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mkdir: cannot create directory ‘/opt/host-conda-bld/linux-aarch64’: Permission denied#1047
@ljw20180420

Description

@ljw20180420
ljw20180420
opened on May 28, 2025

My recipe is

{% set name = "rearr" %}
{% set version = "1.0.0" %}

package:
  name: {{ name|lower }}
  version: {{ version }}

source:
  url: https://github.com/ljw20180420/sx_lcy/archive/refs/tags/conda_pkg.tar.gz
  sha256: 6f3d15d029dc05bb02ce8f2a21eec4054c7abc86bcfb59520b649ab04647cfef

build:
  run_exports:
    - {{ pin_subpackage(name, max_pin="x") }}
  script:
    # install rearrangement
    - mkdir -p core/Rearrangement/build
    - cd core/Rearrangement/build
    - cmake -DCMAKE_BUILD_TYPE=Release ..
    - make
    - mkdir -p $PREFIX/bin
    - cp ./rearrangement $PREFIX/bin/
    - cd $SRC_DIR
    - mkdir -p $PREFIX/share/awk/
    - cp core/Rearrangement/correct_micro_homology.awk $PREFIX/share/awk/
    # install removeDup
    - cp core/removeDuplicates.md $PREFIX/bin/
    # install demultiplex
    - cp core/demultiplex/demultiplex.md $PREFIX/bin/
    - cp core/demultiplex/getAlignPos.awk $PREFIX/share/awk/
    # install getSxCsvFileRef
    - cp sx/getSxCsvFileRef/getSxCsvFileRef.md $PREFIX/bin/
    - cp sx/getSxCsvFileRef/getSxCsvFileTarget.pl $PREFIX/bin/
    - cp sx/getSxCsvFileRef/getSxRefFile.pl $PREFIX/bin/
    - cp sx/getSxCsvFileRef/sxTargetSam2Bed.awk $PREFIX/share/awk/
    # install cutR2Adapter
    - cp sx/sxCutR2AdapterFilterCumulate/sxCutR2AdapterFilterCumulate.md $PREFIX/bin/
    - cp sx/sxCutR2AdapterFilterCumulate/sxCumulateToMapCutAdaptSpliter.awk $PREFIX/share/awk/
    # install sxInderSpliter
    - cp sx/sxExtractSpliter.md $PREFIX/bin/
    # install workflow
    - mkdir -p $PREFIX/share/rearr
    - cp workFlow.mak $PREFIX/share/rearr/
    - cp runWorkFlow.md $PREFIX/bin/
  number: 0
  skip: True # [not linux]

requirements:
  build:
    - make
    - cmake
    - {{ compiler('cxx') }}
  run:
    - make
    - gawk
    - perl
    - samtools
    - bedtools
    - bowtie2
    - python
    - cutadapt
    - numpy

test:
  commands:
    - python -m unittest test.test_suite_no_genome
  source_files:
    - test

about:
  home: https://github.com/ljw20180420/sx_lcy
  summary: 'Chimeric alignment of CRISPR-seq'
  description: |
    rearr is a package to demultiplex and align CRISPR-seq data.
  license: MIT
  license_family: MIT
  license_file: LICENSE.md
  doc_url: https://ljw20180420.github.io/sx_lcy
  dev_url: https://github.com/ljw20180420/sx_lcy

extra:
  recipe-maintainers:
    - ljw

I build the conda package in docker.

