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conda package: r-filelock Linux aarch64 support #10

Open Yikun opened 1 year ago

Yikun commented 1 year ago

When build bioconductor-biocfilecache

The r-filelock conda package missing Linux aarch64: https://github.com/conda-forge/r-filelock-feedstock/tree/main

Yikun commented 1 year ago

@martin-g Would you mind taking a look?

martin-g commented 1 year ago

https://github.com/conda-forge/r-filelock-feedstock/pull/8

martin-g commented 1 year ago

https://github.com/conda-forge/conda-forge-pinning-feedstock/pull/4732

Yikun commented 1 year ago

Good job, also cc @XingYuuuuu

martin-g commented 1 year ago

https://github.com/conda-forge/conda-forge-pinning-feedstock/pull/4732 has been merged but https://anaconda.org/conda-forge/r-filelock still does not have a linux-aarch64 label. I'll give it a day for a new build before asking the Conda people whether something more is needed.

martin-g commented 1 year ago

https://github.com/conda-forge/r-filelock-feedstock/pull/9 (automatically created!) needs to be merged before seeing the new aarch64 build at https://anaconda.org/conda-forge/r-filelock

Yikun commented 1 year ago

image

https://anaconda.org/conda-forge/r-filelock Linux aarch64 already generated.

martin-g commented 1 year ago

Nice! Let's test the Bioconda package build too!

martin-g commented 1 year ago

It fails with a new reason but I don't quite understand it:

❯ ./build-recipes.sh ./recipes bioconductor-biocfilecache                                                                                                                                                  (biotest) 
Recipes: bioconductor-biocfilecache

Going to build recipe 'bioconductor-biocfilecache'
05:53:07 BIOCONDA INFO Considering total of 1 recipes (bioconductor-biocfilecache).
05:53:07 BIOCONDA INFO Processing 1 recipes (bioconductor-biocfilecache).
05:53:07 BIOCONDA INFO Generating DAG
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 1.16
05:53:07 BIOCONDA INFO 1 recipes to build and test: 
bioconductor-biocfilecache
05:53:07 BIOCONDA INFO Determining expected packages for recipes/bioconductor-biocfilecache
05:53:07 CONDA_BUILD 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.
Updating build index: /home/mgrigorov/miniconda3/envs/biotest/conda-bld

05:53:08 CONDA_BUILD WARNING No numpy version specified in conda_build_config.yaml.  Falling back to default numpy value of 1.16
Adding in variants from internal_defaults
05:53:08 CONDA_BUILD INFO Adding in variants from internal_defaults
Adding in variants from /home/mgrigorov/miniconda3/envs/biotest/conda_build_config.yaml
05:53:08 CONDA_BUILD INFO Adding in variants from /home/mgrigorov/miniconda3/envs/biotest/conda_build_config.yaml
Adding in variants from /home/mgrigorov/git/bioconda/bioconda-utils/bioconda_utils/bioconda_utils-conda_build_config.yaml
05:53:08 CONDA_BUILD INFO Adding in variants from /home/mgrigorov/git/bioconda/bioconda-utils/bioconda_utils/bioconda_utils-conda_build_config.yaml
Adding in variants from argument_variants
05:53:09 CONDA_BUILD INFO Adding in variants from argument_variants
Attempting to finalize metadata for bioconductor-biocfilecache
anaconda/cloud/conda-forge/linux-aarch64                    Using cache
anaconda/cloud/conda-forge/noarch                           Using cache
anaconda/pkgs/main/linux-aarch64                            Using cache
anaconda/pkgs/main/noarch                                   Using cache
anaconda/pkgs/r/linux-aarch64                               Using cache
anaconda/pkgs/r/noarch                                      Using cache
warning  Could not parse mod/etag header
anaconda/pkgs/msys2/noarch                                  Using cache
05:53:09 CONDA_BUILD INFO Attempting to finalize metadata for bioconductor-biocfilecache
Reloading output folder: /home/mgrigorov/miniconda3/envs/biotest/conda-bld
Transaction

