Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-25 17:42 -0400 (Tue, 25 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" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 2295/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
zellkonverter 1.14.1 (landing page) Luke Zappia
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | TIMEOUT | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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: 1.14.1 |
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_1.14.1.tar.gz |
StartedAt: 2024-06-24 13:44:37 -0400 (Mon, 24 Jun 2024) |
EndedAt: 2024-06-24 14:24:37 -0400 (Mon, 24 Jun 2024) |
EllapsedTime: 2400.0 seconds |
RetCode: None |
Status: TIMEOUT |
CheckDir: zellkonverter.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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_1.14.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/zellkonverter.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-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 Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * 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 ‘/Users/biocbuild/bbs-3.19-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 40.540 5.087 60.991 writeH5AD 6.649 0.685 7.738 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ Running ‘testthat.R’
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-x86_64/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 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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 0.320 0.102 0.386
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-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") 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: /private/var/cache/basilisk/1.16.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.10.2 added / updated specs: - python=3.11.5 The following NEW packages will be INSTALLED: bzip2 conda-forge/osx-64::bzip2-1.0.8-h10d778d_5 ca-certificates conda-forge/osx-64::ca-certificates-2024.6.2-h8857fd0_0 libexpat conda-forge/osx-64::libexpat-2.6.2-h73e2aa4_0 libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5 libsqlite conda-forge/osx-64::libsqlite-3.46.0-h1b8f9f3_0 libzlib conda-forge/osx-64::libzlib-1.3.1-h87427d6_1 ncurses conda-forge/osx-64::ncurses-6.5-h5846eda_0 openssl conda-forge/osx-64::openssl-3.3.1-h87427d6_0 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 python conda-forge/osx-64::python-3.11.5-h30d4d87_0_cpython readline conda-forge/osx-64::readline-8.2-h9e318b2_1 setuptools conda-forge/noarch::setuptools-70.1.0-pyhd8ed1ab_0 tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1 tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0 wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 xz conda-forge/osx-64::xz-5.2.6-h775f41a_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: /private/var/cache/basilisk/1.16.0/zellkonverter/1.14.1/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 NEW packages will be INSTALLED: anndata conda-forge/noarch::anndata-0.10.2-pyhd8ed1ab_0 array-api-compat conda-forge/noarch::array-api-compat-1.7.1-pyhd8ed1ab_0 c-ares conda-forge/osx-64::c-ares-1.28.1-h10d778d_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/osx-64::h5py-3.10.0-nompi_py311he02c01d_100 hdf5 conda-forge/osx-64::hdf5-1.14.2-nompi_hedada53_100 krb5 conda-forge/osx-64::krb5-1.21.2-hb884880_0 libaec conda-forge/osx-64::libaec-1.1.3-h73e2aa4_0 libblas conda-forge/osx-64::libblas-3.9.0-20_osx64_openblas libcblas conda-forge/osx-64::libcblas-3.9.0-20_osx64_openblas libcurl conda-forge/osx-64::libcurl-8.8.0-hf9fcc65_0 libcxx