Merge branch 'master' into update_tcoffe

.github/workflows/Bulk.yml

@@ -7,12 +7,13 @@ jobs:
   build-linux:
     name: Bulk Linux Builds
     if: "contains(github.event.head_commit.message, '[ci run]')"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
       max-parallel: 6
       matrix:
         runner: [0, 1, 2, 3, 4, 5]
+        # runner: [0]
     steps:
       - uses: actions/checkout@v4
         with:
@@ -58,7 +59,7 @@ jobs:
             --worker-offset ${{ matrix.runner }} --n-workers 6 \
             --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers \
             --lint --record-build-failures --skiplist-leafs \
-            --exclude bioconda-repodata-patches
+            --exclude bioconda-repodata-patches # --subdag-depth 5
           conda clean -y --all
 
   build-osx:
@@ -67,9 +68,9 @@ jobs:
     runs-on: macos-13
     strategy:
       fail-fast: false
-      max-parallel: 4
+      max-parallel: 3
       matrix:
-        runner: [0, 1, 2, 3]
+        runner: [0, 1, 2]
     steps:
       - uses: actions/checkout@v4
         with:
@@ -117,9 +118,9 @@ jobs:
           python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")'
           echo '============'
           bioconda-utils build recipes config.yml \
-            --worker-offset ${{ matrix.runner }} --n-workers 4 \
+            --worker-offset ${{ matrix.runner }} --n-workers 3 \
             --lint --anaconda-upload --record-build-failures --skiplist-leafs \
-            --exclude bioconda-repodata-patches
+            --exclude bioconda-repodata-patches # --subdag-depth 5
           conda clean -y --all
 
   build-osx-arm:

.github/workflows/CommentResponder.yml

@@ -6,7 +6,7 @@ on:
 
 jobs:
   comment:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     name: bioconda-bot comment
     if: >-
       (
@@ -31,7 +31,7 @@ jobs:
       run: bioconda-bot comment
 
   repost:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     name: bioconda-bot repost
     if: >-
       (
@@ -53,7 +53,7 @@ jobs:
       run: bioconda-bot comment
 
   merge:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     name: bioconda-bot merge
     if: >-
       (
@@ -78,7 +78,7 @@ jobs:
           for merging the PR.
 
   update:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     name: bioconda-bot update
     if: >-
       (

.github/workflows/PR.yml

@@ -8,7 +8,7 @@ concurrency:
 jobs:
   lint:
     name: Lint
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     strategy:
       fail-fast: true
       max-parallel: 13
@@ -54,7 +54,7 @@ jobs:
 
   build-linux:
     name: Linux Tests
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     strategy:
       fail-fast: true
       max-parallel: 13

.github/workflows/build-failures.yml

@@ -14,7 +14,7 @@ jobs:
   update-build-failure-page:
     name: Update build failure page
     if: ${{ github.repository == 'bioconda/bioconda-recipes' && !contains(github.event.head_commit.message, '[ci skip]') }}
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v4
         with:

.github/workflows/master.yml

@@ -7,7 +7,7 @@ jobs:
   build-linux:
     name: Linux Upload
     if: github.repository == 'bioconda/bioconda-recipes'
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
       max-parallel: 13

build-fail-blacklist

@@ -97,8 +97,6 @@ recipes/wtforms-components
 recipes/xmlbuilder
 
 # the following packages have open PRs labeled with "Move to conda-forge"
-recipes/perl-alien-build
-recipes/perl-alien-libxml2
 recipes/perl-date-manip
 recipes/perl-datetime-timezone
 recipes/perl-devel-checklib
@@ -118,7 +116,6 @@ recipes/perl-sereal-decoder
 recipes/perl-sereal-encoder
 recipes/perl-term-progressbar
 recipes/perl-uri
-recipes/perl-xml-libxml
 recipes/scoop
 recipes/wheezy.template
 
