Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-09 21:32 -0500 (Sat, 09 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 2283/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
zellkonverter 1.16.0 (landing page) Luke Zappia
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the zellkonverter package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/zellkonverter.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. |
Package: zellkonverter |
Version: 1.16.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings zellkonverter_1.16.0.tar.gz |
StartedAt: 2024-11-09 16:27:00 -0500 (Sat, 09 Nov 2024) |
EndedAt: 2024-11-09 16:36:10 -0500 (Sat, 09 Nov 2024) |
EllapsedTime: 550.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: zellkonverter.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings zellkonverter_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/zellkonverter.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘zellkonverter/DESCRIPTION’ ... OK * this is package ‘zellkonverter’ version ‘1.16.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/zellkonverter.Rcheck/00install.out’ for details. * checking installed package size ... OK * checking package directory ... OK * 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 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 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 ... OK * 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’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed AnnData-Conversion 7.917 0.851 10.292 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/zellkonverter.Rcheck/00check.log’ for details.
zellkonverter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL zellkonverter ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * 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)
zellkonverter.Rcheck/tests/spelling.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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. > if (requireNamespace("spelling", quietly = TRUE)) { + spelling::spell_check_test( + vignettes = TRUE, + error = FALSE, + skip_on_cran = TRUE + ) + } NULL > > proc.time() user system elapsed 0.070 0.016 0.083
zellkonverter.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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") Retrieving notices: ...working... done Channels: - conda-forge Platform: osx-arm64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/zellkonverter/1.16.0/zellkonverterAnnDataEnv-0.10.6 added / updated specs: - python=3.12.2 The following packages will be downloaded: package | build ---------------------------|----------------- python-3.12.2 |hdf0ec26_0_cpython 12.5 MB conda-forge ------------------------------------------------------------ Total: 12.5 MB The following NEW packages will be INSTALLED: bzip2 conda-forge/osx-arm64::bzip2-1.0.8-h99b78c6_7 ca-certificates conda-forge/osx-arm64::ca-certificates-2024.8.30-hf0a4a13_0 libexpat conda-forge/osx-arm64::libexpat-2.6.4-h286801f_0 libffi conda-forge/osx-arm64::libffi-3.4.2-h3422bc3_5 libsqlite conda-forge/osx-arm64::libsqlite-3.47.0-hbaaea75_1 libzlib conda-forge/osx-arm64::libzlib-1.3.1-h8359307_2 ncurses conda-forge/osx-arm64::ncurses-6.5-h7bae524_1 