  Prefix: /home/mgrigorov/miniconda3/envs/biotest

  Nothing to do

Reloading output folder: /home/mgrigorov/miniconda3/envs/biotest/conda-bld
Transaction

  Prefix: /home/mgrigorov/miniconda3/envs/biotest

  Updating specs:

   - r-dbi
   - r-httr
   - r-dbplyr[version='>=1.0.0']
   - r-base=4.2
   - r-filelock
   - r-rsqlite
   - r-curl
   - r-dplyr

  Package                                           Version  Build                     Channel                                                           Size
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
  Install:
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

  + _openmp_mutex                                       4.5  2_gnu                     mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       24kB
  + _r-mutex                                          1.0.1  anacondar_1               mirrors.aliyun.com/anaconda/cloud/conda-forge/noarch               4kB
  + _sysroot_linux-aarch64_curr_repodata_hack             4  h57d6b7b_13               mirrors.aliyun.com/anaconda/cloud/conda-forge/noarch              21kB
  + binutils_impl_linux-aarch64                        2.40  h870a726_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64        6MB
  + bwidget                                          1.9.14  h8af1aa0_1                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      122kB
  + bzip2                                             1.0.8  hf897c2e_4                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      405kB
  + c-ares                                           1.19.1  h31becfc_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      117kB
  + ca-certificates                               2023.7.22  hcefe29a_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      150kB
  + cairo                                            1.16.0  h3b99fb1_1016             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64        1MB
  + curl                                              8.2.1  h4e8248e_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       92kB
  + expat                                             2.5.0  hd600fc2_1                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      126kB
  + font-ttf-dejavu-sans-mono                          2.37  hab24e00_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/noarch             397kB
  + font-ttf-inconsolata                              3.000  h77eed37_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/noarch              97kB
  + font-ttf-source-code-pro                          2.038  h77eed37_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/noarch             701kB
  + font-ttf-ubuntu                                    0.83  hab24e00_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/noarch               2MB
  + fontconfig                                       2.14.2  ha9a116f_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      280kB
  + fonts-conda-ecosystem                                 1  0                         mirrors.aliyun.com/anaconda/cloud/conda-forge/noarch               4kB
  + fonts-conda-forge                                     1  0                         mirrors.aliyun.com/anaconda/cloud/conda-forge/noarch               4kB
  + freetype                                         2.12.1  hbbbf32d_1                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      639kB
  + fribidi                                          1.0.10  hb9de7d4_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      116kB
  + gcc_impl_linux-aarch64                           13.1.0  h07080d6_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       49MB
  + gettext                                          0.21.1  ha18d298_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64        5MB
  + gfortran_impl_linux-aarch64                      13.1.0  h8a08e1f_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       13MB
  + graphite2                                        1.3.13  h7fd3ca4_1001             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      107kB
  + gsl                                                 2.7  h294027d_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64        4MB
  + gxx_impl_linux-aarch64                           13.1.0  h07080d6_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       12MB
  + harfbuzz                                          7.3.0  h8428050_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64        1MB
  + icu                                                72.1  hcf00150_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       12MB
  + kernel-headers_linux-aarch64                     4.18.0  h5b4a56d_13               mirrors.aliyun.com/anaconda/cloud/conda-forge/noarch               1MB
  + keyutils                                          1.6.1  h4e544f5_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      112kB
  + krb5                                             1.21.1  hc419048_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64        1MB
  + ld_impl_linux-aarch64                              2.40  h2d8c526_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      739kB
  + lerc                                              4.0.0  h4de3ea5_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      262kB
  + libblas                                           3.9.0  17_linuxaarch64_openblas  mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       15kB
  + libcblas                                          3.9.0  17_linuxaarch64_openblas  mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       14kB
  + libcurl                                           8.2.1  h4e8248e_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      383kB
  + libdeflate                                         1.18  hb4cce97_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       67kB
  + libedit                                    3.1.20191231  he28a2e2_2                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      134kB
  + libev                                              4.33  h516909a_1                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      106kB
  + libexpat                                          2.5.0  hd600fc2_1                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       77kB
  + libffi                                            3.4.2  h3557bc0_5                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       59kB
  + libgcc-devel_linux-aarch64                       13.1.0  hb5b3640_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64        2MB
