| Back to Build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-06-06 11:00:41 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
|
To the developers/maintainers of the scviR package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1843/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scviR 1.1.0 (landing page) Vincent Carey
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | |||||||||
| Package: scviR |
| Version: 1.1.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD build --keep-empty-dirs --no-resave-data scviR |
| StartedAt: 2023-06-05 15:02:03 -0000 (Mon, 05 Jun 2023) |
| EndedAt: 2023-06-05 15:10:48 -0000 (Mon, 05 Jun 2023) |
| EllapsedTime: 525.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/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
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/1.13.0/scviR/1.1.0/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-2023.5.7-hcefe29a_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-13.1.0-h2b4548d_0
libgomp conda-forge/linux-aarch64::libgomp-13.1.0-h2b4548d_0
libnsl conda-forge/linux-aarch64::libnsl-2.0.0-hf897c2e_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.42.0-h194ca79_0
libuuid conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0
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-3.1.1-h31becfc_1
pip conda-forge/noarch::pip-23.1.2-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-67.7.2-pyhd8ed1ab_0
sqlite conda-forge/linux-aarch64::sqlite-3.42.0-h3b3482f_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/1.13.0/scviR/1.1.0/bsklenv
added / updated specs:
- python=3.8.13
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates conda-forge::ca-certificates-2023.5.7~ --> 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: 23.5.0
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/1.13.0/scviR/1.1.0/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-3.9.0-17_linuxaarch64_openblas
libcblas conda-forge/linux-aarch64::libcblas-3.9.0-17_linuxaarch64_openblas
libgfortran-ng conda-forge/linux-aarch64::libgfortran-ng-13.1.0-he9431aa_0
libgfortran5 conda-forge/linux-aarch64::libgfortran5-13.1.0-h24e4805_0
liblapack conda-forge/linux-aarch64::liblapack-3.9.0-17_linuxaarch64_openblas
libopenblas conda-forge/linux-aarch64::libopenblas-0.3.23-pthreads_hd703e6f_0
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-13.1.0-h452befe_0
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-2023.3-pyhd8ed1ab_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
The following packages will be UPDATED:
ca-certificates pkgs/main::ca-certificates-2023.01.10~ --> conda-forge::ca-certificates-2023.5.7-hcefe29a_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: 23.5.0
Please update conda by running
$ conda update -n base -c defaults conda
Collecting scvi-tools==0.20.0
Using cached scvi_tools-0.20.0-py3-none-any.whl (330 kB)
Collecting scanpy==1.9.1
Using cached scanpy-1.9.1-py3-none-any.whl (2.0 MB)
Collecting matplotlib==3.6.3
Using cached matplotlib-3.6.3-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (11.6 MB)
Collecting anndata>=0.7.5 (from scvi-tools==0.20.0)
Using cached anndata-0.9.1-py3-none-any.whl (102 kB)
Collecting chex (from scvi-tools==0.20.0)
Using cached chex-0.1.7-py3-none-any.whl (89 kB)
Collecting docrep>=0.3.2 (from scvi-tools==0.20.0)
Using cached docrep-0.3.2.tar.gz (33 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting flax (from scvi-tools==0.20.0)
Using cached flax-0.6.10-py3-none-any.whl (226 kB)
Collecting h5py>=2.9.0 (from scvi-tools==0.20.0)
Using cached h5py-3.8.0-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (8.6 MB)
Collecting jax>=0.3 (from scvi-tools==0.20.0)
Using cached jax-0.4.11.tar.gz (1.3 MB)
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
INFO: pip is looking at multiple versions of scvi-tools to determine which version is compatible with other requirements. This could take a while.
ERROR: Ignored the following versions that require a different python version: 1.0.0 Requires-Python >=3.9; 1.0.0b0 Requires-Python >=3.9
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 [doinit] (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
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/1.13.0/scviR/1.1.0/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-2023.5.7-hcefe29a_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-13.1.0-h2b4548d_0
libgomp conda-forge/linux-aarch64::libgomp-13.1.0-h2b4548d_0
libnsl conda-forge/linux-aarch64::libnsl-2.0.0-hf897c2e_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.42.0-h194ca79_0
libuuid conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0
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-3.1.1-h31becfc_1
pip conda-forge/noarch::pip-23.1.2-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-67.7.2-pyhd8ed1ab_0
sqlite conda-forge/linux-aarch64::sqlite-3.42.0-h3b3482f_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/1.13.0/scviR/1.1.0/bsklenv
added / updated specs:
- python=3.8.13
The following packages will be SUPERSEDED by a higher-priority channel:
ca-certificates conda-forge::ca-certificates-2023.5.7~ --> 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: 23.5.0
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/1.13.0/scviR/1.1.0/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-3.9.0-17_linuxaarch64_openblas
libcblas conda-forge/linux-aarch64::libcblas-3.9.0-17_linuxaarch64_openblas
libgfortran-ng conda-forge/linux-aarch64::libgfortran-ng-13.1.0-he9431aa_0
libgfortran5 conda-forge/linux-aarch64::libgfortran5-13.1.0-h24e4805_0
liblapack conda-forge/linux-aarch64::liblapack-3.9.0-17_linuxaarch64_openblas
libopenblas conda-forge/linux-aarch64::libopenblas-0.3.23-pthreads_hd703e6f_0
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-13.1.0-h452befe_0
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-2023.3-pyhd8ed1ab_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
The following packages will be UPDATED:
ca-certificates pkgs/main::ca-certificates-2023.01.10~ --> conda-forge::ca-certificates-2023.5.7-hcefe29a_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: 23.5.0
Please update conda by running
$ conda update -n base -c defaults conda
Collecting scvi-tools==0.20.0
Using cached scvi_tools-0.20.0-py3-none-any.whl (330 kB)
Collecting scanpy==1.9.1
Using cached scanpy-1.9.1-py3-none-any.whl (2.0 MB)
Collecting matplotlib==3.6.3
Using cached matplotlib-3.6.3-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (11.6 MB)
Collecting anndata>=0.7.5 (from scvi-tools==0.20.0)
Using cached anndata-0.9.1-py3-none-any.whl (102 kB)
Collecting chex (from scvi-tools==0.20.0)
Using cached chex-0.1.7-py3-none-any.whl (89 kB)
Collecting docrep>=0.3.2 (from scvi-tools==0.20.0)
Using cached docrep-0.3.2.tar.gz (33 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting flax (from scvi-tools==0.20.0)
Using cached flax-0.6.10-py3-none-any.whl (226 kB)
Collecting h5py>=2.9.0 (from scvi-tools==0.20.0)
Using cached h5py-3.8.0-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (8.6 MB)
Collecting jax>=0.3 (from scvi-tools==0.20.0)
Using cached jax-0.4.11.tar.gz (1.3 MB)
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
INFO: pip is looking at multiple versions of scvi-tools to determine which version is compatible with other requirements. This could take a while.
ERROR: Ignored the following versions that require a different python version: 1.0.0 Requires-Python >=3.9; 1.0.0b0 Requires-Python >=3.9
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 [getdat2] (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