bioconda-utils build --docker --mulled-test --packages rearr

The output is

10:33:14 BIOCONDA INFO Considering total of 1 recipes (rearr).
10:33:14 BIOCONDA INFO Processing 1 recipes (rearr).
10:33:14 BIOCONDA INFO Using docker image quay.io/bioconda/bioconda-utils-build-env-cos7:3.7.2 for building.
10:33:14 BIOCONDA INFO Generating DAG
Loading Recipes: 100%|████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 76.22it/s]
10:33:14 BIOCONDA INFO 1 recipes to build and test: 
rearr
10:33:14 BIOCONDA INFO Determining expected packages for recipes/rearr
WARNING: 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.
WARNING: No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.22
Adding in variants from internal_defaults
Adding in variants from /home/ljw/wuqiang/sx/bioconda-recipes/.conda/conda_build_config.yaml
Adding in variants from /home/ljw/wuqiang/sx/bioconda-recipes/.conda/lib/python3.10/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml
conda-forge/osx-arm64: 120MB [00:15, 8.13MB/s]                                        | 0/10 [00:00<?, ?files/s]
conda-forge/linux-aarch64: 132MB [00:19, 7.14MB/s]                            | 1/10 [00:19<02:56, 19.57s/files]
bioconda/linux-aarch64: 2.90MB [00:00, 4.78MB/s]                              | 2/10 [00:24<01:25, 10.69s/files]
bioconda/osx: 24.5MB [00:03, 7.40MB/s]                                        | 3/10 [00:24<00:43,  6.18s/files]
conda-forge/linux: 322MB [00:30, 11.0MB/s]                                    | 4/10 [00:29<00:32,  5.45s/files]
conda-forge/osx: 266MB [00:43, 6.48MB/s]████████                              | 5/10 [00:43<00:42,  8.52s/files]
bioconda/osx-arm64: 1.11MB [00:11, 103kB/s]███████████                        | 6/10 [00:54<00:38,  9.52s/files]
bioconda/linux: 31.2MB [00:25, 1.29MB/s]/s]]
bioconda/noarch: 31.4MB [00:01, 30.8MB/s]█████████████████████████            | 8/10 [00:55<00:10,  5.04s/files]
conda-forge/noarch: 126MB [00:37, 3.52MB/s]█████████████████████████████      | 9/10 [00:57<00:04,  4.22s/files]
Downloading: 100%|███████████████████████████████████████████████████████████| 10/10 [01:02<00:00,  6.25s/files]
Adding in variants from argument_variants
Attempting to finalize metadata for rearrs] 
Reloading output folder: ...working... done
Getting pinned dependencies: ...working... done
Reloading output folder: ...working... done
Getting pinned dependencies: ...working... done
10:36:36 BIOCONDA INFO BUILD START recipes/rearr
10:36:37 BIOCONDA INFO Starting build for recipes/rearr Free disk space: 349828.51 MB. Free memory: 49167.61 MB (76.67%)
10:36:37 BIOCONDA INFO (COMMAND) docker system df
10:36:37 BIOCONDA INFO (OUT) TYPE            TOTAL     ACTIVE    SIZE      RECLAIMABLE
10:36:37 BIOCONDA INFO (OUT) Images          48        0         43.95GB   43.95GB (100%)
10:36:37 BIOCONDA INFO (OUT) Containers      0         0         0B        0B
10:36:37 BIOCONDA INFO (OUT) Local Volumes   557       0         139GB     139GB (100%)
10:36:37 BIOCONDA INFO (OUT) Build Cache     1215      0         125.2GB   125.2GB
10:36:37 BIOCONDA INFO (COMMAND) docker ps -a
10:36:37 BIOCONDA INFO (OUT) CONTAINER ID   IMAGE     COMMAND   CREATED   STATUS    PORTS     NAMES
10:36:37 BIOCONDA INFO (COMMAND) docker run -t --net host --rm -v /tmp/tmpn3x46m2e/build_script.bash:/opt/build_script.bash -v /home/ljw/wuqiang/sx/bioconda-recipes/.conda/conda-bld:/opt/host-conda-bld -v /home/ljw/wuqiang/sx/bioconda-recipes/recipes/rearr:/opt/recipe -e LC_ADDRESS=en_US.UTF-8 -e LC_NAME=en_US.UTF-8 -e LC_MONETARY=en_US.UTF-8 -e LC_PAPER=en_US.UTF-8 -e LANG=en_US.UTF-8 -e LC_IDENTIFICATION=en_US.UTF-8 -e LC_TELEPHONE=en_US.UTF-8 -e LC_MEASUREMENT=en_US.UTF-8 -e LC_TIME=en_US.UTF-8 -e LC_NUMERIC=en_US.UTF-8 -e HOST_USER_ID=1000 quay.io/bioconda/bioconda-utils-build-env-cos7:3.7.2 /bin/bash /opt/build_script.bash
10:36:41 BIOCONDA INFO (OUT) 2025-05-28T02:36:41 Subdir: linux-64 Gathering repodata
10:36:41 BIOCONDA INFO (OUT) 2025-05-28T02:36:41 linux-64 Writing pre-patch repodata
10:36:41 BIOCONDA INFO (OUT) 2025-05-28T02:36:41 linux-64 Applying patch instructions
10:36:41 BIOCONDA INFO (OUT) 2025-05-28T02:36:41 linux-64 Writing patched repodata
10:36:41 BIOCONDA INFO (OUT) 2025-05-28T02:36:41 linux-64 Building current_repodata subset
10:36:41 BIOCONDA INFO (OUT) 2025-05-28T02:36:41 linux-64 Writing current_repodata subset
10:36:41 BIOCONDA INFO (OUT) 2025-05-28T02:36:41 linux-64 Writing index HTML
10:36:41 BIOCONDA INFO (OUT) 2025-05-28T02:36:41 Subdir: linux-aarch64 Gathering repodata
10:36:41 BIOCONDA INFO (OUT) 2025-05-28T02:36:41 linux-aarch64 Writing pre-patch repodata
10:36:41 BIOCONDA INFO (OUT) 2025-05-28T02:36:41 linux-aarch64 Applying patch instructions
10:36:41 BIOCONDA INFO (OUT) 2025-05-28T02:36:41 linux-aarch64 Writing patched repodata
10:36:41 BIOCONDA INFO (OUT) 2025-05-28T02:36:41 linux-aarch64 Building current_repodata subset
10:36:41 BIOCONDA INFO (OUT) 2025-05-28T02:36:41 linux-aarch64 Writing current_repodata subset
10:36:41 BIOCONDA INFO (OUT) 2025-05-28T02:36:41 linux-aarch64 Writing index HTML
10:36:41 BIOCONDA INFO (OUT) 2025-05-28T02:36:41 Subdir: noarch Gathering repodata
10:36:41 BIOCONDA INFO (OUT) 2025-05-28T02:36:41 noarch Writing pre-patch repodata
10:36:41 BIOCONDA INFO (OUT) 2025-05-28T02:36:41 noarch Applying patch instructions
10:36:41 BIOCONDA INFO (OUT) 2025-05-28T02:36:41 noarch Writing patched repodata
10:36:41 BIOCONDA INFO (OUT) 2025-05-28T02:36:41 noarch Building current_repodata subset
10:36:41 BIOCONDA INFO (OUT) 2025-05-28T02:36:41 noarch Writing current_repodata subset
10:36:41 BIOCONDA INFO (OUT) 2025-05-28T02:36:41 noarch Writing index HTML
10:36:42 BIOCONDA INFO (OUT) mkdir: cannot create directory ‘/opt/host-conda-bld/linux-aarch64’: Permission denied
10:36:42 BIOCONDA ERROR COMMAND FAILED (exited with 1): docker run -t --net host --rm -v /tmp/tmpn3x46m2e/build_script.bash:/opt/build_script.bash -v /home/ljw/wuqiang/sx/bioconda-recipes/.conda/conda-bld:/opt/host-conda-bld -v /home/ljw/wuqiang/sx/bioconda-recipes/recipes/rearr:/opt/recipe -e LC_ADDRESS=en_US.UTF-8 -e LC_NAME=en_US.UTF-8 -e LC_MONETARY=en_US.UTF-8 -e LC_PAPER=en_US.UTF-8 -e LANG=en_US.UTF-8 -e LC_IDENTIFICATION=en_US.UTF-8 -e LC_TELEPHONE=en_US.UTF-8 -e LC_MEASUREMENT=en_US.UTF-8 -e LC_TIME=en_US.UTF-8 -e LC_NUMERIC=en_US.UTF-8 -e HOST_USER_ID=1000 quay.io/bioconda/bioconda-utils-build-env-cos7:3.7.2 /bin/bash /opt/build_script.bash