  + libgcc-ng                                        13.1.0  h2b4548d_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      457kB
  + libgfortran-ng                                   13.1.0  he9431aa_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       23kB
  + libgfortran5                                     13.1.0  h24e4805_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64        1MB
  + libglib                                          2.76.4  h0464669_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64        3MB
  + libgomp                                          13.1.0  h2b4548d_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      423kB
  + libiconv                                           1.17  h9cdd2b7_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64        1MB
  + libjpeg-turbo                                   2.1.5.1  hb4cce97_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      500kB
  + liblapack                                         3.9.0  17_linuxaarch64_openblas  mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       15kB
  + libnghttp2                                       1.52.0  h250e5c5_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      673kB
  + libopenblas                                      0.3.23  pthreads_hd703e6f_0       mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64        4MB
  + libpng                                           1.6.39  hf9034f9_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      299kB
  + libsanitizer                                     13.1.0  h452befe_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64        4MB
  + libssh2                                          1.11.0  h492db2e_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      284kB
  + libstdcxx-devel_linux-aarch64                    13.1.0  hb5b3640_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64        8MB
  + libstdcxx-ng                                     13.1.0  h452befe_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64        4MB
  + libtiff                                           4.5.1  h360e80f_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      454kB
  + libuuid                                          2.38.1  hb4cce97_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       36kB
  + libwebp-base                                      1.3.1  h31becfc_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      364kB
  + libxcb                                             1.15  h2a766a3_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      389kB
  + libxml2                                          2.11.4  h164fba4_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      750kB
  + libzlib                                          1.2.13  h31becfc_5                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       67kB
  + make                                                4.3  h309ac5b_1                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      497kB
  + ncurses                                             6.4  h2e1726e_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      921kB
  + openssl                                           3.1.1  h31becfc_1                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64        3MB
  + pango                                           1.50.14  hb4276a1_1                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      454kB
  + pcre2                                             10.40  he7b27c6_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64        2MB
  + pixman                                           0.40.0  hb9de7d4_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      551kB
  + pthread-stubs                                       0.4  hb9de7d4_1001             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64        6kB
  + r-askpass                                           1.1  r42h25e906a_4             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       31kB
  + r-base                                            4.2.3  haa72b06_6                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64     Cached
  + r-bit                                             4.0.5  r42h25e906a_1             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64        1MB
  + r-bit64                                           4.0.5  r42h25e906a_2             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      516kB
  + r-blob                                            1.2.4  r42hc72bb7e_1             mirrors.aliyun.com/anaconda/cloud/conda-forge/noarch              66kB
  + r-cachem                                          1.0.8  r42h25e906a_1             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       76kB
  + r-cli                                             3.6.1  r42h93f32a7_1             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64        1MB
  + r-cpp11                                           0.4.5  r42hc72bb7e_0             mirrors.aliyun.com/anaconda/cloud/conda-forge/noarch             236kB
  + r-crayon                                          1.5.2  r42hc72bb7e_2             mirrors.aliyun.com/anaconda/cloud/conda-forge/noarch             166kB
  + r-curl                                            5.0.1  r42h8aed89a_0             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      456kB
  + r-dbi                                             1.1.3  r42hc72bb7e_2             mirrors.aliyun.com/anaconda/cloud/conda-forge/noarch             713kB
  + r-dbplyr                                          2.3.3  r42hc72bb7e_0             mirrors.aliyun.com/anaconda/cloud/conda-forge/noarch               1MB
  + r-dplyr                                           1.1.2  r42h93f32a7_1             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64        1MB
  + r-ellipsis                                        0.3.2  r42h25e906a_2             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       44kB
  + r-fansi                                           1.0.4  r42h25e906a_1             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      321kB
  + r-fastmap                                         1.1.1  r42h93f32a7_1             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       73kB
  + r-filelock                                        1.0.2  r42h9d23599_1004          mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       31kB
  + r-generics                                        0.1.3  r42hc72bb7e_2             mirrors.aliyun.com/anaconda/cloud/conda-forge/noarch              91kB
