===============================
R CMD BUILD
===============================
* 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... done
## Package Plan ##
environment location: /home/pkgbuild/.cache/R/basilisk/1.11.2/scviR/0.99.1/bsklenv
added / updated specs:
- python=3.8.13
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
ca-certificates conda-forge/linux-64::ca-certificates-2022.12.7-ha878542_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-h41732ed_0
libffi conda-forge/linux-64::libffi-3.3-h58526e2_2
libgcc-ng conda-forge/linux-64::libgcc-ng-12.2.0-h65d4601_19
libgomp conda-forge/linux-64::libgomp-12.2.0-h65d4601_19
libsqlite conda-forge/linux-64::libsqlite-3.40.0-h753d276_0
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-12.2.0-h46fd767_19
libzlib conda-forge/linux-64::libzlib-1.2.13-h166bdaf_4
ncurses conda-forge/linux-64::ncurses-6.3-h27087fc_1
openssl conda-forge/linux-64::openssl-1.1.1t-h0b41bf4_0
pip conda-forge/noarch::pip-23.0.1-pyhd8ed1ab_0
python pkgs/main/linux-64::python-3.8.13-haa1d7c7_1
readline conda-forge/linux-64::readline-8.1.2-h0f457ee_0
setuptools conda-forge/noarch::setuptools-67.4.0-pyhd8ed1ab_0
sqlite conda-forge/linux-64::sqlite-3.40.0-h4ff8645_0
tk conda-forge/linux-64::tk-8.6.12-h27826a3_0
wheel conda-forge/noarch::wheel-0.38.4-pyhd8ed1ab_0
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0
zlib conda-forge/linux-64::zlib-1.2.13-h166bdaf_4
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/pkgbuild/.cache/R/basilisk/1.11.2/scviR/0.99.1/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-h06a4308_0
The following packages will be SUPERSEDED by a higher-priority channel:
openssl conda-forge::openssl-1.1.1t-h0b41bf4_0 --> pkgs/main::openssl-1.1.1t-h7f8727e_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/pkgbuild/.cache/R/basilisk/1.11.2/scviR/0.99.1/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-64::libblas-3.9.0-16_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-16_linux64_openblas
libgfortran-ng conda-forge/linux-64::libgfortran-ng-12.2.0-h69a702a_19
libgfortran5 conda-forge/linux-64::libgfortran5-12.2.0-h337968e_19
liblapack conda-forge/linux-64::liblapack-3.9.0-16_linux64_openblas
libopenblas conda-forge/linux-64::libopenblas-0.3.21-pthreads_h78a6416_3
numpy conda-forge/linux-64::numpy-1.23.1-py38h3a7f9d9_0
pandas conda-forge/linux-64::pandas-1.4.4-py38h47df419_0
python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
python_abi conda-forge/linux-64::python_abi-3.8-2_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-ha878542_0
openssl pkgs/main::openssl-1.1.1t-h7f8727e_0 --> conda-forge::openssl-1.1.1t-h0b41bf4_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
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_12_x86_64.manylinux2010_x86_64.whl (9.4 MB)
Collecting jax>=0.3
Using cached jax-0.4.4-py3-none-any.whl
Requirement already satisfied: pandas>=1.0 in /home/pkgbuild/.cache/R/basilisk/1.11.2/scviR/0.99.1/bsklenv/lib/python3.8/site-packages (from scvi-tools==0.20.0) (1.4.4)
Collecting torchmetrics>=0.11.0
Using cached torchmetrics-0.11.1-py3-none-any.whl (517 kB)
Collecting chex
Using cached chex-0.1.6-py3-none-any.whl (87 kB)
Collecting numpyro
Using cached numpyro-0.11.0-py3-none-any.whl (300 kB)
Collecting pytorch-lightning<1.10.0,>=1.9.0
Using cached pytorch_lightning-1.9.3-py3-none-any.whl (826 kB)
Collecting pyro-ppl>=1.6.0
Using cached pyro_ppl-1.8.4-py3-none-any.whl (730 kB)
Collecting torch>=1.8.0
Using cached torch-1.13.1-cp38-cp38-manylinux1_x86_64.whl (887.4 MB)
Collecting scikit-learn>=0.21.2