conda-forge/osx-64::libcxx-17.0.6-h88467a6_0 libedit conda-forge/osx-64::libedit-3.1.20191231-h0678c8f_2 libev conda-forge/osx-64::libev-4.33-h10d778d_2 libgfortran conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_3 libgfortran5 conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_3 liblapack conda-forge/osx-64::liblapack-3.9.0-20_osx64_openblas libnghttp2 conda-forge/osx-64::libnghttp2-1.58.0-h64cf6d3_1 libopenblas conda-forge/osx-64::libopenblas-0.3.25-openmp_hfef2a42_0 libssh2 conda-forge/osx-64::libssh2-1.11.0-hd019ec5_0 llvm-openmp conda-forge/osx-64::llvm-openmp-18.1.8-h15ab845_0 natsort conda-forge/noarch::natsort-8.4.0-pyhd8ed1ab_0 numpy conda-forge/osx-64::numpy-1.26.0-py311hc44ba51_0 packaging conda-forge/noarch::packaging-23.2-pyhd8ed1ab_0 pandas conda-forge/osx-64::pandas-2.1.1-py311hab14417_1 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/osx-64::python_abi-3.11-4_cp311 pytz conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0 scipy conda-forge/osx-64::scipy-1.11.3-py311h16c3c4d_1 six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 zstd conda-forge/osx-64::zstd-1.5.6-h915ae27_0 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done 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: /private/var/cache/basilisk/1.16.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.9.2 added / updated specs: - python=3.11.5 The following NEW packages will be INSTALLED: bzip2 conda-forge/osx-64::bzip2-1.0.8-h10d778d_5 ca-certificates conda-forge/osx-64::ca-certificates-2024.6.2-h8857fd0_0 libexpat conda-forge/osx-64::libexpat-2.6.2-h73e2aa4_0 libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5 libsqlite conda-forge/osx-64::libsqlite-3.46.0-h1b8f9f3_0 libzlib conda-forge/osx-64::libzlib-1.3.1-h87427d6_1 ncurses conda-forge/osx-64::ncurses-6.5-h5846eda_0 openssl conda-forge/osx-64::openssl-3.3.1-h87427d6_0 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 python conda-forge/osx-64::python-3.11.5-h30d4d87_0_cpython readline conda-forge/osx-64::readline-8.2-h9e318b2_1 setuptools conda-forge/noarch::setuptools-70.1.0-pyhd8ed1ab_0 tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1 tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0 wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 xz conda-forge/osx-64::xz-5.2.6-h775f41a_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: /private/var/cache/basilisk/1.16.0/zellkonverter/1.14.1/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 NEW packages will be INSTALLED: anndata conda-forge/noarch::anndata-0.9.2-pyhd8ed1ab_0 c-ares conda-forge/osx-64::c-ares-1.28.1-h10d778d_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-64::h5py-3.9.0-nompi_py311hf255e76_103 hdf5 conda-forge/osx-64::hdf5-1.14.2-nompi_hedada53_100 krb5 conda-forge/osx-64::krb5-1.21.2-hb884880_0 libaec conda-forge/osx-64::libaec-1.1.3-h73e2aa4_0 libblas conda-forge/osx-64::libblas-3.9.0-20_osx64_openblas libcblas conda-forge/osx-64::libcblas-3.9.0-20_osx64_openblas libcurl conda-forge/osx-64::libcurl-8.8.0-hf9fcc65_0 libcxx conda-forge/osx-64::libcxx-17.0.6-h88467a6_0 libedit conda-forge/osx-64::libedit-3.1.20191231-h0678c8f_2 libev conda-forge/osx-64::libev-4.33-h10d778d_2 libgfortran conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_3 libgfortran5 conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_3 liblapack conda-forge/osx-64::liblapack-3.9.0-20_osx64_openblas libnghttp2 conda-forge/osx-64::libnghttp2-1.58.0-h64cf6d3_1 libopenblas conda-forge/osx-64::libopenblas-0.3.25-openmp_hfef2a42_0 libssh2 conda-forge/osx-64::libssh2-1.11.0-hd019ec5_0 llvm-openmp conda-forge/osx-64::llvm-openmp-18.1.8-h15ab845_0 