  + r-glue                                            1.6.2  r42h25e906a_2             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      153kB
  + r-httr                                            1.4.6  r42hc72bb7e_1             mirrors.aliyun.com/anaconda/cloud/conda-forge/noarch             487kB
  + r-jsonlite                                        1.8.7  r42h25e906a_0             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      641kB
  + r-lifecycle                                       1.0.3  r42hc72bb7e_2             mirrors.aliyun.com/anaconda/cloud/conda-forge/noarch             122kB
  + r-magrittr                                        2.0.3  r42h25e906a_2             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      210kB
  + r-memoise                                         2.0.1  r42hc72bb7e_2             mirrors.aliyun.com/anaconda/cloud/conda-forge/noarch              56kB
  + r-mime                                             0.12  r42h25e906a_2             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       54kB
  + r-openssl                                         2.0.6  r42h2a8de3c_1             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      640kB
  + r-pillar                                          1.9.0  r42hc72bb7e_1             mirrors.aliyun.com/anaconda/cloud/conda-forge/noarch             618kB
  + r-pkgconfig                                       2.0.3  r42hc72bb7e_3             mirrors.aliyun.com/anaconda/cloud/conda-forge/noarch              26kB
  + r-plogr                                           0.2.0  r42hc72bb7e_1005          mirrors.aliyun.com/anaconda/cloud/conda-forge/noarch              22kB
  + r-purrr                                           1.0.1  r42h25e906a_1             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      489kB
  + r-r6                                              2.5.1  r42hc72bb7e_2             mirrors.aliyun.com/anaconda/cloud/conda-forge/noarch              91kB
  + r-rlang                                           1.1.1  r42h93f32a7_1             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64        2MB
  + r-rsqlite                                         2.3.1  r42h93f32a7_1             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64        1MB
  + r-stringi                                        1.7.12  r42heb6e581_2             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      896kB
  + r-stringr                                         1.5.0  r42h785f33e_1             mirrors.aliyun.com/anaconda/cloud/conda-forge/noarch             296kB
  + r-sys                                             3.4.2  r42h25e906a_1             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       50kB
  + r-tibble                                          3.2.1  r42h25e906a_2             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      612kB
  + r-tidyr                                           1.3.0  r42h93f32a7_1             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64        1MB
  + r-tidyselect                                      1.2.0  r42h4571c7f_1             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      216kB
  + r-utf8                                            1.2.3  r42h25e906a_1             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      148kB
  + r-vctrs                                           0.6.3  r42h93f32a7_0             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64        1MB
  + r-withr                                           2.5.0  r42hc72bb7e_2             mirrors.aliyun.com/anaconda/cloud/conda-forge/noarch             239kB
  + readline                                            8.2  h8fc344f_1                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      294kB
  + sed                                                 4.8  ha0d5d3d_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      289kB
  + sysroot_linux-aarch64                              2.17  h5b4a56d_13               mirrors.aliyun.com/anaconda/cloud/conda-forge/noarch              16MB
  + tk                                               8.6.12  hd8af866_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64        4MB
  + tktable                                            2.10  hcd05d48_3                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       90kB
  + xorg-kbproto                                      1.0.7  h3557bc0_1002             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       27kB
  + xorg-libice                                       1.1.1  h7935292_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       60kB
  + xorg-libsm                                        1.2.4  h5a01bc2_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       29kB
  + xorg-libx11                                       1.8.6  h055a233_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      850kB
  + xorg-libxau                                      1.0.11  h31becfc_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       15kB
  + xorg-libxdmcp                                     1.1.3  h3557bc0_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       20kB
  + xorg-libxext                                      1.3.4  h2a766a3_2                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       51kB
  + xorg-libxrender                                  0.9.11  h7935292_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       37kB
  + xorg-libxt                                        1.3.0  h7935292_1                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      384kB
  + xorg-renderproto                                 0.11.1  h3557bc0_1002             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       10kB
  + xorg-xextproto                                    7.3.0  h2a766a3_1003             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       30kB
  + xorg-xproto                                      7.0.31  h3557bc0_1007             mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       75kB
  + xz                                                5.2.6  h9cdd2b7_0                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      441kB
  + zlib                                             1.2.13  h31becfc_5                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64       96kB
  + zstd                                              1.5.2  h4c53e97_7                mirrors.aliyun.com/anaconda/cloud/conda-forge/linux-aarch64      406kB