Using cached scikit_learn-1.2.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (9.8 MB)
Collecting h5py>=2.9.0
Using cached h5py-3.8.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.7 MB)
Collecting ml-collections>=0.1.1
Using cached ml_collections-0.1.1-py3-none-any.whl
Collecting openpyxl>=3.0
Using cached openpyxl-3.1.1-py2.py3-none-any.whl (249 kB)
Collecting tqdm>=4.56.0
Using cached tqdm-4.64.1-py2.py3-none-any.whl (78 kB)
Collecting optax
Using cached optax-0.1.4-py3-none-any.whl (154 kB)
Collecting mudata>=0.1.2
Using cached mudata-0.2.1-py3-none-any.whl (23 kB)
Collecting jaxlib
Using cached jaxlib-0.4.4-cp38-cp38-manylinux2014_x86_64.whl (72.6 MB)
Collecting docrep>=0.3.2
Using cached docrep-0.3.2-py3-none-any.whl
Collecting flax
Using cached flax-0.6.4-py3-none-any.whl (204 kB)
Collecting rich>=12.0.0
Using cached rich-13.3.1-py3-none-any.whl (239 kB)
Collecting anndata>=0.7.5
Using cached anndata-0.8.0-py3-none-any.whl (96 kB)
Requirement already satisfied: numpy>=1.17.0 in /home/pkgbuild/.cache/R/basilisk/1.11.2/scviR/0.99.1/bsklenv/lib/python3.8/site-packages (from scvi-tools==0.20.0) (1.23.1)
Collecting scipy
Using cached scipy-1.10.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.5 MB)
Collecting natsort
Using cached natsort-8.2.0-py3-none-any.whl (37 kB)
Collecting networkx>=2.3
Using cached networkx-3.0-py3-none-any.whl (2.0 MB)
Collecting packaging
Using cached packaging-23.0-py3-none-any.whl (42 kB)
Collecting seaborn
Using cached seaborn-0.12.2-py3-none-any.whl (293 kB)
Collecting joblib
Using cached joblib-1.2.0-py3-none-any.whl (297 kB)
Collecting numba>=0.41.0
Using cached numba-0.56.4-cp38-cp38-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.5 MB)
Collecting patsy
Using cached patsy-0.5.3-py2.py3-none-any.whl (233 kB)
Collecting session-info
Using cached session_info-1.0.0-py3-none-any.whl
Collecting umap-learn>=0.3.10
Using cached umap_learn-0.5.3-py3-none-any.whl
Collecting statsmodels>=0.10.0rc2
Using cached statsmodels-0.13.5-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (9.9 MB)
Collecting contourpy>=1.0.1
Using cached contourpy-1.0.7-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (300 kB)
Collecting pillow>=6.2.0
Using cached Pillow-9.4.0-cp38-cp38-manylinux_2_28_x86_64.whl (3.4 MB)
Collecting pyparsing>=2.2.1
Using cached pyparsing-3.0.9-py3-none-any.whl (98 kB)
Collecting cycler>=0.10
Using cached cycler-0.11.0-py3-none-any.whl (6.4 kB)
Collecting kiwisolver>=1.0.1
Using cached kiwisolver-1.4.4-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.2 MB)
Collecting fonttools>=4.22.0
Using cached fonttools-4.38.0-py3-none-any.whl (965 kB)
Requirement already satisfied: python-dateutil>=2.7 in /home/pkgbuild/.cache/R/basilisk/1.11.2/scviR/0.99.1/bsklenv/lib/python3.8/site-packages (from matplotlib==3.6.3) (2.8.2)
Requirement already satisfied: six in /home/pkgbuild/.cache/R/basilisk/1.11.2/scviR/0.99.1/bsklenv/lib/python3.8/site-packages (from docrep>=0.3.2->scvi-tools==0.20.0) (1.16.0)
Collecting opt-einsum
Using cached opt_einsum-3.3.0-py3-none-any.whl (65 kB)
Collecting contextlib2
Using cached contextlib2-21.6.0-py2.py3-none-any.whl (13 kB)
Collecting absl-py
Using cached absl_py-1.4.0-py3-none-any.whl (126 kB)
Collecting PyYAML
Using cached PyYAML-6.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (701 kB)
Requirement already satisfied: setuptools in /home/pkgbuild/.cache/R/basilisk/1.11.2/scviR/0.99.1/bsklenv/lib/python3.8/site-packages (from numba>=0.41.0->scanpy==1.9.1) (67.4.0)
Collecting llvmlite<0.40,>=0.39.0dev0