@@ -217,7 +214,6 @@ recipes/pureclip
 recipes/hulk
 recipes/bolt-lmm
 recipes/unitig-counter
-recipes/probcons
 recipes/spydrpick
 recipes/bctools
 recipes/group_humann2_uniref_abundances_to_go
@@ -310,7 +306,6 @@ recipes/vqsr_cnn
 recipes/mqc
 recipes/roprofile
 recipes/chanjo
-recipes/phylip
 recipes/gqt
 recipes/diamond_add_taxonomy
 recipes/shapemapper
@@ -609,7 +604,6 @@ recipes/fastuniq
 recipes/fgap
 recipes/funcannot
 recipes/genepender
-recipes/ghostx
 recipes/ls-gkm
 recipes/mosaik
 recipes/ngmerge

recipes/10x_bamtofastq/meta.yaml

@@ -5,7 +5,7 @@ package:
   version: {{ version }}
 
 build:
-  number: 2
+  number: 3
 
 source:
   url: https://github.com/10XGenomics/bamtofastq/archive/refs/tags/v{{ version }}.tar.gz

recipes/2pg_cartesian/meta.yaml

@@ -10,7 +10,7 @@ source:
 
 build:
   skip: True  #[osx]
-  number: 7
+  number: 8
 
 requirements:
   build:

recipes/3seq/build_failure.linux-aarch64.yaml

@@ -0,0 +1,104 @@
+recipe_sha: 482ec77add88952c9953d6e21d2a0ca92d37689cd8dc5aafb1e998e5f1749d35  # 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: |-
+  -- Detecting CXX compile features
+  -- Detecting CXX compile features - done
+  -- Configuring done (0.4s)
+  -- Generating done (0.0s)
+  -- Build files have been written to: $SRC_DIR/build
+  [  3%] Building CXX object CMakeFiles/3seq.dir/source/3Seq.cpp.o
+  [  7%] Building CXX object CMakeFiles/3seq.dir/source/run-mode/CheckPRun.cpp.o
+  [ 10%] Building CXX object CMakeFiles/3seq.dir/source/run-mode/FullRun.cpp.o
+  [ 14%] Building CXX object CMakeFiles/3seq.dir/source/data/bio/Genome.cpp.o
+  [ 17%] Building CXX object CMakeFiles/3seq.dir/source/data/bio/GenomeSet.cpp.o
+  [ 21%] Building CXX object CMakeFiles/3seq.dir/source/run-mode/GenPRun.cpp.o
+  [ 25%] Building CXX object CMakeFiles/3seq.dir/source/run-mode/HelpRun.cpp.o
+  [ 28%] Building CXX object CMakeFiles/3seq.dir/source/run-mode/InfoRun.cpp.o
+  [ 32%] Building CXX object CMakeFiles/3seq.dir/source/Interface.cpp.o
+  [ 35%] Building CXX object CMakeFiles/3seq.dir/source/run-mode/MatchRun.cpp.o
+  [ 39%] Building CXX object CMakeFiles/3seq.dir/source/data/bio/Nucleotide.cpp.o
+  [ 42%] Building CXX object CMakeFiles/3seq.dir/source/stat/PTable.cpp.o
+  [ 46%] Building CXX object CMakeFiles/3seq.dir/source/stat/PTableFile.cpp.o
+  [ 50%] Building CXX object CMakeFiles/3seq.dir/source/run-mode/Run.cpp.o
+  [ 53%] Building CXX object CMakeFiles/3seq.dir/source/data/bio/Sequence.cpp.o
+  [ 57%] Building CXX object CMakeFiles/3seq.dir/source/data/file/SequenceFile.cpp.o
+  [ 60%] Building CXX object CMakeFiles/3seq.dir/source/run-mode/SingleBpRun.cpp.o
+  [ 64%] Building CXX object CMakeFiles/3seq.dir/source/stat/stat.cpp.o
+  [ 67%] Building CXX object CMakeFiles/3seq.dir/source/util/String.cpp.o
+  [ 71%] Building CXX object CMakeFiles/3seq.dir/source/data/file/TextFile.cpp.o
+  [ 75%] Building CXX object CMakeFiles/3seq.dir/source/data/bio/Triplet.cpp.o
+  [ 78%] Building CXX object CMakeFiles/3seq.dir/source/run-mode/TripletRun.cpp.o
+  [ 82%] Building CXX object CMakeFiles/3seq.dir/source/util/Util.cpp.o
+  [ 85%] Building CXX object CMakeFiles/3seq.dir/source/run-mode/VersionRun.cpp.o
+  [ 89%] Building CXX object CMakeFiles/3seq.dir/source/run-mode/WriteRun.cpp.o
+  [ 92%] Building CXX object CMakeFiles/3seq.dir/source/AppInfo.cpp.o
+  [ 96%] Building CXX object CMakeFiles/3seq.dir/source/run-mode/RFullRun.cpp.o
+  [100%] Linking CXX executable 3seq
+  [100%] Built target 3seq
+  --2024-12-13 03:19:32--  https://www.dropbox.com/s/zac4wotgdmm3mvb/pvaluetable.2017.700.tgz
+  Resolving www.dropbox.com (www.dropbox.com)... 162.125.6.18, 2620:100:601c:18::a27d:612
+  Connecting to www.dropbox.com (www.dropbox.com)|162.125.6.18|:443... connected.
+  HTTP request sent, awaiting response... 302 Found
+  Location: https://www.dropbox.com/scl/fi/vss650bd06nfjfjs2chw5/pvaluetable.2017.700.tgz?rlkey=tgnqupam50kv57ckl7fbdbgtm [following]
+  --2024-12-13 03:19:32--  https://www.dropbox.com/scl/fi/vss650bd06nfjfjs2chw5/pvaluetable.2017.700.tgz?rlkey=tgnqupam50kv57ckl7fbdbgtm
+  Reusing existing connection to www.dropbox.com:443.
+  HTTP request sent, awaiting response... 302 Found
+  Location: https://ucdc0812fd3f0d759ad1863f8deb.dl.dropboxusercontent.com/cd/0/inline/CgKT93TYemZCjT--ige0eEZpvkGsxchqZlmk5pGYcMW2d1oWMutdGgNm4xrQLdwCgCYTUYgrKgGxZodi88k1PpY65F5q8bFbL82b1xO8AyXgEuQccS_yGU4NU6SNxHPQ494/file# [following]
+  --2024-12-13 03:19:33--  https://ucdc0812fd3f0d759ad1863f8deb.dl.dropboxusercontent.com/cd/0/inline/CgKT93TYemZCjT--ige0eEZpvkGsxchqZlmk5pGYcMW2d1oWMutdGgNm4xrQLdwCgCYTUYgrKgGxZodi88k1PpY65F5q8bFbL82b1xO8AyXgEuQccS_yGU4NU6SNxHPQ494/file
+  Resolving ucdc0812fd3f0d759ad1863f8deb.dl.dropboxusercontent.com (ucdc0812fd3f0d759ad1863f8deb.dl.dropboxusercontent.com)... 162.125.6.15, 2620:100:601c:15::a27d:60f
+  Connecting to ucdc0812fd3f0d759ad1863f8deb.dl.dropboxusercontent.com (ucdc0812fd3f0d759ad1863f8deb.dl.dropboxusercontent.com)|162.125.6.15|:443... connected.
+  HTTP request sent, awaiting response... 302 Found
+  Location: /cd/0/inline2/CgKpK5UQm_6483X6-NYh7sC9Gwp1gRPAvs9-22s4_owWzC92xAKPn0by2RukudDuwqSN9LKsBJAeDlC_OUNFZG1peOoCGBhynPjHsC8cMgV_f4T-xxklkS1RpY0FbAGyQxYPBj23jT-hjK3e9X4uoWcyuA_rj9YXu5htQXE52472Mm5MA0B0C3pgZgyrPdwU9jbbf-WVSM5SvZnWWCY8ZOU4eFmVVhidGdRGkgmWN6NpGBJxs09LLDcs-cSX_zMLRiG6Pdj6fI-Qa_Zauxx_PCWtmRwxY3yKwClN4S6ZUXBfqNbVIgQ9Ztg7csOagUFQRnFVQE4EgUlUy8v1-nbb9_iURbSjzQXbA5Ul_mXzV4MfsA/file [following]