openssl conda-forge/osx-arm64::openssl-3.3.2-h8359307_0 pip conda-forge/noarch::pip-24.3.1-pyh8b19718_0 python conda-forge/osx-arm64::python-3.12.2-hdf0ec26_0_cpython readline conda-forge/osx-arm64::readline-8.2-h92ec313_1 setuptools conda-forge/noarch::setuptools-75.3.0-pyhd8ed1ab_0 tk conda-forge/osx-arm64::tk-8.6.13-h5083fa2_1 tzdata conda-forge/noarch::tzdata-2024b-hc8b5060_0 wheel conda-forge/noarch::wheel-0.45.0-pyhd8ed1ab_0 xz conda-forge/osx-arm64::xz-5.2.6-h57fd34a_0 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Channels: - conda-forge Platform: osx-arm64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ==> WARNING: A newer version of conda exists. <== current version: 24.3.0 latest version: 24.9.2 Please update conda by running $ conda update -n base -c conda-forge conda # All requested packages already installed. Channels: - conda-forge Platform: osx-arm64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ==> WARNING: A newer version of conda exists. <== current version: 24.3.0 latest version: 24.9.2 Please update conda by running $ conda update -n base -c conda-forge conda ## Package Plan ## environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/zellkonverter/1.16.0/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 packages will be downloaded: package | build ---------------------------|----------------- anndata-0.10.6 | pyhd8ed1ab_0 96 KB conda-forge c-ares-1.34.3 | h5505292_0 175 KB conda-forge h5py-3.10.0 |nompi_py312hac0f6fd_101 1.0 MB conda-forge numpy-1.26.4 | py312h8442bc7_0 5.8 MB conda-forge pandas-2.2.1 | py312h88edd18_0 13.8 MB conda-forge scipy-1.12.0 | py312h9d7df2b_2 14.8 MB conda-forge ------------------------------------------------------------ Total: 35.7 MB 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-1.9.1-pyhd8ed1ab_0 c-ares conda-forge/osx-arm64::c-ares-1.34.3-h5505292_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-1.2.2-pyhd8ed1ab_0 h5py conda-forge/osx-arm64::h5py-3.10.0-nompi_py312hac0f6fd_101 hdf5 conda-forge/osx-arm64::hdf5-1.14.3-nompi_hec07895_105 krb5 conda-forge/osx-arm64::krb5-1.21.3-h237132a_0 libaec conda-forge/osx-arm64::libaec-1.1.3-hebf3989_0 libblas conda-forge/osx-arm64::libblas-3.9.0-25_osxarm64_openblas libcblas conda-forge/osx-arm64::libcblas-3.9.0-25_osxarm64_openblas libcurl conda-forge/osx-arm64::libcurl-8.10.1-h13a7ad3_0 libcxx conda-forge/osx-arm64::libcxx-19.1.3-ha82da77_0 libedit conda-forge/osx-arm64::libedit-3.1.20191231-hc8eb9b7_2 libev conda-forge/osx-arm64::libev-4.33-h93a5062_2 libgfortran conda-forge/osx-arm64::libgfortran-5.0.0-13_2_0_hd922786_3 libgfortran5 conda-forge/osx-arm64::libgfortran5-13.2.0-hf226fd6_3 liblapack conda-forge/osx-arm64::liblapack-3.9.0-25_osxarm64_openblas libnghttp2 conda-forge/osx-arm64::libnghttp2-1.64.0-h6d7220d_0 libopenblas conda-forge/osx-arm64::libopenblas-0.3.28-openmp_hf332438_1 libssh2 conda-forge/osx-arm64::libssh2-1.11.0-h7a5bd25_0 llvm-openmp conda-forge/osx-arm64::llvm-openmp-19.1.3-hb52a8e5_0 natsort conda-forge/noarch::natsort-8.4.0-pyhd8ed1ab_0 numpy conda-forge/osx-arm64::numpy-1.26.4-py312h8442bc7_0 packaging conda-forge/noarch::packaging-24.0-pyhd8ed1ab_0 pandas conda-forge/osx-arm64::pandas-2.2.1-py312h88edd18_0 python-dateutil conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0 python-tzdata conda-forge/noarch::python-tzdata-2024.2-pyhd8ed1ab_0 python_abi conda-forge/osx-arm64::python_abi-3.12-5_cp312 pytz conda-forge/noarch::pytz-2024.2-pyhd8ed1ab_0 scipy conda-forge/osx-arm64::scipy-1.12.0-py312h9d7df2b_2 six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 zstd conda-forge/osx-arm64::zstd-1.5.6-hb46c0d2_0 Downloading and Extracting Packages: ...working... done Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Channels: - conda-forge Platform: osx-arm64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/zellkonverter/1.16.0/zellkonverterAnnDataEnv-0.10.2 added / updated specs: - python=3.11.5 The following packages will be downloaded: package | build ---------------------------|----------------- python-3.11.5 |h47c9636_0_cpython 14.0 MB conda-forge ------------------------------------------------------------ Total: 14.0 MB The following NEW packages will be INSTALLED: bzip2 conda-forge/osx-arm64::bzip2-1.0.8-h99b78c6_7 ca-certificates conda-forge/osx-arm64::ca-certificates-2024.8.30-hf0a4a13_0 libexpat conda-forge/osx-arm64::libexpat-2.6.4-h286801f_0 libffi conda-forge/osx-arm64::libffi-3.4.2-h3422bc3_5 libsqlite conda-forge/osx-arm64::libsqlite-3.47.0-hbaaea75_1 libzlib conda-forge/osx-arm64::libzlib-1.3.1-h8359307_2 ncurses conda-forge/osx-arm64::ncurses-6.5-h7bae524_1 openssl conda-forge/osx-arm64::openssl-3.3.2-h8359307_0 pip conda-forge/noarch::pip-24.3.1-pyh8b19718_0 python conda-forge/osx-arm64::python-3.11.5-h47c9636_0_cpython readline conda-forge/osx-arm64::readline-8.2-h92ec313_1 setuptools conda-forge/noarch::setuptools-75.3.0-pyhd8ed1ab_0 tk conda-forge/osx-arm64::tk-8.6.13-h5083fa2_1 tzdata conda-forge/noarch::tzdata-2024b-hc8b5060_0 wheel conda-forge/noarch::wheel-0.45.0-pyhd8ed1ab_0 xz conda-forge/osx-arm64::xz-5.2.6-h57fd34a_0 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Channels: - conda-forge Platform: osx-arm64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ==> WARNING: A newer version of conda exists. <== current version: 24.3.0 latest version: 24.9.2 Please update conda by running $ conda update -n base -c conda-forge conda # All requested packages already installed. Channels: - conda-forge Platform: osx-arm64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ==> WARNING: A newer version of conda exists. <== current version: 24.3.0 latest version: 24.9.2 Please update conda by running $ conda update -n base -c conda-forge conda ## Package Plan ## environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/zellkonverter/1.16.0/zellkonverterAnnDataEnv-0.10.2 added / updated specs: - anndata=0.10.2 - h5py=3.10.0 - hdf5=1.14.2 - natsort=8.4.0 - numpy=1.26.0 - packaging=23.2 - pandas=2.1.1 - python[version='3.11.5.*,3.11.5.