Using cached llvmlite-0.39.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (34.6 MB)
Collecting importlib-metadata
Using cached importlib_metadata-6.0.0-py3-none-any.whl (21 kB)
Collecting et-xmlfile
Using cached et_xmlfile-1.1.0-py3-none-any.whl (4.7 kB)
Requirement already satisfied: pytz>=2020.1 in /home/pkgbuild/.cache/R/basilisk/1.11.2/scviR/0.99.1/bsklenv/lib/python3.8/site-packages (from pandas>=1.0->scvi-tools==0.20.0) (2022.7.1)
Collecting pyro-api>=0.1.1
Using cached pyro_api-0.1.2-py3-none-any.whl (11 kB)
Collecting lightning-utilities>=0.6.0.post0
Using cached lightning_utilities-0.7.1-py3-none-any.whl (18 kB)
Collecting fsspec[http]>2021.06.0
Using cached fsspec-2023.1.0-py3-none-any.whl (143 kB)
Collecting typing-extensions>=4.0.0
Using cached typing_extensions-4.5.0-py3-none-any.whl (27 kB)
Collecting pygments<3.0.0,>=2.14.0
Using cached Pygments-2.14.0-py3-none-any.whl (1.1 MB)
Collecting markdown-it-py<3.0.0,>=2.1.0
Using cached markdown_it_py-2.2.0-py3-none-any.whl (84 kB)
Collecting threadpoolctl>=2.0.0
Using cached threadpoolctl-3.1.0-py3-none-any.whl (14 kB)
Collecting nvidia-cublas-cu11==11.10.3.66
Using cached nvidia_cublas_cu11-11.10.3.66-py3-none-manylinux1_x86_64.whl (317.1 MB)
Collecting nvidia-cudnn-cu11==8.5.0.96
Using cached nvidia_cudnn_cu11-8.5.0.96-2-py3-none-manylinux1_x86_64.whl (557.1 MB)
Collecting nvidia-cuda-nvrtc-cu11==11.7.99
Using cached nvidia_cuda_nvrtc_cu11-11.7.99-2-py3-none-manylinux1_x86_64.whl (21.0 MB)
Collecting nvidia-cuda-runtime-cu11==11.7.99
Using cached nvidia_cuda_runtime_cu11-11.7.99-py3-none-manylinux1_x86_64.whl (849 kB)
Requirement already satisfied: wheel in /home/pkgbuild/.cache/R/basilisk/1.11.2/scviR/0.99.1/bsklenv/lib/python3.8/site-packages (from nvidia-cublas-cu11==11.10.3.66->torch>=1.8.0->scvi-tools==0.20.0) (0.38.4)
Collecting pynndescent>=0.5
Using cached pynndescent-0.5.8-py3-none-any.whl
Collecting dm-tree>=0.1.5
Using cached dm_tree-0.1.8-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (152 kB)
Collecting toolz>=0.9.0
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Collecting orbax
Using cached orbax-0.1.2-py3-none-any.whl (73 kB)
Collecting msgpack
Using cached msgpack-1.0.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (322 kB)
Collecting tensorstore
Using cached tensorstore-0.1.32-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.4 MB)
Collecting multipledispatch
Using cached multipledispatch-0.6.0-py3-none-any.whl (11 kB)
Collecting stdlib-list
Using cached stdlib_list-0.8.0-py3-none-any.whl (63 kB)
Collecting aiohttp!=4.0.0a0,!=4.0.0a1
Using cached aiohttp-3.8.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.0 MB)
Collecting requests
Using cached requests-2.28.2-py3-none-any.whl (62 kB)
Collecting mdurl~=0.1
Using cached mdurl-0.1.2-py3-none-any.whl (10.0 kB)
Collecting zipp>=0.5
Downloading zipp-3.15.0-py3-none-any.whl (6.8 kB)
Collecting importlib_resources
Using cached importlib_resources-5.12.0-py3-none-any.whl (36 kB)
Collecting etils
Using cached etils-1.0.0-py3-none-any.whl (146 kB)
Collecting cached_property
Using cached cached_property-1.5.2-py2.py3-none-any.whl (7.6 kB)
Collecting aiosignal>=1.1.2
Using cached aiosignal-1.3.1-py3-none-any.whl (7.6 kB)
Collecting async-timeout<5.0,>=4.0.0a3
Using cached async_timeout-4.0.2-py3-none-any.whl (5.8 kB)
Collecting charset-normalizer<4.0,>=2.0
Using cached charset_normalizer-3.0.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (195 kB)
Collecting attrs>=17.3.0
Using cached attrs-22.2.0-py3-none-any.whl (60 kB)