+  --2024-12-13 03:19:33--  https://ucdc0812fd3f0d759ad1863f8deb.dl.dropboxusercontent.com/cd/0/inline2/CgKpK5UQm_6483X6-NYh7sC9Gwp1gRPAvs9-22s4_owWzC92xAKPn0by2RukudDuwqSN9LKsBJAeDlC_OUNFZG1peOoCGBhynPjHsC8cMgV_f4T-xxklkS1RpY0FbAGyQxYPBj23jT-hjK3e9X4uoWcyuA_rj9YXu5htQXE52472Mm5MA0B0C3pgZgyrPdwU9jbbf-WVSM5SvZnWWCY8ZOU4eFmVVhidGdRGkgmWN6NpGBJxs09LLDcs-cSX_zMLRiG6Pdj6fI-Qa_Zauxx_PCWtmRwxY3yKwClN4S6ZUXBfqNbVIgQ9Ztg7csOagUFQRnFVQE4EgUlUy8v1-nbb9_iURbSjzQXbA5Ul_mXzV4MfsA/file
+  Reusing existing connection to ucdc0812fd3f0d759ad1863f8deb.dl.dropboxusercontent.com:443.
+  HTTP request sent, awaiting response... 200 OK
+  Length: 205243295 (196M) [application/x-gtar]
+  Saving to: '/opt/conda/conda-bld/3seq_1734059853486/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/share/3seq/pvaluetable.2017.700.tgz'
+
+  pvaluetable.2017.70   0%[                    ]       0  --.-KB/s               pvaluetable.2017.70   4%[                    ]   8.00M  --.-KB/s               pvaluetable.2017.70   4%[                    ]   8.02M  5.50MB/s               pvaluetable.2017.70  22%[===>                ]  44.92M  27.1MB/s               pvaluetable.2017.70  31%[=====>              ]  60.77M  32.7MB/s               pvaluetable.2017.70  41%[=======>            ]  82.02M  39.8MB/s               pvaluetable.2017.70  52%[=========>          ] 102.64M  45.2MB/s               pvaluetable.2017.70  63%[===========>        ] 123.52M  49.8MB/s               pvaluetable.2017.70  71%[=============>      ] 139.77M  52.1MB/s               pvaluetable.2017.70  86%[================>   ] 169.27M  58.7MB/s               pvaluetable.2017.70 100%[===================>] 195.73M  65.1MB/s    in 3.0s
+
+  2024-12-13 03:19:37 (65.1 MB/s) - '/opt/conda/conda-bld/3seq_1734059853486/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/share/3seq/pvaluetable.2017.700.tgz' saved [205243295/205243295]
+
+
+  Resource usage statistics from building 3seq:
+     Process count: 10
+     CPU time: Sys=0:00:00.9, User=0:00:08.8
+     Memory: 159.3M
+     Disk usage: 20.4K
+     Time elapsed: 0:00:34.1
+
+
+  Packaging 3seq
+  Packaging 3seq-1.8-h163da20_5
+  number of files: 3
+  Warning: rpath /opt/conda/conda-bld/3seq_1734059853486/_build_env/lib is outside prefix /opt/conda/conda-bld/3seq_1734059853486/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol (removing it)
+  patchelf: open: Text file busy
+     INFO: sysroot: '/opt/conda/conda-bld/3seq_1734059853486/_build_env/aarch64-conda-linux-gnu/sysroot/' files: '['usr/share/zoneinfo', 'usr/share/locale/zh_TW/LC_MESSAGES/libc.mo', 'usr/share/locale/zh_CN/LC_MESSAGES/libc.mo', 'usr/share/locale/vi/LC_MESSAGES/libc.mo']'
+     INFO (3seq,bin/3seq): Needed DSO lib/libstdc.so.6 found in conda-forge/linux-aarch64::libstdcxx==14.2.0=h3f4de04_1
+     INFO (3seq,bin/3seq): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libm.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_18
+     INFO (3seq,bin/3seq): Needed DSO lib/libgcc_s.so.1 found in conda-forge/linux-aarch64::libgcc==14.2.0=he277a41_1
+     INFO (3seq,bin/3seq): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/libc.so.6 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_18
+     INFO (3seq,bin/3seq): Needed DSO aarch64-conda-linux-gnu/sysroot/lib64/ld-linux-aarch64.so.1 found in CDT/compiler package conda-forge/noarch::sysroot_linux-aarch64==2.17=h5b4a56d_18
+  Fixing permissions
+  Packaged license file/s.
+  Traceback (most recent call last):
+    File "/opt/conda/bin/conda-build", line 11, in <module>
+      sys.exit(execute())
+    File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute
+      api.build(
+    File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build
+      return build_tree(
+    File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree
+      packages_from_this = build(
+    File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2765, in build
+      newly_built_packages = bundlers[pkg_type](
+    File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 1889, in bundle_conda
+      output["checksums"] = create_info_files(
+    File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 1417, in create_info_files
+      files_with_prefix = get_files_with_prefix(m, replacements, files, prefix)
+    File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 1016, in get_files_with_prefix
+      files_with_prefix = [
+    File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 1020, in <listcomp>
+      if open(os.path.join(prefix, f), "rb").read().find(b"\x00") != -1
+  OSError: [Errno 26] Text file busy: '/opt/conda/conda-bld/3seq_1734059853486/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin/3seq'
+# Last 100 lines of the build log.