  Summary:

  Install: 132 packages

  Total download: 195MB

───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

Traceback (most recent call last):
  File "/home/mgrigorov/miniconda3/envs/biotest/bin/bioconda-utils", line 33, in <module>
    sys.exit(load_entry_point('bioconda-utils', 'console_scripts', 'bioconda-utils')())
  File "/home/mgrigorov/git/bioconda/bioconda-utils/bioconda_utils/cli.py", line 1024, in main
    argh.dispatch_commands([
  File "/home/mgrigorov/miniconda3/envs/biotest/lib/python3.8/site-packages/argh/dispatching.py", line 328, in dispatch_commands
    dispatch(parser, *args, **kwargs)
  File "/home/mgrigorov/miniconda3/envs/biotest/lib/python3.8/site-packages/argh/dispatching.py", line 174, in dispatch
    for line in lines:
  File "/home/mgrigorov/miniconda3/envs/biotest/lib/python3.8/site-packages/argh/dispatching.py", line 277, in _execute_command
    for line in result:
  File "/home/mgrigorov/miniconda3/envs/biotest/lib/python3.8/site-packages/argh/dispatching.py", line 260, in _call
    result = function(*positional, **keywords)
  File "<boltons.funcutils.FunctionBuilder-5>", line 2, in build
  File "/home/mgrigorov/git/bioconda/bioconda-utils/bioconda_utils/cli.py", line 133, in wrapper
    func(*args, **kwargs)
  File "<boltons.funcutils.FunctionBuilder-4>", line 2, in build
  File "/home/mgrigorov/git/bioconda/bioconda-utils/bioconda_utils/cli.py", line 62, in wrapper
    func(*args, **kwargs)
  File "/home/mgrigorov/git/bioconda/bioconda-utils/bioconda_utils/cli.py", line 474, in build
    success = build_recipes(recipe_folder, config, recipes,
  File "/home/mgrigorov/git/bioconda/bioconda-utils/bioconda_utils/build.py", line 323, in build_recipes
    pkg_paths = utils.get_package_paths(recipe, check_channels, force=force)
  File "/home/mgrigorov/git/bioconda/bioconda-utils/bioconda_utils/utils.py", line 1140, in get_package_paths
    platform, metas = _load_platform_metas(recipe, finalize=True)
  File "/home/mgrigorov/git/bioconda/bioconda-utils/bioconda_utils/utils.py", line 1040, in _load_platform_metas
    return platform, load_all_meta(recipe, config=config, finalize=finalize)
  File "/home/mgrigorov/git/bioconda/bioconda-utils/bioconda_utils/utils.py", line 450, in load_all_meta
    metas = [
  File "/home/mgrigorov/git/bioconda/bioconda-utils/bioconda_utils/utils.py", line 453, in <listcomp>
    for (meta, _, _) in api.render(
  File "/home/mgrigorov/miniconda3/envs/biotest/lib/python3.8/site-packages/conda_build/api.py", line 49, in render
    for od, om in meta.get_output_metadata_set(
  File "/home/mgrigorov/miniconda3/envs/biotest/lib/python3.8/site-packages/conda_build/metadata.py", line 2120, in get_output_metadata_set
    conda_packages = finalize_outputs_pass(ref_metadata, conda_packages, pass_no=0,
  File "/home/mgrigorov/miniconda3/envs/biotest/lib/python3.8/site-packages/conda_build/metadata.py", line 781, in finalize_outputs_pass
    fm = finalize_metadata(om, parent_metadata=parent_metadata,
  File "/home/mgrigorov/miniconda3/envs/biotest/lib/python3.8/site-packages/conda_build/render.py", line 546, in finalize_metadata
    build_unsat, host_unsat = add_upstream_pins(m,
  File "/home/mgrigorov/miniconda3/envs/biotest/lib/python3.8/site-packages/conda_build/render.py", line 408, in add_upstream_pins
    host_deps, host_unsat, extra_run_specs_from_host = _read_upstream_pin_files(m, 'host',
  File "/home/mgrigorov/miniconda3/envs/biotest/lib/python3.8/site-packages/conda_build/render.py", line 378, in _read_upstream_pin_files
    extra_run_specs = get_upstream_pins(m, actions, env)
  File "/home/mgrigorov/miniconda3/envs/biotest/lib/python3.8/site-packages/conda_build/render.py", line 364, in get_upstream_pins
    loc, dist = execute_download_actions(m, actions, env=env, package_subset=pkg)[pkg]
  File "/home/mgrigorov/miniconda3/envs/biotest/lib/python3.8/site-packages/conda_build/render.py", line 331, in execute_download_actions
    _loc = os.path.join(pkg_dir, index[pkg].fn)
KeyError: Dist(channel='http://mirrors.aliyun.com/anaconda/cloud/conda-forge', dist_name='r-curl-5.0.1-r42h8aed89a_0', name='r-curl', fmt='.conda', version='5.0.1', build_string='r42h8aed89a_0', build_number=0, base_url=None, platform=None)
martin-g commented 1 year ago