Collecting multidict<7.0,>=4.5
Using cached multidict-6.0.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (121 kB)
Collecting yarl<2.0,>=1.0
Using cached yarl-1.8.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (262 kB)
Collecting frozenlist>=1.1.1
Using cached frozenlist-1.3.3-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (161 kB)
Collecting certifi>=2017.4.17
Using cached certifi-2022.12.7-py3-none-any.whl (155 kB)
Collecting idna<4,>=2.5
Using cached idna-3.4-py3-none-any.whl (61 kB)
Collecting urllib3<1.27,>=1.21.1
Using cached urllib3-1.26.14-py2.py3-none-any.whl (140 kB)
Installing collected packages: stdlib-list, pyro-api, msgpack, dm-tree, charset-normalizer, cached_property, zipp, urllib3, typing-extensions, tqdm, toolz, threadpoolctl, tensorstore, session-info, scipy, PyYAML, pyparsing, pygments, pillow, patsy, packaging, opt-einsum, nvidia-cuda-runtime-cu11, nvidia-cuda-nvrtc-cu11, nvidia-cublas-cu11, networkx, natsort, multipledispatch, multidict, mdurl, llvmlite, kiwisolver, joblib, idna, h5py, fsspec, frozenlist, fonttools, etils, et-xmlfile, docrep, cycler, contourpy, contextlib2, certifi, attrs, async-timeout, absl-py, yarl, scikit-learn, requests, openpyxl, nvidia-cudnn-cu11, ml-collections, matplotlib, markdown-it-py, lightning-utilities, jaxlib, jax, importlib_resources, importlib-metadata, aiosignal, torch, statsmodels, seaborn, rich, numpyro, numba, chex, anndata, aiohttp, torchmetrics, pyro-ppl, pynndescent, optax, mudata, umap-learn, pytorch-lightning, scanpy, orbax, flax, scvi-tools
Successfully installed PyYAML-6.0 absl-py-1.4.0 aiohttp-3.8.4 aiosignal-1.3.1 anndata-0.8.0 async-timeout-4.0.2 attrs-22.2.0 cached_property-1.5.2 certifi-2022.12.7 charset-normalizer-3.0.1 chex-0.1.6 contextlib2-21.6.0 contourpy-1.0.7 cycler-0.11.0 dm-tree-0.1.8 docrep-0.3.2 et-xmlfile-1.1.0 etils-1.0.0 flax-0.6.4 fonttools-4.38.0 frozenlist-1.3.3 fsspec-2023.1.0 h5py-3.8.0 idna-3.4 importlib-metadata-6.0.0 importlib_resources-5.12.0 jax-0.4.4 jaxlib-0.4.4 joblib-1.2.0 kiwisolver-1.4.4 lightning-utilities-0.7.1 llvmlite-0.39.1 markdown-it-py-2.2.0 matplotlib-3.6.3 mdurl-0.1.2 ml-collections-0.1.1 msgpack-1.0.4 mudata-0.2.1 multidict-6.0.4 multipledispatch-0.6.0 natsort-8.2.0 networkx-3.0 numba-0.56.4 numpyro-0.11.0 nvidia-cublas-cu11-11.10.3.66 nvidia-cuda-nvrtc-cu11-11.7.99 nvidia-cuda-runtime-cu11-11.7.99 nvidia-cudnn-cu11-8.5.0.96 openpyxl-3.1.1 opt-einsum-3.3.0 optax-0.1.4 orbax-0.1.2 packaging-23.0 patsy-0.5.3 pillow-9.4.0 pygments-2.14.0 pynndescent-0.5.8 pyparsing-3.0.9 pyro-api-0.1.2 pyro-ppl-1.8.4 pytorch-lightning-1.9.3 requests-2.28.2 rich-13.3.1 scanpy-1.9.1 scikit-learn-1.2.1 scipy-1.10.1 scvi-tools-0.20.0 seaborn-0.12.2 session-info-1.0.0 statsmodels-0.13.5 stdlib-list-0.8.0 tensorstore-0.1.32 threadpoolctl-3.1.0 toolz-0.12.0 torch-1.13.1 torchmetrics-0.11.1 tqdm-4.64.1 typing-extensions-4.5.0 umap-learn-0.5.3 urllib3-1.26.14 yarl-1.8.2 zipp-3.15.0
Quitting from lines 26-31 (citeseq_tut.Rmd)
Error: processing vignette 'citeseq_tut.Rmd' failed with diagnostics:
FileNotFoundError: [Errno 2] Unable to open file (unable to open file: name = '/home/pkgbuild/.cache/R/BiocFileCache/56ffb361275cb_demo2.h5ad', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
--- failed re-building ‘citeseq_tut.Rmd’
--- re-building ‘compch12.Rmd’ using rmarkdown
Quitting from lines 40-42 (compch12.Rmd)
Error: processing vignette 'compch12.Rmd' failed with diagnostics:
cannot open the connection
--- 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
===============================
