Vincent Carey
| Snapshot Date: 2025-03-17 13:40 -0400 (Mon, 17 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/scviR |
| git_branch: devel |
| git_last_commit: 97c87b8 |
| git_last_commit_date: 2024-10-29 11:18:41 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-18 11:49 -0400 (Tue, 18 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4537 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4543 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4459 |
| 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 | ||||
| Package 1926/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scviR 1.7.0 (landing page) Vincent Carey
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: scviR |
| Version: 1.7.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data scviR |
| StartedAt: 2025-03-18 02:32:08 -0000 (Tue, 18 Mar 2025) |
| EndedAt: 2025-03-18 03:02:47 -0000 (Tue, 18 Mar 2025) |
| EllapsedTime: 1838.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/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
Channels:
- conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.19.1/scviR/1.7.0/bsklenv
added / updated specs:
- python=3.10
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-h68df207_7
ca-certificates conda-forge/linux-aarch64::ca-certificates-2025.1.31-hcefe29a_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.43-h80caac9_4
libffi conda-forge/linux-aarch64::libffi-3.4.6-he21f813_0
libgcc conda-forge/linux-aarch64::libgcc-14.2.0-he277a41_2
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-14.2.0-he9431aa_2
libgomp conda-forge/linux-aarch64::libgomp-14.2.0-he277a41_2
liblzma conda-forge/linux-aarch64::liblzma-5.6.4-h86ecc28_0
libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.49.1-h5eb1b54_2
libuuid conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_0
libxcrypt conda-forge/linux-aarch64::libxcrypt-4.4.36-h31becfc_1
libzlib conda-forge/linux-aarch64::libzlib-1.3.1-h86ecc28_2
ncurses conda-forge/linux-aarch64::ncurses-6.5-ha32ae93_3
openssl conda-forge/linux-aarch64::openssl-3.4.1-hd08dc88_0
pip conda-forge/noarch::pip-25.0.1-pyh8b19718_0
python conda-forge/linux-aarch64::python-3.10.16-h57b00e1_1_cpython
readline conda-forge/linux-aarch64::readline-8.2-h8382b9d_2
setuptools conda-forge/noarch::setuptools-75.8.2-pyhff2d567_0
tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0
tzdata conda-forge/noarch::tzdata-2025a-h78e105d_0
wheel conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Channels:
- conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 24.11.3
latest version: 25.1.1
Please update conda by running
$ conda update -n base -c conda-forge conda
# All requested packages already installed.
Channels:
- conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 24.11.3
latest version: 25.1.1
Please update conda by running
$ conda update -n base -c conda-forge conda
## Package Plan ##
environment location: /home/biocbuild/.cache/R/basilisk/1.19.1/scviR/1.7.0/bsklenv
added / updated specs:
- numpy=1.24.4
- pandas=1.5.3
- python[version='3.10.*,3.10.*']
The following NEW packages will be INSTALLED:
libblas conda-forge/linux-aarch64::libblas-3.9.0-31_h1a9f1db_openblas
libcblas conda-forge/linux-aarch64::libcblas-3.9.0-31_hab92f65_openblas
libgfortran conda-forge/linux-aarch64::libgfortran-14.2.0-he9431aa_2
libgfortran5 conda-forge/linux-aarch64::libgfortran5-14.2.0-hb6113d0_2
liblapack conda-forge/linux-aarch64::liblapack-3.9.0-31_h411afd4_openblas
libopenblas conda-forge/linux-aarch64::libopenblas-0.3.29-pthreads_h9d3fd7e_0
libstdcxx conda-forge/linux-aarch64::libstdcxx-14.2.0-h3f4de04_2
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-14.2.0-hf1166c9_2
numpy conda-forge/linux-aarch64::numpy-1.24.4-py310h7f380f4_0
pandas conda-forge/linux-aarch64::pandas-1.5.3-py310hc3d6b01_1
python-dateutil conda-forge/noarch::python-dateutil-2.9.0.post0-pyhff2d567_1
python_abi conda-forge/linux-aarch64::python_abi-3.10-5_cp310
pytz conda-forge/noarch::pytz-2025.1-pyhd8ed1ab_0
six conda-forge/noarch::six-1.17.0-pyhd8ed1ab_0
Downloading and Extracting Packages: ...working... done
Preparing transaction: - \ | done
Verifying transaction: - \ | / - \ | / - \ | / - \ done
Executing transaction: / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done
Collecting anndata==0.10.1