*'] - scipy=1.11.3 The following packages will be downloaded: package | build ---------------------------|----------------- anndata-0.10.2 | pyhd8ed1ab_0 94 KB conda-forge h5py-3.10.0 |nompi_py311h393cb7e_100 1.0 MB conda-forge hdf5-1.14.2 |nompi_h3aba7b3_100 3.3 MB conda-forge numpy-1.26.0 | py311hb8f3215_0 6.5 MB conda-forge packaging-23.2 | pyhd8ed1ab_0 48 KB conda-forge pandas-2.1.1 | py311h9e438b8_1 13.7 MB conda-forge scipy-1.11.3 | py311h93d07a4_1 14.4 MB conda-forge ------------------------------------------------------------ Total: 39.0 MB The following NEW packages will be INSTALLED: anndata conda-forge/noarch::anndata-0.10.2-pyhd8ed1ab_0 array-api-compat conda-forge/noarch::array-api-compat-1.9.1-pyhd8ed1ab_0 c-ares conda-forge/osx-arm64::c-ares-1.34.3-h5505292_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-1.2.2-pyhd8ed1ab_0 h5py conda-forge/osx-arm64::h5py-3.10.0-nompi_py311h393cb7e_100 hdf5 conda-forge/osx-arm64::hdf5-1.14.2-nompi_h3aba7b3_100 krb5 conda-forge/osx-arm64::krb5-1.21.3-h237132a_0 libaec conda-forge/osx-arm64::libaec-1.1.3-hebf3989_0 libblas conda-forge/osx-arm64::libblas-3.9.0-20_osxarm64_openblas libcblas conda-forge/osx-arm64::libcblas-3.9.0-20_osxarm64_openblas libcurl conda-forge/osx-arm64::libcurl-8.10.1-h13a7ad3_0 libcxx conda-forge/osx-arm64::libcxx-19.1.3-ha82da77_0 libedit conda-forge/osx-arm64::libedit-3.1.20191231-hc8eb9b7_2 libev conda-forge/osx-arm64::libev-4.33-h93a5062_2 libgfortran conda-forge/osx-arm64::libgfortran-5.0.0-13_2_0_hd922786_3 libgfortran5 conda-forge/osx-arm64::libgfortran5-13.2.0-hf226fd6_3 liblapack conda-forge/osx-arm64::liblapack-3.9.0-20_osxarm64_openblas libnghttp2 conda-forge/osx-arm64::libnghttp2-1.64.0-h6d7220d_0 libopenblas conda-forge/osx-arm64::libopenblas-0.3.25-openmp_h6c19121_0 libssh2 conda-forge/osx-arm64::libssh2-1.11.0-h7a5bd25_0 llvm-openmp conda-forge/osx-arm64::llvm-openmp-19.1.3-hb52a8e5_0 natsort conda-forge/noarch::natsort-8.4.0-pyhd8ed1ab_0 numpy conda-forge/osx-arm64::numpy-1.26.0-py311hb8f3215_0 packaging conda-forge/noarch::packaging-23.2-pyhd8ed1ab_0 pandas conda-forge/osx-arm64::pandas-2.1.1-py311h9e438b8_1 python-dateutil conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0 python-tzdata conda-forge/noarch::python-tzdata-2024.2-pyhd8ed1ab_0 python_abi conda-forge/osx-arm64::python_abi-3.11-5_cp311 pytz conda-forge/noarch::pytz-2024.2-pyhd8ed1ab_0 scipy conda-forge/osx-arm64::scipy-1.11.3-py311h93d07a4_1 six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 zstd conda-forge/osx-arm64::zstd-1.5.6-hb46c0d2_0 Downloading and Extracting Packages: ...working... done Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Channels: - conda-forge Platform: osx-arm64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/zellkonverter/1.16.0/zellkonverterAnnDataEnv-0.9.2 added / updated specs: - python=3.11.5 The following NEW packages will be INSTALLED: bzip2 conda-forge/osx-arm64::bzip2-1.0.8-h99b78c6_7 ca-certificates conda-forge/osx-arm64::ca-certificates-2024.8.30-hf0a4a13_0 libexpat conda-forge/osx-arm64::libexpat-2.6.4-h286801f_0 libffi conda-forge/osx-arm64::libffi-3.4.2-h3422bc3_5 libsqlite conda-forge/osx-arm64::libsqlite-3.47.0-hbaaea75_1 libzlib conda-forge/osx-arm64::libzlib-1.3.1-h8359307_2 ncurses conda-forge/osx-arm64::ncurses-6.5-h7bae524_1 openssl conda-forge/osx-arm64::openssl-3.3.2-h8359307_0 pip conda-forge/noarch::pip-24.3.1-pyh8b19718_0 python conda-forge/osx-arm64::python-3.11.5-h47c9636_0_cpython readline conda-forge/osx-arm64::readline-8.2-h92ec313_1 setuptools conda-forge/noarch::setuptools-75.3.0-pyhd8ed1ab_0 tk conda-forge/osx-arm64::tk-8.6.13-h5083fa2_1 tzdata