It seems the error is just a weird way to say that the download of a package (r-curl in the above error) has timed out. Executing the same command several times always fail with a different package and on the next attempt the respective package is listed as Cached

martin-g commented 1 year ago

After doing the above command several times finally all is cached and the build proceeds to:

...
06:40:32 BIOCONDA INFO (OUT) An HTTP error occurred when trying to retrieve this URL.
06:40:32 BIOCONDA INFO (OUT) HTTP errors are often intermittent, and a simple retry will get you on your way.
06:40:32 BIOCONDA INFO (OUT) Downloading https://depot.galaxyproject.org/software/bioconductor-biocfilecache/bioconductor-biocfilecache_2.8.1_src_all.tar.gz
06:40:32 BIOCONDA INFO (OUT) INFO:conda_build.source:Downloading https://depot.galaxyproject.org/software/bioconductor-biocfilecache/bioconductor-biocfilecache_2.8.1_src_all.tar.gz
06:40:32 BIOCONDA INFO (OUT) DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): depot.galaxyproject.org:443
06:40:34 BIOCONDA INFO (OUT) DEBUG:urllib3.connectionpool:https://depot.galaxyproject.org:443 "GET /software/bioconductor-biocfilecache/bioconductor-biocfilecache_2.8.1_src_all.tar.gz HTTP/1.1" 404 153
06:40:34 BIOCONDA INFO (OUT) Error: HTTP 404 NOT FOUND for url <https://depot.galaxyproject.org/software/bioconductor-biocfilecache/bioconductor-biocfilecache_2.8.1_src_all.tar.gz>
06:40:34 BIOCONDA INFO (OUT) Elapsed: 00:01.281473
06:40:34 BIOCONDA INFO (OUT) 
06:40:34 BIOCONDA INFO (OUT) An HTTP error occurred when trying to retrieve this URL.
06:40:34 BIOCONDA INFO (OUT) HTTP errors are often intermittent, and a simple retry will get you on your way.
06:40:34 BIOCONDA INFO (OUT) WARNING:conda_build.source:Error: HTTP 404 NOT FOUND for url <https://depot.galaxyproject.org/software/bioconductor-biocfilecache/bioconductor-biocfilecache_2.8.1_src_all.tar.gz>
06:40:34 BIOCONDA INFO (OUT) Elapsed: 00:01.281473
06:40:34 BIOCONDA INFO (OUT) 
06:40:34 BIOCONDA INFO (OUT) An HTTP error occurred when trying to retrieve this URL.
06:40:34 BIOCONDA INFO (OUT) HTTP errors are often intermittent, and a simple retry will get you on your way.
06:40:34 BIOCONDA INFO (OUT) Traceback (most recent call last):
06:40:34 BIOCONDA INFO (OUT)   File "/opt/conda/bin/conda-mambabuild", line 10, in <module>
06:40:34 BIOCONDA INFO (OUT)     sys.exit(main())
06:40:34 BIOCONDA INFO (OUT)   File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 239, in main
06:40:34 BIOCONDA INFO (OUT)     call_conda_build(action, config)
