.13.0
 recipes/bioconductor-ropls/1.2.14
-recipes/r-seurat/1.4.0.16
 recipes/r-speaq/1.2.1
 recipes/bioconductor-cummerbund/2.8.2
 recipes/bioconductor-cummerbund/2.12.1
@@ -775,23 +765,6 @@ recipes/bioconductor-gladiatox
 recipes/bioconductor-biocgenerics
 
 # Build and rendering failures that are breaking bulk and the nightly uploads
-recipes/samtools/0.1.19
-recipes/samtools/1.1
-recipes/last/490
-recipes/last/638
-recipes/last/874
-recipes/kat/2.0.8
-recipes/gromacs
-recipes/braker
-recipes/bowtie2/2.2.1
-recipes/bowtie2/2.2.4
-recipes/bowtie2/2.2.5
-recipes/bedtools/2.19.1
-recipes/bedtools/2.20.1
-recipes/bedtools/2.22
-recipes/bedtools/2.23.0
-recipes/bcftools
-recipes/bcftools/1.3.1
 recipes/sqt
 recipes/tepid
 recipes/aragorn/1.2.38
@@ -903,10 +876,7 @@ recipes/gromacs/2018
 recipes/hr2
 recipes/indelfixer
 recipes/je-suite
-recipes/mafft/7.305
-recipes/mafft/7.310
 recipes/mdust
-recipes/meme/4.11.2
 recipes/metacherchant
 recipes/mgltools
 recipes/mira
@@ -937,7 +907,6 @@ recipes/regtools
 recipes/repeatscout
 recipes/rnacode/0.3
 recipes/rna-seqc
-recipes/rnashapes/2.1.6
 recipes/rnastructure
 recipes/rnastructure/5.7
 recipes/rnastructure/6.0
@@ -953,15 +922,11 @@ recipes/socru
 recipes/ssake
 recipes/subread
 recipes/tantan
-recipes/tophat2/2.0.13
 recipes/tophat-recondition
 recipes/tracer
-recipes/trimmomatic/0.32
-recipes/trimmomatic/0.33
 recipes/vcfsamplecompare
 recipes/watchdog-wms
 recipes/wdltool
-recipes/weblogo/2.8.2
 recipes/womtool
 recipes/xtandem
 recipes/yaha

recipes/bcftools/1.3.1/build.sh

@@ -2,4 +2,5 @@
 
 export CPPFLAGS="-I$PREFIX/include"
 export LDFLAGS="-L$PREFIX/lib"
-make prefix=$PREFIX CPPFLAGS=$CPPFLAGS LDFLAGS=$LDFLAGS plugins install
+make all prefix=${PREFIX} CC=${CC} LDFLAGS="$LDFLAGS" CFLAGS="$CFLAGS"
+make install prefix=${PREFIX} CC=${CC} LDFLAGS="$LDFLAGS" CFLAGS="$CFLAGS"

recipes/bcftools/1.3.1/meta.yaml

@@ -1,20 +1,14 @@
-about:
-  home: https://github.com/samtools/bcftools
-  license: MIT
-  summary: BCFtools is a set of utilities that manipulate variant calls in the Variant
-    Call Format (VCF) and its binary counterpart BCF. All commands work transparently
-    with both VCFs and BCFs, both uncompressed and BGZF-compressed.  Most commands
-    accept VCF, bgzipped VCF and BCF with filetype detected automatically even when
-    streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed
-    VCF and BCF and streams will work in most, but not all situations.
-
-build:
-  number: 4
-
 package:
   name: bcftools
   version: '1.3.1'
 
+source:
+  sha256: 12c37a4054cbf1980223e2b3a80a7fdb3fd850324a4ba6832e38fdba91f1b924
+  url: https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2
+
+build:
+  number: 5
+
 requirements:
   build:
     - {{ compiler('c') }}
@@ -23,16 +17,23 @@ requirements:
   run:
     - zlib
 
-source:
-  sha256: 12c37a4054cbf1980223e2b3a80a7fdb3fd850324a4ba6832e38fdba91f1b924
-  url: https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2
-
 test:
   commands:
     - "bcftools -h > /dev/null"
     - bcftools --version
     - bcftools plugin -lv
 
+about:
+  home: https://github.com/samtools/bcftools
+  license: MIT
+  license_file: "LICENSE"
+  summary: BCFtools is a set of utilities that manipulate variant calls in the Variant
+    Call Format (VCF) and its binary counterpart BCF. All commands work transparently
+    with both VCFs and BCFs, both uncompressed and BGZF-compressed.  Most commands
+    accept VCF, bgzipped VCF and BCF with filetype detected automatically even when
+    streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed
+    VCF and BCF and streams will work in most, but not all situations.
+
 extra:
   identifiers:
     - biotools:bcftools

recipes/bcftools/meta.yaml

@@ -1,19 +1,16 @@
 {% set version="1.9" %}
-about:
-  home: https://github.com/samtools/bcftools
-  license: MIT
-  summary: BCFtools is a set of utilities that manipulate variant calls in the Variant
-    Call Format (VCF) and its binary counterpart BCF. All commands work transparently
-    with both VCFs and BCFs, both uncompressed and BGZF-compressed.  Most commands
-    accept VCF, bgzipped VCF and BCF with filetype detected automatically even when
-    streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed
-    VCF and BCF and streams will work in most, but not all situations.
 
-build:
-  number: 3
 package:
   name: bcftools
   version: {{ version }}
+
+build:
+  number: 4
+
+source:
+  url: https://github.com/samtools/bcftools/releases/download/{{ version }}/bcftools-{{ version }}.tar.bz2
+  sha256: 6f36d0e6f16ec4acf88649fb1565d443acf0ba40f25a9afd87f14d14d13070c8
+
 requirements:
   build:
     - {{ compiler('c') }}
@@ -33,17 +30,23 @@ requirements:
     - zlib
     - libdeflate
 
-source:
-  url: https://github.com/samtools/bcftools/releases/download/{{ version }}/bcftools-{{ version }}.tar.bz2
-  sha256: 6f36d0e6f16ec4acf88649fb1565d443acf0ba40f25a9afd87f14d14d13070c8
-
 test:
   commands:
     - bcftools -h
     - bcftools --version
     - bcftools plugin -lv
     #- plot-vcfstats -h 2>&1 | grep -q "Plots output of "
 
+about:
+  home: https://github.com/samtools/bcftools
+  license: MIT
+  summary: BCFtools is a set of utilities that manipulate variant calls in the Variant
+    Call Format (VCF) and its binary counterpart BCF. All commands work transparently
+    with both VCFs and BCFs, both uncompressed and BGZF-compressed.  Most commands
+    accept VCF, bgzipped VCF and BCF with filetype detected automatically even when
+    streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed
+    VCF and BCF and streams will work in most, but not all situations.
+
 extra:
   identifiers:
     - biotools:bcftools

recipes/bedtools/2.19.1/build.sh

@@ -4,6 +4,6 @@ export CFLAGS="-I$PREFIX/include"
 export LDFLAGS="-L$PREFIX/lib"
 export CPATH=${PREFIX}/include
 
-make
+make prefix=$PREFIX CXX=$CXX CC=$CC LDFLAGS="-L$PREFIX/lib"
 mkdir -p $PREFIX/bin
 mv bin/* $PREFIX/bin/