conda-forge/noarch::tzdata-2024b-hc8b5060_0 wheel conda-forge/noarch::wheel-0.45.0-pyhd8ed1ab_0 xz conda-forge/osx-arm64::xz-5.2.6-h57fd34a_0 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Channels: - conda-forge Platform: osx-arm64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ==> WARNING: A newer version of conda exists. <== current version: 24.3.0 latest version: 24.9.2 Please update conda by running $ conda update -n base -c conda-forge conda # All requested packages already installed. Channels: - conda-forge Platform: osx-arm64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ==> WARNING: A newer version of conda exists. <== current version: 24.3.0 latest version: 24.9.2 Please update conda by running $ conda update -n base -c conda-forge conda ## Package Plan ## environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/zellkonverter/1.16.0/zellkonverterAnnDataEnv-0.9.2 added / updated specs: - anndata=0.9.2 - h5py=3.9.0 - hdf5=1.14.2 - natsort=8.4.0 - numpy=1.26.0 - packaging=23.2 - pandas=2.1.1 - python[version='3.11.5.*,3.11.5.*'] - scipy=1.11.3 The following packages will be downloaded: package | build ---------------------------|----------------- anndata-0.9.2 | pyhd8ed1ab_0 85 KB conda-forge h5py-3.9.0 |nompi_py311h4794d1a_103 1.1 MB conda-forge ------------------------------------------------------------ Total: 1.2 MB The following NEW packages will be INSTALLED: anndata conda-forge/noarch::anndata-0.9.2-pyhd8ed1ab_0 c-ares conda-forge/osx-arm64::c-ares-1.34.3-h5505292_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 h5py conda-forge/osx-arm64::h5py-3.9.0-nompi_py311h4794d1a_103 hdf5 conda-forge/osx-arm64::hdf5-1.14.2-nompi_h3aba7b3_100 krb5 conda-forge/osx-arm64::krb5-1.21.3-h237132a_0 libaec conda-forge/osx-arm64::libaec-1.1.3-hebf3989_0 libblas conda-forge/osx-arm64::libblas-3.9.0-20_osxarm64_openblas libcblas conda-forge/osx-arm64::libcblas-3.9.0-20_osxarm64_openblas libcurl conda-forge/osx-arm64::libcurl-8.10.1-h13a7ad3_0 libcxx conda-forge/osx-arm64::libcxx-19.1.3-ha82da77_0 libedit conda-forge/osx-arm64::libedit-3.1.20191231-hc8eb9b7_2 libev conda-forge/osx-arm64::libev-4.33-h93a5062_2 libgfortran conda-forge/osx-arm64::libgfortran-5.0.0-13_2_0_hd922786_3 libgfortran5 conda-forge/osx-arm64::libgfortran5-13.2.0-hf226fd6_3 liblapack conda-forge/osx-arm64::liblapack-3.9.0-20_osxarm64_openblas libnghttp2 conda-forge/osx-arm64::libnghttp2-1.64.0-h6d7220d_0 libopenblas conda-forge/osx-arm64::libopenblas-0.3.25-openmp_h6c19121_0 libssh2 conda-forge/osx-arm64::libssh2-1.11.0-h7a5bd25_0 llvm-openmp conda-forge/osx-arm64::llvm-openmp-19.1.3-hb52a8e5_0 natsort conda-forge/noarch::natsort-8.4.0-pyhd8ed1ab_0 numpy conda-forge/osx-arm64::numpy-1.26.0-py311hb8f3215_0 packaging conda-forge/noarch::packaging-23.2-pyhd8ed1ab_0 pandas conda-forge/osx-arm64::pandas-2.1.1-py311h9e438b8_1 python-dateutil conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0 python-tzdata conda-forge/noarch::python-tzdata-2024.2-pyhd8ed1ab_0 python_abi conda-forge/osx-arm64::python_abi-3.11-5_cp311 pytz conda-forge/noarch::pytz-2024.2-pyhd8ed1ab_0 scipy conda-forge/osx-arm64::scipy-1.11.3-py311h93d07a4_1 six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 zstd