10:36:42 BIOCONDA ERROR BUILD FAILED recipes/rearr
10:36:42 BIOCONDA INFO Finished build for recipes/rearr Free disk space: 349828.51 MB. Free memory: 49191.39 MB (76.70%)
10:36:42 BIOCONDA INFO (COMMAND) docker system df
10:36:43 BIOCONDA INFO (OUT) TYPE            TOTAL     ACTIVE    SIZE      RECLAIMABLE
10:36:43 BIOCONDA INFO (OUT) Images          48        0         43.95GB   43.95GB (100%)
10:36:43 BIOCONDA INFO (OUT) Containers      0         0         0B        0B
10:36:43 BIOCONDA INFO (OUT) Local Volumes   557       0         139GB     139GB (100%)
10:36:43 BIOCONDA INFO (OUT) Build Cache     1215      0         125.2GB   125.2GB
10:36:43 BIOCONDA INFO (COMMAND) docker ps -a
10:36:43 BIOCONDA INFO (OUT) CONTAINER ID   IMAGE     COMMAND   CREATED   STATUS    PORTS     NAMES
10:36:43 BIOCONDA INFO (COMMAND) conda build purge
10:36:43 BIOCONDA INFO (COMMAND) docker container prune -f
10:36:43 BIOCONDA ERROR BUILD SUMMARY: of 1 recipes, 1 failed and 0 were skipped. Details of recipes and environments follow.
10:36:43 BIOCONDA ERROR BUILD SUMMARY: FAILED recipe recipes/rearr