Using cached anndata-0.10.1-py3-none-any.whl.metadata (6.4 kB)
Collecting docrep==0.3.2
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==0.8.1
Using cached flax-0.8.1-py3-none-any.whl.metadata (10 kB)
Collecting jax==0.4.23
Using cached jax-0.4.23-py3-none-any.whl.metadata (24 kB)
Collecting jaxlib==0.4.23
Using cached jaxlib-0.4.23-cp310-cp310-manylinux2014_aarch64.whl.metadata (2.1 kB)
Collecting optax==0.1.9
Using cached optax-0.1.9-py3-none-any.whl.metadata (6.7 kB)
Collecting scipy==1.12.0
Using cached scipy-1.12.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (112 kB)
Collecting scikit-learn==1.4.0
Using cached scikit_learn-1.4.0-1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (11 kB)
Collecting rich==13.7.1
Using cached rich-13.7.1-py3-none-any.whl.metadata (18 kB)
Collecting h5py==3.9.0
Using cached h5py-3.9.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (2.5 kB)
Collecting torch==1.13.1
Using cached torch-1.13.1-cp310-cp310-manylinux2014_aarch64.whl.metadata (23 kB)
Collecting lightning==2.1.4
Using cached lightning-2.1.4-py3-none-any.whl.metadata (57 kB)
Collecting torchmetrics==0.11.0
Using cached torchmetrics-0.11.0-py3-none-any.whl.metadata (16 kB)
Collecting tqdm==4.66.2
Using cached tqdm-4.66.2-py3-none-any.whl.metadata (57 kB)
Collecting ml-collections==0.1.1
Using cached ml_collections-0.1.1.tar.gz (77 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting mudata==0.2.3
Using cached mudata-0.2.3-py3-none-any.whl.metadata (4.7 kB)
Collecting scvi-tools==1.1.2
Using cached scvi_tools-1.1.2-py3-none-any.whl.metadata (12 kB)
Collecting scanpy==1.9.5
Using cached scanpy-1.9.5-py3-none-any.whl.metadata (5.9 kB)
Collecting matplotlib==3.7.3
Using cached matplotlib-3.7.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (5.7 kB)
Collecting scikit-misc==0.3.1
Using cached scikit_misc-0.3.1.tar.gz (302 kB)
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'
Installing backend dependencies: started
Installing backend dependencies: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'error'
error: subprocess-exited-with-error
× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [10 lines of output]
+ meson setup /home/biocbuild/tmp/pip-install-5l58l1qv/scikit-misc_a70d54d6f4c5468c96c4e4095920ae42 /home/biocbuild/tmp/pip-install-5l58l1qv/scikit-misc_a70d54d6f4c5468c96c4e4095920ae42/.mesonpy-cexaysnm -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/home/biocbuild/tmp/pip-install-5l58l1qv/scikit-misc_a70d54d6f4c5468c96c4e4095920ae42/.mesonpy-cexaysnm/meson-python-native-file.ini
The Meson build system
Version: 1.7.0
Source dir: /home/biocbuild/tmp/pip-install-5l58l1qv/scikit-misc_a70d54d6f4c5468c96c4e4095920ae42
Build dir: /home/biocbuild/tmp/pip-install-5l58l1qv/scikit-misc_a70d54d6f4c5468c96c4e4095920ae42/.mesonpy-cexaysnm
Build type: native build
../meson.build:5:11: ERROR: Command `/home/biocbuild/tmp/pip-install-5l58l1qv/scikit-misc_a70d54d6f4c5468c96c4e4095920ae42/skmisc/_build_utils/version_please.py` failed with status 127.
A full log can be found at /home/biocbuild/tmp/pip-install-5l58l1qv/scikit-misc_a70d54d6f4c5468c96c4e4095920ae42/.mesonpy-cexaysnm/meson-logs/meson-log.txt
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
Quitting from citeseq_tut.Rmd:42-48 [doinit]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `setupBasiliskEnv()`:
! failed to install additional packages via pip
---
Backtrace:
▆
1. └─scviR::getCiteseq5k10kPbmcs()
2. └─scviR::anndataR()
3. └─basilisk::basiliskStart(bsklenv)
4. └─basilisk::obtainEnvironmentPath(env)
5. └─basilisk::setupBasiliskEnv(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 1089.7 MB
Quitting from compch12.Rmd:49-53 [getdat2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `download.file()`:
! download from 'https://mghp.osn.xsede.org/bir190004-bucket01/BiocScviR/full_5k10k_totalVI.h5ad' failed
---
Backtrace:
▆
1. └─scviR::getTotalVI5k10kAdata()
2. └─scviR:::.osn_bucket_to_cache("full_5k10k_totalVI.h5ad")
3. └─utils::download.file(target, tf)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'compch12.Rmd' failed with diagnostics:
download from 'https://mghp.osn.xsede.org/bir190004-bucket01/BiocScviR/full_5k10k_totalVI.h5ad' failed
--- 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