BiocCheckGitClone('scviR')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: scviR
─ PackageVersion: 0.99.1
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2942/6d93c49803cf7a245f90dcb91d7445329b8883ae/scviR
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2942/6d93c49803cf7a245f90dcb91d7445329b8883ae/scviR.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
Apple clang version 12.0.0 (clang-1200.0.32.29)
GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scviR/DESCRIPTION’ ... OK
* this is package ‘scviR’ version ‘0.99.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘scviR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [19s/21s] OK
* checking whether the package can be loaded with stated dependencies ... [19s/21s] OK
* checking whether the package can be unloaded cleanly ... [19s/21s] OK
* checking whether the namespace can be loaded with stated dependencies ... [18s/20s] OK
* checking whether the namespace can be unloaded cleanly ... [18s/21s] OK
* checking loading without being on the library search path ... [19s/22s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [61s/67s] NOTE
get_subclustering_features: warning in topTable(lm1, p, n = n): partial
argument match of 'n' to 'number'
.osn_bucket_to_cache: no visible global function definition for
‘download.file’
adt_profiles: no visible global function definition for ‘rowSds’
cache_citeseq_5k10k_pbmcs: no visible global function definition for
‘download.file’
cache_citeseq_5k10k_tutvae: no visible global function definition for
‘download.file’
get_subcl_LM: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
download.file model.matrix rowSds
Consider adding
importFrom("stats", "model.matrix")
importFrom("utils", "download.file")
to your NAMESPACE file.
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [118s/148s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_subcl_LM 14.177 0.772 16.674
cache_citeseq_5k10k_tutvae 12.057 2.851 24.440
get_subclustering_features 10.618 0.117 12.073
get_ch12_allsce 9.040 0.252 10.326
anndataR 7.081 1.692 9.536
adt_profiles 5.881 0.236 6.791
get_citeseq_tutvae 3.875 1.749 15.415
get_totalVI_normalized_5k10k 4.521 0.198 5.266
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test.R’ [32s/36s]
[32s/36s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [9s/10s] OK
* DONE
Status: 2 NOTEs
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2942/6d93c49803cf7a245f90dcb91d7445329b8883ae/scviR.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('scviR_0.99.1.tar.gz')
===============================
─ BiocCheckVersion: 1.35.9
─ BiocVersion: 3.17
─ Package: scviR
─ PackageVersion: 0.99.1
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp8NsZQx/file16be051982a54/scviR
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmp8NsZQx/file16be076ca7657
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2942/6d93c49803cf7a245f90dcb91d7445329b8883ae/scviR.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 4.2 to 4.3.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
ImmunoOncology
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of scviR...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 23 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 5% of man pages use at least one of these tags.
* NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 82 lines (6%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 131 lines
(9%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 14 NOTES
See the scviR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.