conda-forge/osx-arm64::zstd-1.5.6-hb46c0d2_0 Downloading and Extracting Packages: ...working... done Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Channels: - conda-forge Platform: osx-arm64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/zellkonverter/1.16.0/zellkonverterAnnDataEnv-0.8.0 added / updated specs: - python=3.8.13 The following packages will be downloaded: package | build ---------------------------|----------------- python-3.8.13 |hd3575e6_0_cpython 12.3 MB conda-forge ------------------------------------------------------------ Total: 12.3 MB The following NEW packages will be INSTALLED: bzip2 conda-forge/osx-arm64::bzip2-1.0.8-h99b78c6_7 ca-certificates conda-forge/osx-arm64::ca-certificates-2024.8.30-hf0a4a13_0 libffi conda-forge/osx-arm64::libffi-3.4.2-h3422bc3_5 libsqlite conda-forge/osx-arm64::libsqlite-3.47.0-hbaaea75_1 libzlib conda-forge/osx-arm64::libzlib-1.3.1-h8359307_2 ncurses conda-forge/osx-arm64::ncurses-6.5-h7bae524_1 openssl conda-forge/osx-arm64::openssl-3.3.2-h8359307_0 pip conda-forge/noarch::pip-24.3.1-pyh8b19718_0 python conda-forge/osx-arm64::python-3.8.13-hd3575e6_0_cpython readline conda-forge/osx-arm64::readline-8.2-h92ec313_1 setuptools conda-forge/noarch::setuptools-75.3.0-pyhd8ed1ab_0 sqlite conda-forge/osx-arm64::sqlite-3.47.0-hcd14bea_1 tk conda-forge/osx-arm64::tk-8.6.13-h5083fa2_1 wheel conda-forge/noarch::wheel-0.45.0-pyhd8ed1ab_0 xz conda-forge/osx-arm64::xz-5.2.6-h57fd34a_0 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Channels: - conda-forge Platform: osx-arm64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ==> WARNING: A newer version of conda exists. <== current version: 24.3.0 latest version: 24.9.2 Please update conda by running $ conda update -n base -c conda-forge conda # All requested packages already installed. Channels: - conda-forge Platform: osx-arm64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ==> WARNING: A newer version of conda exists. <== current version: 24.3.0 latest version: 24.9.2 Please update conda by running $ conda update -n base -c conda-forge conda ## Package Plan ## environment location: /Users/biocbuild/Library/Caches/org.R-project.R/R/basilisk/1.18.0/zellkonverter/1.16.0/zellkonverterAnnDataEnv-0.8.0 added / updated specs: - anndata=0.8.0 - h5py=3.6.0 - hdf5=1.12.1 - natsort=8.1.0 - numpy=1.22.3 - packaging=21.3 - pandas=1.4.2 - python[version='3.8.13.*,3.8.13.*'] - scipy=1.7.3 - sqlite=3.38.2 The following packages will be downloaded: package | build ---------------------------|----------------- anndata-0.8.0 | pyhd8ed1ab_1 74 KB conda-forge h5py-3.6.0 |nompi_py38hacf61ce_100 1.1 MB conda-forge importlib_metadata-8.5.0 | hd8ed1ab_0 9 KB conda-forge natsort-8.1.0 | pyhd8ed1ab_0 35 KB conda-forge numpy-1.22.3 | py38h4084d66_2 5.7 MB conda-forge packaging-21.3 | pyhd8ed1ab_0 36 KB conda-forge pandas-1.4.2 | py38h6724fcd_2 11.6 MB conda-forge scipy-1.7.3 | py38h7b4f323_1 19.1 MB conda-forge sqlite-3.38.2 | h7e3ccbd_0 1.7 MB conda-forge ------------------------------------------------------------ Total: 39.3 MB The following NEW packages will be INSTALLED: anndata conda-forge/noarch::anndata-0.8.0-pyhd8ed1ab_1 c-ares conda-forge/osx-arm64::c-ares-1.34.3-h5505292_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 