The content of build_script.bash

#!/bin/bash
set -eo pipefail

# Add the host's mounted conda-bld dir so that we can use its contents as
# dependencies for building this recipe.
#
# Note that if the directory didn't exist on the host, then the staging area
# will exist in the container but will be empty.  Channels expect at least
# a linux-64/linux-aarch64 and noarch directory within that directory, so we
# make sure it exists before adding the channel.
# Also ensure conda-build's local channel directory exists the same way.
for local_channel in '/opt/conda/conda-bld' '/opt/host-conda-bld'; do
  mkdir -p "${local_channel}"/linux-64
  mkdir -p "${local_channel}"/linux-aarch64
  mkdir -p "${local_channel}"/noarch
  conda index "${local_channel}"
done
conda config --add channels file:///opt/host-conda-bld 2> >(
    grep -vF "Warning: 'file:///opt/host-conda-bld' already in 'channels' list, moving to the top" >&2
)

# Pass on conda_pkg_format ("2" for .conda instead of .tar.bz2) from host's conda-build config.
test -n '' && conda config --set conda_build.pkg_format ''

# The actual building...
# we explicitly point to the meta.yaml, in order to keep
# conda-build from building all subdirectories
conda-build -c file:///opt/host-conda-bld --override-channels --no-anaconda-upload -c conda-forge -c bioconda -e /opt/host-conda-bld/conda_build_config_0_-e_conda_build_config.yaml -e /opt/host-conda-bld/conda_build_config_1_-e_bioconda_utils-conda_build_config.yaml /opt/recipe/meta.yaml 2>&1

# copy all built packages to the staging area
find /opt/conda/conda-bld \
  -name src_cache -prune -o \
  -type f \( -name '*.tar.bz2' -o -name '*.conda' \) -print0 |
  xargs -0 -- cp -t '/opt/host-conda-bld/linux-64' --
#While technically better, this is slower and more prone to breaking
#cp `conda-build --override-channels --no-anaconda-upload -c conda-forge -c bioconda -e /opt/host-conda-bld/conda_build_config_0_-e_conda_build_config.yaml -e /opt/host-conda-bld/conda_build_config_1_-e_bioconda_utils-conda_build_config.yaml /opt/recipe/meta.yaml --output | grep -e '\.tar\.bz2$' -e '\.conda$')` /opt/host-conda-bld/linux-64
conda index /opt/host-conda-bld
# Ensure permissions are correct on the host.
HOST_USER=1000
chown $HOST_USER:$HOST_USER /opt/host-conda-bld/linux-64/*

The key error is

mkdir: cannot create directory ‘/opt/host-conda-bld/linux-aarch64’: Permission denied

According to the command

docker run -t --net host --rm -v /tmp/tmpn3x46m2e/build_build_script.bash -v /home/ljw/wuqiang/sx/bioconda-recipes/.conda/conda-bld:/opt/host-conda-bld -v /home/ljw/wuqiang/sx/bioconda-recipes/recipes/rearr:/opt/recipe -e LC_ADDRESS=en_US.UTF-8 -e LC_NAME=en_US.UTF-8 -e LC_MONETARY=en_US.UTF-8 -e LC_PAPER=en_US.UTF-8 -e LANG=en_US.UTF-8 -e LC_IDENTIFICATION=en_US.UTF-8 -e LC_TELEPHONE=en_US.UTF-8 -e LC_MEASUREMENT=en_US.UTF-8 -e LC_TIME=en_US.UTF-8 -e LC_NUMERIC=en_US.UTF-8 -e HOST_USER_ID=1000 quay.io/bioconda/bioconda-utils-build-env-cos7:3.7.2 /bin/bash /opt/build_script.bash

build_script.bash tries to create a directory linux-aarch64 in /opt/host-conda-bld/ in docker as user conda. /opt/host-conda-bld/ is bind to /home/ljw/wuqiang/sx/bioconda-recipes/.conda/conda-bld on my host, so docker user conda has not permission. My host is linux-64. Why build_script.bash also build linux-aarch64? build_script.bash also tries to create directories linux-64 and noarch in /opt/host-conda-bld/. That works because linux-64 and noarch have been created by bioconda-utils build automatically on my host before the execution of build_script.bash in docker.

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