Back to Long Tests report for BioC 3.19 |
This page was generated on 2024-06-22 23:55 -0400 (Sat, 22 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4758 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4492 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4506 |
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 33/33 | Hostname | OS / Arch | CHECK | |||||||
zellkonverter 1.14.1 (landing page) Luke Zappia
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | |||||||
palomino3 | Windows Server 2022 Datacenter / x64 | ERROR | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | ||||||||
To the developers/maintainers of the zellkonverter package: - 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. |
Package: zellkonverter |
Version: 1.14.1 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no zellkonverter_1.14.1.tar.gz |
StartedAt: 2024-06-22 16:31:42 -0400 (Sat, 22 Jun 2024) |
EndedAt: 2024-06-22 16:56:17 -0400 (Sat, 22 Jun 2024) |
EllapsedTime: 1475.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: zellkonverter.Rcheck |
Warnings: 0 |
zellkonverter.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(zellkonverter) Registered S3 method overwritten by 'zellkonverter': method from py_to_r.pandas.core.arrays.categorical.Categorical reticulate > > test_check("zellkonverter") 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: /var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6 added / updated specs: - python=3.12.2 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 bzip2 conda-forge/linux-64::bzip2-1.0.8-hd590300_5 ca-certificates conda-forge/linux-64::ca-certificates-2024.6.2-hbcca054_0 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-hf3520f5_7 libexpat conda-forge/linux-64::libexpat-2.6.2-h59595ed_0 libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5 libgcc-ng conda-forge/linux-64::libgcc-ng-13.2.0-h77fa898_11 libgomp conda-forge/linux-64::libgomp-13.2.0-h77fa898_11 libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0 libsqlite conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0 libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 libxcrypt conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 libzlib conda-forge/linux-64::libzlib-1.3.1-h4ab18f5_1 ncurses conda-forge/linux-64::ncurses-6.5-h59595ed_0 openssl conda-forge/linux-64::openssl-3.3.1-h4ab18f5_0 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 python conda-forge/linux-64::python-3.12.2-hab00c5b_0_cpython readline conda-forge/linux-64::readline-8.2-h8228510_1 setuptools conda-forge/noarch::setuptools-70.1.0-pyhd8ed1ab_0 tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0 wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 xz conda-forge/linux-64::xz-5.2.6-h166bdaf_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 ==> WARNING: A newer version of conda exists. <== current version: 4.12.0 latest version: 24.5.0 Please update conda by running $ conda update -n base -c defaults conda # All requested packages already installed. 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 ==> WARNING: A newer version of conda exists. <== current version: 4.12.0 latest version: 24.5.0 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6 added / updated specs: - anndata=0.10.6 - h5py=3.10.0 - hdf5=1.14.3 - natsort=8.4.0 - numpy=1.26.4 - packaging=24.0 - pandas=2.2.1 - python[version='3.12.2.*,3.12.2.*'] - scipy=1.12.0 The following NEW packages will be INSTALLED: anndata conda-forge/noarch::anndata-0.10.6-pyhd8ed1ab_0 array-api-compat conda-forge/noarch::array-api-compat-1.7.1-pyhd8ed1ab_0 c-ares conda-forge/linux-64::c-ares-1.28.1-hd590300_0 cached-property conda-forge/noarch::cached-property-1.5.2-hd8ed1ab_1 cached_property conda-forge/noarch::cached_property-1.5.2-pyha770c72_1 exceptiongroup conda-forge/noarch::exceptiongroup-1.2.0-pyhd8ed1ab_2 h5py conda-forge/linux-64::h5py-3.10.0-nompi_py312h1b477d7_101 hdf5 conda-forge/linux-64::hdf5-1.14.3-nompi_hdf9ad27_105 keyutils conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0 krb5 conda-forge/linux-64::krb5-1.21.2-h659d440_0 libaec conda-forge/linux-64::libaec-1.1.3-h59595ed_0 libblas conda-forge/linux-64::libblas-3.9.0-22_linux64_openblas libcblas conda-forge/linux-64::libcblas-3.9.0-22_linux64_openblas libcurl conda-forge/linux-64::libcurl-8.8.0-hca28451_0 libedit conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2 libev conda-forge/linux-64::libev-4.33-hd590300_2 libgfortran-ng conda-forge/linux-64::libgfortran-ng-13.2.0-h69a702a_11 libgfortran5 conda-forge/linux-64::libgfortran5-13.2.0-h3d2ce59_11 liblapack conda-forge/linux-64::liblapack-3.9.0-22_linux64_openblas libnghttp2 conda-forge/linux-64::libnghttp2-1.58.0-h47da74e_1 libopenblas conda-forge/linux-64::libopenblas-0.3.27-pthreads_h413a1c8_0 libssh2 conda-forge/linux-64::libssh2-1.11.0-h0841786_0 libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-13.2.0-hc0a3c3a_11 natsort conda-forge/noarch::natsort-8.4.0-pyhd8ed1ab_0 numpy conda-forge/linux-64::numpy-1.26.4-py312heda63a1_0 packaging conda-forge/noarch::packaging-24.0-pyhd8ed1ab_0 pandas conda-forge/linux-64::pandas-2.2.1-py312hfb8ada1_0 python-dateutil conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0 python-tzdata conda-forge/noarch::python-tzdata-2024.1-pyhd8ed1ab_0 python_abi conda-forge/linux-64::python_abi-3.12-4_cp312 pytz conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0 scipy conda-forge/linux-64::scipy-1.12.0-py312heda63a1_2 six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 zstd conda-forge/linux-64::zstd-1.5.6-ha6fb4c9_0 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done /var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024. warnings.warn( /var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024. warnings.warn( /var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024. warnings.warn( /var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024. warnings.warn( /var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024. warnings.warn( /var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024. warnings.warn( /var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024. warnings.warn( /var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024. warnings.warn( /var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:1818: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`. utils.warn_names_duplicates("obs") /var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:1818: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`. utils.warn_names_duplicates("obs") /var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024. warnings.warn( /var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:1818: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`. utils.warn_names_duplicates("obs") /var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:1818: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`. utils.warn_names_duplicates("obs") /var/cache/basilisk/1.17.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.6/lib/python3.12/site-packages/anndata/_core/anndata.py:430: FutureWarning: The dtype argument is deprecated and will be removed in late 2024. warnings.warn( [ FAIL 0 | WARN 0 | SKIP 0 | PASS 199 ] > > proc.time() user system elapsed 918.035 325.441 1351.906
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no zellkonverter_1.14.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc-longtests/meat/zellkonverter.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’ * checking for file ‘zellkonverter/DESCRIPTION’ ... OK * this is package ‘zellkonverter’ version ‘1.14.1’ * 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 ‘zellkonverter’ can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See ‘/home/biocbuild/bbs-3.19-bioc-longtests/meat/zellkonverter.Rcheck/00install.out’ for details. * checking installed package size ... OK * checking package 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... 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 ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... SKIPPED * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in shell scripts ... OK * checking files in ‘vignettes’ ... SKIPPED * checking examples ... SKIPPED * checking for unstated dependencies in ‘longtests’ ... OK * checking tests in ‘longtests’ ... Running ‘testthat.R’ OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc-longtests/meat/zellkonverter.Rcheck/00check.log’ for details.
zellkonverter.Rcheck/00install.out
* installing *source* package ‘zellkonverter’ ... ** using non-staged installation via StagedInstall field ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (zellkonverter)