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This page was generated on 2023-03-27 05:50:43 -0000 (Mon, 27 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" 6083
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD results for scviR on kunpeng1


To the developers/maintainers of the scviR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scviR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1843/2195HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scviR 0.99.9  (landing page)
Vincent Carey
Snapshot Date: 2023-03-24 01:40:07 -0000 (Fri, 24 Mar 2023)
git_url: https://git.bioconductor.org/packages/scviR
git_branch: devel
git_last_commit: 6936132
git_last_commit_date: 2023-03-10 16:42:08 -0000 (Fri, 10 Mar 2023)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    ERROR  skipped

Summary

Package: scviR
Version: 0.99.9
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data scviR
StartedAt: 2023-03-24 17:07:56 -0000 (Fri, 24 Mar 2023)
EndedAt: 2023-03-24 17:40:01 -0000 (Fri, 24 Mar 2023)
EllapsedTime: 1925.6 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data scviR
###
##############################################################################
##############################################################################


* checking for file ‘scviR/DESCRIPTION’ ... OK
* preparing ‘scviR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘citeseq_tut.Rmd’ using rmarkdown
trying URL 'https://mghp.osn.xsede.org/bir190004-bucket01/BiocScviR/pbmc_citeseq_5k10k.h5ad.gz'
Content type 'application/octet-stream' length 51844928 bytes (49.4 MB)
==================================================
downloaded 49.4 MB

Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.11.3/scviR/0.99.9/bsklenv

  added / updated specs:
    - python=3.8.13


The following NEW packages will be INSTALLED:

  _openmp_mutex      conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu
  bzip2              conda-forge/linux-aarch64::bzip2-1.0.8-hf897c2e_4
  ca-certificates    conda-forge/linux-aarch64::ca-certificates-2022.12.7-h4fd8a4c_0
  ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.40-h2d8c526_0
  libffi             conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5
  libgcc-ng          conda-forge/linux-aarch64::libgcc-ng-12.2.0-h607ecd0_19
  libgomp            conda-forge/linux-aarch64::libgomp-12.2.0-h607ecd0_19
  libnsl             conda-forge/linux-aarch64::libnsl-2.0.0-hf897c2e_0
  libsqlite          conda-forge/linux-aarch64::libsqlite-3.40.0-hf9034f9_0
  libuuid            conda-forge/linux-aarch64::libuuid-2.32.1-hf897c2e_1000
  libzlib            conda-forge/linux-aarch64::libzlib-1.2.13-h4e544f5_4
  ncurses            conda-forge/linux-aarch64::ncurses-6.3-headf329_1
  openssl            conda-forge/linux-aarch64::openssl-3.1.0-hb4cce97_0
  pip                conda-forge/noarch::pip-23.0.1-pyhd8ed1ab_0
  python             conda-forge/linux-aarch64::python-3.8.13-h92ab765_0_cpython
  readline           conda-forge/linux-aarch64::readline-8.2-h8fc344f_1
  setuptools         conda-forge/noarch::setuptools-67.6.0-pyhd8ed1ab_0
  sqlite             conda-forge/linux-aarch64::sqlite-3.40.0-h69ca7e5_0
  tk                 conda-forge/linux-aarch64::tk-8.6.12-hd8af866_0
  wheel              conda-forge/noarch::wheel-0.40.0-pyhd8ed1ab_0
  xz                 conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.11.3/scviR/0.99.9/bsklenv

  added / updated specs:
    - python=3.8.13


The following packages will be UPDATED:

  ca-certificates    conda-forge::ca-certificates-2022.12.~ --> pkgs/main::ca-certificates-2023.01.10-hd43f75c_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 23.1.0

Please update conda by running

    $ conda update -n base -c defaults conda


Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.11.3/scviR/0.99.9/bsklenv

  added / updated specs:
    - numpy=1.23.1
    - pandas=1.4.4
    - python=3.8.13


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    numpy-1.23.1               |   py38ha80beb7_0         6.6 MB  conda-forge
    pandas-1.4.4               |   py38h2fe58aa_0        12.3 MB  conda-forge
    ------------------------------------------------------------
                                           Total:        18.9 MB