06:40:34 BIOCONDA INFO (OUT)   File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 211, in call_conda_build
06:40:34 BIOCONDA INFO (OUT)     result = api.build(
06:40:34 BIOCONDA INFO (OUT)   File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 186, in build
06:40:34 BIOCONDA INFO (OUT)     return build_tree(
06:40:34 BIOCONDA INFO (OUT)   File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3088, in build_tree
06:40:34 BIOCONDA INFO (OUT)     packages_from_this = build(metadata, stats,
06:40:34 BIOCONDA INFO (OUT)   File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2138, in build
06:40:34 BIOCONDA INFO (OUT)     try_download(m, no_download_source=False, raise_error=True)
06:40:34 BIOCONDA INFO (OUT)   File "/opt/conda/lib/python3.8/site-packages/conda_build/render.py", line 649, in try_download
06:40:34 BIOCONDA INFO (OUT)     source.provide(metadata)
06:40:34 BIOCONDA INFO (OUT)   File "/opt/conda/lib/python3.8/site-packages/conda_build/source.py", line 859, in provide
06:40:34 BIOCONDA INFO (OUT)     unpack(source_dict, src_dir, metadata.config.src_cache, recipe_path=metadata.path,
06:40:34 BIOCONDA INFO (OUT)   File "/opt/conda/lib/python3.8/site-packages/conda_build/source.py", line 139, in unpack
06:40:34 BIOCONDA INFO (OUT)     src_path, unhashed_fn = download_to_cache(cache_folder, recipe_path, source_dict, verbose)
06:40:34 BIOCONDA INFO (OUT)   File "/opt/conda/lib/python3.8/site-packages/conda_build/source.py", line 95, in download_to_cache
06:40:34 BIOCONDA INFO (OUT)     raise RuntimeError("Could not download %s" % url)
06:40:34 BIOCONDA INFO (OUT) RuntimeError: Could not download https://depot.galaxyproject.org/software/bioconductor-biocfilecache/bioconductor-biocfilecache_2.8.1_src_all.tar.gz
06:40:41 BIOCONDA ERROR COMMAND FAILED (exited with 1): docker run -t --net host --rm -v /tmp/tmpw965yqcf/build_script.bash:/opt/build_script.bash -v /home/mgrigorov/miniconda3/envs/biotest/conda-bld/:/opt/host-conda-bld -v /home/mgrigorov/git/bioconda/bioconda-recipes/recipes/bioconductor-biocfilecache:/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 ghcr.io/yikun/bioconda-utils-build-env-cos7-aarch64 /bin/bash /opt/build_script.bash

06:40:41 BIOCONDA ERROR BUILD FAILED recipes/bioconductor-biocfilecache
06:40:41 BIOCONDA INFO (COMMAND) conda build purge
06:40:42 BIOCONDA ERROR BUILD SUMMARY: of 1 recipes, 1 failed and 0 were skipped. Details of recipes and environments follow.
06:40:42 BIOCONDA ERROR BUILD SUMMARY: FAILED recipe recipes/bioconductor-biocfilecache

https://depot.galaxyproject.org/software/bioconductor-biocfilecache/bioconductor-biocfilecache_2.8.1_src_all.tar.gz gives 404 !