h5py conda-forge/osx-arm64::h5py-3.6.0-nompi_py38hacf61ce_100 hdf5 conda-forge/osx-arm64::hdf5-1.12.1-nompi_hd9dbc9e_104 importlib-metadata conda-forge/noarch::importlib-metadata-8.5.0-pyha770c72_0 importlib_metadata conda-forge/noarch::importlib_metadata-8.5.0-hd8ed1ab_0 krb5 conda-forge/osx-arm64::krb5-1.21.3-h237132a_0 libblas conda-forge/osx-arm64::libblas-3.9.0-20_osxarm64_openblas libcblas conda-forge/osx-arm64::libcblas-3.9.0-20_osxarm64_openblas libcurl conda-forge/osx-arm64::libcurl-8.8.0-h7b6f9a7_1 libcxx conda-forge/osx-arm64::libcxx-19.1.3-ha82da77_0 libedit conda-forge/osx-arm64::libedit-3.1.20191231-hc8eb9b7_2 libev conda-forge/osx-arm64::libev-4.33-h93a5062_2 libgfortran conda-forge/osx-arm64::libgfortran-5.0.0-13_2_0_hd922786_3 libgfortran5 conda-forge/osx-arm64::libgfortran5-13.2.0-hf226fd6_3 liblapack conda-forge/osx-arm64::liblapack-3.9.0-20_osxarm64_openblas libnghttp2 conda-forge/osx-arm64::libnghttp2-1.58.0-ha4dd798_1 libopenblas conda-forge/osx-arm64::libopenblas-0.3.25-openmp_h6c19121_0 libssh2 conda-forge/osx-arm64::libssh2-1.11.0-h7a5bd25_0 llvm-openmp conda-forge/osx-arm64::llvm-openmp-19.1.3-hb52a8e5_0 natsort conda-forge/noarch::natsort-8.1.0-pyhd8ed1ab_0 numpy conda-forge/osx-arm64::numpy-1.22.3-py38h4084d66_2 packaging conda-forge/noarch::packaging-21.3-pyhd8ed1ab_0 pandas conda-forge/osx-arm64::pandas-1.4.2-py38h6724fcd_2 pyparsing conda-forge/noarch::pyparsing-3.1.4-pyhd8ed1ab_0 python-dateutil conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0 python_abi conda-forge/osx-arm64::python_abi-3.8-5_cp38 pytz conda-forge/noarch::pytz-2024.2-pyhd8ed1ab_0 scipy conda-forge/osx-arm64::scipy-1.7.3-py38h7b4f323_1 six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 typing_extensions conda-forge/noarch::typing_extensions-4.12.2-pyha770c72_0 zipp conda-forge/noarch::zipp-3.20.2-pyhd8ed1ab_0 zlib conda-forge/osx-arm64::zlib-1.2.13-hfb2fe0b_6 zstd conda-forge/osx-arm64::zstd-1.5.6-hb46c0d2_0 The following packages will be DOWNGRADED: libsqlite 3.47.0-hbaaea75_1 --> 3.46.0-hfb93653_0 libzlib 1.3.1-h8359307_2 --> 1.2.13-hfb2fe0b_6 sqlite 3.47.0-hcd14bea_1 --> 3.38.2-h7e3ccbd_0 Downloading and Extracting Packages: ...working... done Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done sys:1: FutureWarning: X.dtype being converted to np.float32 from float64. In the next version of anndata (0.9) conversion will not be automatic. Pass dtype explicitly to avoid this warning. Pass `AnnData(X, dtype=X.dtype, ...)` to get the future behavour. [ FAIL 0 | WARN 28 | SKIP 6 | PASS 152 ] ══ Skipped tests (6) ═══════════════════════════════════════════════════════════ • On CRAN (4): 'test-read.R:192:5', 'test-read.R:234:5', 'test-zzz-anndata.R:6:5', 'test-zzz-anndata.R:63:5' • On Mac aarch64 (2): 'test-read.R:70:5', 'test-write.R:164:5' [ FAIL 0 | WARN 28 | SKIP 6 | PASS 152 ] > > proc.time() user system elapsed 122.896 42.731 258.488
zellkonverter.Rcheck/zellkonverter-Ex.timings
name | user | system | elapsed | |
AnnData-Conversion | 7.917 | 0.851 | 10.292 | |
AnnData-Environment | 0.002 | 0.001 | 0.003 | |
readH5AD | 0.274 | 0.021 | 0.298 | |
setZellkonverterVerbose | 0.001 | 0.000 | 0.000 | |
writeH5AD | 1.156 | 0.135 | 1.306 | |