The following NEW packages will be INSTALLED:

  libblas            conda-forge/linux-aarch64::libblas-3.9.0-16_linuxaarch64_openblas
  libcblas           conda-forge/linux-aarch64::libcblas-3.9.0-16_linuxaarch64_openblas
  libgfortran-ng     conda-forge/linux-aarch64::libgfortran-ng-12.2.0-he9431aa_19
  libgfortran5       conda-forge/linux-aarch64::libgfortran5-12.2.0-hf695500_19
  liblapack          conda-forge/linux-aarch64::liblapack-3.9.0-16_linuxaarch64_openblas
  libopenblas        conda-forge/linux-aarch64::libopenblas-0.3.21-pthreads_h6cb6f83_3
  libstdcxx-ng       conda-forge/linux-aarch64::libstdcxx-ng-12.2.0-hc13a102_19
  numpy              conda-forge/linux-aarch64::numpy-1.23.1-py38ha80beb7_0
  pandas             conda-forge/linux-aarch64::pandas-1.4.4-py38h2fe58aa_0
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
  python_abi         conda-forge/linux-aarch64::python_abi-3.8-3_cp38
  pytz               conda-forge/noarch::pytz-2022.7.1-pyhd8ed1ab_0
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0

The following packages will be SUPERSEDED by a higher-priority channel:

  ca-certificates    pkgs/main::ca-certificates-2023.01.10~ --> conda-forge::ca-certificates-2022.12.7-h4fd8a4c_0



Downloading and Extracting Packages

numpy-1.23.1         | 6.6 MB    |            |   0% 
numpy-1.23.1         | 6.6 MB    |            |   0% 
numpy-1.23.1         | 6.6 MB    | 5          |   6% 
numpy-1.23.1         | 6.6 MB    | #          |  11% 
numpy-1.23.1         | 6.6 MB    | #5         |  16% 
numpy-1.23.1         | 6.6 MB    | ##1        |  22% 
numpy-1.23.1         | 6.6 MB    | ###1       |  32% 
numpy-1.23.1         | 6.6 MB    | ####5      |  45% 
numpy-1.23.1         | 6.6 MB    | #####6     |  57% 
numpy-1.23.1         | 6.6 MB    | ######6    |  66% 
numpy-1.23.1         | 6.6 MB    | #######2   |  73% 
numpy-1.23.1         | 6.6 MB    | #######8   |  78% 
numpy-1.23.1         | 6.6 MB    | ########7  |  87% 
numpy-1.23.1         | 6.6 MB    | #########1 |  92% 
numpy-1.23.1         | 6.6 MB    | #########5 |  95% 
numpy-1.23.1         | 6.6 MB    | #########8 |  98% 
numpy-1.23.1         | 6.6 MB    | ########## | 100% 

pandas-1.4.4         | 12.3 MB   |            |   0% 
pandas-1.4.4         | 12.3 MB   |            |   0% 
pandas-1.4.4         | 12.3 MB   |            |   1% 
pandas-1.4.4         | 12.3 MB   | 1          |   1% 
pandas-1.4.4         | 12.3 MB   | 1          |   2% 
pandas-1.4.4         | 12.3 MB   | 2          |   3% 
pandas-1.4.4         | 12.3 MB   | 3          |   3% 
pandas-1.4.4         | 12.3 MB   | 3          |   4% 
pandas-1.4.4         | 12.3 MB   | 4          |   4% 
pandas-1.4.4         | 12.3 MB   | 5          |   5% 
pandas-1.4.4         | 12.3 MB   | 5          |   6% 
pandas-1.4.4         | 12.3 MB   | 6          |   7% 
pandas-1.4.4         | 12.3 MB   | 7          |   8% 
pandas-1.4.4         | 12.3 MB   | 8          |   8% 
pandas-1.4.4         | 12.3 MB   | 9          |  10% 
pandas-1.4.4         | 12.3 MB   | ##         |  21% 
pandas-1.4.4         | 12.3 MB   | ###        |  30% 
pandas-1.4.4         | 12.3 MB   | ###4       |  34% 
pandas-1.4.4         | 12.3 MB   | ###7       |  37% 
pandas-1.4.4         | 12.3 MB   | ####       |  40% 
pandas-1.4.4         | 12.3 MB   | ####4      |  44% 
pandas-1.4.4         | 12.3 MB   | ####9      |  49% 
pandas-1.4.4         | 12.3 MB   | #####3     |  54% 
pandas-1.4.4         | 12.3 MB   | ######1    |  62% 
pandas-1.4.4         | 12.3 MB   | ######4    |  64% 
pandas-1.4.4         | 12.3 MB   | ######7    |  67% 
pandas-1.4.4         | 12.3 MB   | ######8    |  69% 
pandas-1.4.4         | 12.3 MB   | #######    |  71% 
pandas-1.4.4         | 12.3 MB   | #######1   |  72% 
pandas-1.4.4         | 12.3 MB   | #######3   |  73% 
pandas-1.4.4         | 12.3 MB   | #######4   |  74% 
pandas-1.4.4         | 12.3 MB   | #######5   |  76% 
pandas-1.4.4         | 12.3 MB   | #######6   |  77% 
pandas-1.4.4         | 12.3 MB   | #######8   |  79% 
pandas-1.4.4         | 12.3 MB   | ########2  |  83% 
pandas-1.4.4         | 12.3 MB   | ########4  |  85% 
pandas-1.4.4         | 12.3 MB   | ########6  |  87% 
pandas-1.4.4         | 12.3 MB   | ########8  |  88% 
pandas-1.4.4         | 12.3 MB   | #########1 |  91% 
pandas-1.4.4         | 12.3 MB   | #########3 |  94% 
pandas-1.4.4         | 12.3 MB   | #########6 |  97% 
pandas-1.4.4         | 12.3 MB   | #########8 |  98% 
pandas-1.4.4         | 12.3 MB   | #########9 | 100% 
pandas-1.4.4         | 12.3 MB   | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 23.1.0