recipes/3seq/meta.yaml

@@ -7,7 +7,7 @@ package:
   version: {{ version }}
 
 build:
-  number: 4
+  number: 5
   run_exports:
     - {{ pin_subpackage("3seq", max_pin="x") }}  
 

recipes/abawaca/meta.yaml

@@ -11,7 +11,7 @@ source:
     - 0001-Use-CXX-and-flags.patch
 
 build:
-  number: 7
+  number: 8
   run_exports:
     - {{ pin_subpackage("abawaca", max_pin="x") }}
 
@@ -37,4 +37,4 @@ extra:
   identifiers:
     - doi:10.1038/nature14486
   additional-platforms:
-    - linux-aarch64
+    - linux-aarch64

recipes/abismal/meta.yaml

@@ -5,7 +5,7 @@ package:
   version: {{ version }}
 
 build:
-  number: 0
+  number: 1
   run_exports:
     # abismal is currently not intended to be stable between minor versions (x.x).
     - {{ pin_subpackage('abismal', max_pin="x.x") }}

recipes/abnumber/meta.yaml

@@ -1,12 +1,12 @@
-{% set version = "0.4.1" %} # Remember to update sha256 below
+{% set version = "0.4.2" %} # Remember to update sha256 below
 
 package:
   name: abnumber
   version: '{{ version }}'
 
 source:
   url: https://github.com/prihoda/abnumber/archive/v{{ version }}.tar.gz
-  sha256: '240c7ccc1f85607ffdd0109f19761ab0488a059ae15e3ccd6066ef36c192a047'
+  sha256: 'b816fee3db6c018f6963a5e4ce2d23b2889251fb42b7b93d42e81805cd418bc5'
 
 build:
   noarch: python
@@ -19,6 +19,7 @@ requirements:
   host:
     - python >=3.6
     - pip
+    - setuptools
   run:
     - python >=3.6
     - biopython

recipes/abpoa/meta.yaml

@@ -10,7 +10,7 @@ source:
   sha256: bb97de2dbdec014f2fb24beb0c85fa0b2073f717f3b68639e1edd89239729e6c
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage(name | lower, max_pin="x") }}