Please update conda by running

    $ conda update -n base -c defaults conda


Collecting scvi-tools==0.20.0
  Downloading scvi_tools-0.20.0-py3-none-any.whl (330 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 330.2/330.2 kB 14.4 MB/s eta 0:00:00
Collecting scanpy==1.9.1
  Downloading scanpy-1.9.1-py3-none-any.whl (2.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 42.4 MB/s eta 0:00:00
Collecting matplotlib==3.6.3
  Downloading matplotlib-3.6.3-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (11.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.6/11.6 MB 1.4 MB/s eta 0:00:00
Collecting jax>=0.3
  Downloading jax-0.4.6.tar.gz (1.2 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 1.4 MB/s eta 0:00:00
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting torchmetrics>=0.11.0
  Downloading torchmetrics-0.11.4-py3-none-any.whl (519 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 519.2/519.2 kB 7.2 MB/s eta 0:00:00
Collecting openpyxl>=3.0
  Downloading openpyxl-3.1.2-py2.py3-none-any.whl (249 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 250.0/250.0 kB 15.7 MB/s eta 0:00:00
Collecting mudata>=0.1.2
  Downloading mudata-0.2.1-py3-none-any.whl (23 kB)
Collecting anndata>=0.7.5
  Using cached anndata-0.8.0-py3-none-any.whl (96 kB)
Collecting pyro-ppl>=1.6.0
  Downloading pyro_ppl-1.8.4-py3-none-any.whl (730 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 730.7/730.7 kB 26.6 MB/s eta 0:00:00
Collecting docrep>=0.3.2
  Downloading docrep-0.3.2.tar.gz (33 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting scikit-learn>=0.21.2
  Downloading scikit_learn-1.2.2-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (9.3 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.3/9.3 MB 1.6 MB/s eta 0:00:00
Collecting scipy
  Downloading scipy-1.10.1-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (31.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 31.0/31.0 MB 1.3 MB/s eta 0:00:00
ERROR: Could not find a version that satisfies the requirement jaxlib (from scvi-tools) (from versions: none)
ERROR: No matching distribution found for jaxlib
Quitting from lines 43-48 (citeseq_tut.Rmd) 
Error: processing vignette 'citeseq_tut.Rmd' failed with diagnostics:
failed to install additional packages via pip
--- failed re-building ‘citeseq_tut.Rmd’

--- re-building ‘compch12.Rmd’ using rmarkdown
trying URL 'https://mghp.osn.xsede.org/bir190004-bucket01/BiocScviR/ch12sce.rda'
Content type 'application/octet-stream' length 58079368 bytes (55.4 MB)
==================================================
downloaded 55.4 MB

trying URL 'https://mghp.osn.xsede.org/bir190004-bucket01/BiocScviR/full_5k10k_totalVI.h5ad'
Content type 'application/octet-stream' length 1216903940 bytes (1160.5 MB)
==================================================
downloaded 1160.5 MB

Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.11.3/scviR/0.99.9/bsklenv

  added / updated specs:
    - python=3.8.13


The following NEW packages will be INSTALLED:

  _openmp_mutex      conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu
  bzip2              conda-forge/linux-aarch64::bzip2-1.0.8-hf897c2e_4
  ca-certificates    conda-forge/linux-aarch64::ca-certificates-2022.12.7-h4fd8a4c_0
  ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.40-h2d8c526_0
  libffi             conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5
  libgcc-ng          conda-forge/linux-aarch64::libgcc-ng-12.2.0-h607ecd0_19
  libgomp            conda-forge/linux-aarch64::libgomp-12.2.0-h607ecd0_19
  libnsl             conda-forge/linux-aarch64::libnsl-2.0.0-hf897c2e_0
  libsqlite          conda-forge/linux-aarch64::libsqlite-3.40.0-hf9034f9_0
  libuuid            conda-forge/linux-aarch64::libuuid-2.32.1-hf897c2e_1000
  libzlib            conda-forge/linux-aarch64::libzlib-1.2.13-h4e544f5_4
  ncurses            conda-forge/linux-aarch64::ncurses-6.3-headf329_1
  openssl            conda-forge/linux-aarch64::openssl-3.1.0-hb4cce97_0
  pip                conda-forge/noarch::pip-23.0.1-pyhd8ed1ab_0
  python             conda-forge/linux-aarch64::python-3.8.13-h92ab765_0_cpython
  readline           conda-forge/linux-aarch64::readline-8.2-h8fc344f_1
  setuptools         conda-forge/noarch::setuptools-67.6.0-pyhd8ed1ab_0
  sqlite             conda-forge/linux-aarch64::sqlite-3.40.0-h69ca7e5_0
  tk                 conda-forge/linux-aarch64::tk-8.6.12-hd8af866_0
  wheel              conda-forge/noarch::wheel-0.40.0-pyhd8ed1ab_0
  xz                 conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.11.3/scviR/0.99.9/bsklenv

  added / updated specs:
    - python=3.8.13


The following packages will be UPDATED:

  ca-certificates    conda-forge::ca-certificates-2022.12.~ --> pkgs/main::ca-certificates-2023.01.10-hd43f75c_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 23.1.0

Please update conda by running

    $ conda update -n base -c defaults conda


Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/biocbuild/.cache/R/basilisk/1.11.3/scviR/0.99.9/bsklenv

  added / updated specs:
    - numpy=1.23.1
    - pandas=1.4.4
    - python=3.8.13


The following NEW packages will be INSTALLED:

  libblas            conda-forge/linux-aarch64::libblas-3.9.0-16_linuxaarch64_openblas
  libcblas           conda-forge/linux-aarch64::libcblas-3.9.0-16_linuxaarch64_openblas
  libgfortran-ng     conda-forge/linux-aarch64::libgfortran-ng-12.2.0-he9431aa_19
  libgfortran5       conda-forge/linux-aarch64::libgfortran5-12.2.0-hf695500_19
  liblapack          conda-forge/linux-aarch64::liblapack-3.9.0-16_linuxaarch64_openblas
  libopenblas        conda-forge/linux-aarch64::libopenblas-0.3.21-pthreads_h6cb6f83_3
  libstdcxx-ng       conda-forge/linux-aarch64::libstdcxx-ng-12.2.0-hc13a102_19
  numpy              conda-forge/linux-aarch64::numpy-1.23.1-py38ha80beb7_0
  pandas             conda-forge/linux-aarch64::pandas-1.4.4-py38h2fe58aa_0
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
  python_abi         conda-forge/linux-aarch64::python_abi-3.8-3_cp38
  pytz               conda-forge/noarch::pytz-2022.7.1-pyhd8ed1ab_0
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0

The following packages will be SUPERSEDED by a higher-priority channel:

  ca-certificates    pkgs/main::ca-certificates-2023.01.10~ --> conda-forge::ca-certificates-2022.12.7-h4fd8a4c_0


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done


==> WARNING: A newer version of conda exists. <==
  current version: 4.12.0
  latest version: 23.1.0

Please update conda by running

    $ conda update -n base -c defaults conda


Collecting scvi-tools==0.20.0
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Collecting tqdm>=4.56.0
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Requirement already satisfied: numpy>=1.17.0 in /home/biocbuild/.cache/R/basilisk/1.11.3/scviR/0.99.9/bsklenv/lib/python3.8/site-packages (from scvi-tools==0.20.0) (1.23.1)
Collecting scipy
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Collecting h5py>=2.9.0
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Requirement already satisfied: pandas>=1.0 in /home/biocbuild/.cache/R/basilisk/1.11.3/scviR/0.99.9/bsklenv/lib/python3.8/site-packages (from scvi-tools==0.20.0) (1.4.4)
Collecting mudata>=0.1.2
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ERROR: Could not find a version that satisfies the requirement jaxlib (from scvi-tools) (from versions: none)
ERROR: No matching distribution found for jaxlib
Quitting from lines 50-52 (compch12.Rmd) 
Error: processing vignette 'compch12.Rmd' failed with diagnostics:
failed to install additional packages via pip
--- failed re-building ‘compch12.Rmd’

--- re-building ‘scviR.Rmd’ using rmarkdown
--- finished re-building ‘scviR.Rmd’

SUMMARY: processing the following files failed:
  ‘citeseq_tut.Rmd’ ‘compch12.Rmd’

Error: Vignette re-building failed.
Execution halted