natsort conda-forge/noarch::natsort-8.4.0-pyhd8ed1ab_0 numpy conda-forge/osx-64::numpy-1.26.0-py311hc44ba51_0 packaging conda-forge/noarch::packaging-23.2-pyhd8ed1ab_0 pandas conda-forge/osx-64::pandas-2.1.1-py311hab14417_1 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/osx-64::python_abi-3.11-4_cp311 pytz conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0 scipy conda-forge/osx-64::scipy-1.11.3-py311h16c3c4d_1 six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 zstd conda-forge/osx-64::zstd-1.5.6-h915ae27_0 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done 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: /private/var/cache/basilisk/1.16.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.8.0 added / updated specs: - python=3.8.13 The following NEW packages will be INSTALLED: bzip2 conda-forge/osx-64::bzip2-1.0.8-h10d778d_5 ca-certificates conda-forge/osx-64::ca-certificates-2024.6.2-h8857fd0_0 libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5 libsqlite conda-forge/osx-64::libsqlite-3.46.0-h1b8f9f3_0 libzlib conda-forge/osx-64::libzlib-1.3.1-h87427d6_1 ncurses conda-forge/osx-64::ncurses-6.5-h5846eda_0 openssl conda-forge/osx-64::openssl-3.3.1-h87427d6_0 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 python conda-forge/osx-64::python-3.8.13-h66c20e1_0_cpython readline conda-forge/osx-64::readline-8.2-h9e318b2_1 setuptools conda-forge/noarch::setuptools-70.1.0-pyhd8ed1ab_0 sqlite conda-forge/osx-64::sqlite-3.46.0-h28673e1_0 tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1 wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 xz conda-forge/osx-64::xz-5.2.6-h775f41a_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: /private/var/cache/basilisk/1.16.0/zellkonverter/1.14.1/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 ---------------------------|----------------- importlib-metadata-7.2.1 | pyha770c72_0 27 KB conda-forge importlib_metadata-7.2.1 | hd8ed1ab_0 9 KB conda-forge ------------------------------------------------------------ Total: 36 KB The following NEW packages will be INSTALLED: anndata conda-forge/noarch::anndata-0.8.0-pyhd8ed1ab_1 c-ares conda-forge/osx-64::c-ares-1.28.1-h10d778d_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-64::h5py-3.6.0-nompi_py38h9f21798_100 hdf5 conda-forge/osx-64::hdf5-1.12.1-nompi_h0aa1fa2_104 importlib-metadata conda-forge/noarch::importlib-metadata-7.2.1-pyha770c72_0 importlib_metadata conda-forge/noarch::importlib_metadata-7.2.1-hd8ed1ab_0 krb5 conda-forge/osx-64::krb5-1.21.2-hb884880_0 libblas conda-forge/osx-64::libblas-3.9.0-20_osx64_openblas libcblas conda-forge/osx-64::libcblas-3.9.0-20_osx64_openblas libcurl conda-forge/osx-64::libcurl-8.8.0-hf9fcc65_0 libcxx conda-forge/osx-64::libcxx-17.0.6-h88467a6_0 libedit conda-forge/osx-64::libedit-3.1.20191231-h0678c8f_2 libev conda-forge/osx-64::libev-4.33-h10d778d_2 libgfortran conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_3 libgfortran5 conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_3 liblapack conda-forge/osx-64::liblapack-3.9.0-20_osx64_openblas libnghttp2 conda-forge/osx-64::libnghttp2-1.58.0-h64cf6d3_1 libopenblas conda-forge/osx-64::libopenblas-0.3.25-openmp_hfef2a42_0 libssh2 conda-forge/osx-64::libssh2-1.11.0-hd019ec5_0 llvm-openmp conda-forge/osx-64::llvm-openmp-18.1.8-h15ab845_0 natsort conda-forge/noarch::natsort-8.1.0-pyhd8ed1ab_0 numpy conda-forge/osx-64::numpy-1.22.3-py38h7eae8df_2 packaging conda-forge/noarch::packaging-21.3-pyhd8ed1ab_0 pandas conda-forge/osx-64::pandas-1.4.2-py38h2b30649_2 pyparsing conda-forge/noarch::pyparsing-3.1.2-pyhd8ed1ab_0 python-dateutil conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0 python_abi conda-forge/osx-64::python_abi-3.8-4_cp38 pytz conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0 scipy conda-forge/osx-64::scipy-1.7.3-py38hfb8b963_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-3.19.2-pyhd8ed1ab_0 zlib conda-forge/osx-64::zlib-1.2.13-h87427d6_6 zstd conda-forge/osx-64::zstd-1.5.6-h915ae27_0 The following packages will be DOWNGRADED: libzlib 1.3.1-h87427d6_1 --> 1.2.13-h87427d6_6 sqlite 3.46.0-h28673e1_0 --> 3.38.2-hb516253_0 Downloading and Extracting Packages importlib-metadata-7 | 27 KB | | 0% importlib-metadata-7 | 27 KB | #####9 | 59% importlib-metadata-7 | 27 KB | ########## | 100% importlib-metadata-7 | 27 KB | ########## | 100% importlib_metadata-7 | 9 KB | | 0% importlib_metadata-7 | 9 KB | ########## | 100% importlib_metadata-7 | 9 KB | ########## | 100% Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done 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: /private/var/cache/basilisk/1.16.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.7.6 added / updated specs: - python=3.7.10 The following NEW packages will be INSTALLED: ca-certificates conda-forge/osx-64::ca-certificates-2024.6.2-h8857fd0_0 libcxx conda-forge/osx-64::libcxx-17.0.6-h88467a6_0 libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5 libsqlite conda-forge/osx-64::libsqlite-3.46.0-h1b8f9f3_0 libzlib conda-forge/osx-64::libzlib-1.3.1-h87427d6_1 ncurses conda-forge/osx-64::ncurses-6.5-h5846eda_0 openssl conda-forge/osx-64::openssl-3.3.1-h87427d6_0 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 python conda-forge/osx-64::python-3.7.10-hf3644f1_104_cpython readline conda-forge/osx-64::readline-8.2-h9e318b2_1 setuptools conda-forge/noarch::setuptools-69.0.3-pyhd8ed1ab_0 sqlite conda-forge/osx-64::sqlite-3.46.0-h28673e1_0 tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1 wheel conda-forge/noarch::wheel-0.42.0-pyhd8ed1ab_0 xz conda-forge/osx-64::xz-5.2.6-h775f41a_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: /private/var/cache/basilisk/1.16.0/zellkonverter/1.14.1/zellkonverterAnnDataEnv-0.7.6 added / updated specs: - anndata=0.7.6 - h5py=3.2.1 - hdf5=1.10.6 - natsort=7.1.1 - numpy=1.20.2 - packaging=20.9 - pandas=1.2.4 - python[version='3.7.10.*,3.7.10.*'] - scipy=1.6.3 - sqlite=3.35.5 The following NEW packages will be INSTALLED: anndata conda-forge/osx-64::anndata-0.7.6-py37hf985489_0 c-ares conda-forge/osx-64::c-ares-1.28.1-h10d778d_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-64::h5py-3.2.1-nompi_py37hdf859c4_100 hdf5 conda-forge/osx-64::hdf5-1.10.6-nompi_hc5d9132_1114 importlib-metadata conda-forge/osx-64::importlib-metadata-4.11.4-py37hf985489_0 importlib_metadata conda-forge/noarch::importlib_metadata-4.11.4-hd8ed1ab_0 krb5 conda-forge/osx-64::krb5-1.20.1-h0165f36_0 libblas conda-forge/osx-64::libblas-3.9.0-20_osx64_openblas libcblas conda-forge/osx-64::libcblas-3.9.0-20_osx64_openblas libcurl conda-forge/osx-64::libcurl-7.87.0-haf73cf8_0 libedit conda-forge/osx-64::libedit-3.1.20191231-h0678c8f_2 libev conda-forge/osx-64::libev-4.33-h10d778d_2 libgfortran conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_3 libgfortran5 conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_3 liblapack conda-forge/osx-64::liblapack-3.9.0-20_osx64_openblas libnghttp2 conda-forge/osx-64::libnghttp2-1.51.0-h0dd9d14_0 libopenblas conda-forge/osx-64::libopenblas-0.3.25-openmp_hfef2a42_0 libssh2 conda-forge/osx-64::libssh2-1.10.0-h7535e13_3 llvm-openmp conda-forge/osx-64::llvm-openmp-18.1.8-h15ab845_0 natsort conda-forge/noarch::natsort-7.1.1-pyhd8ed1ab_0 numpy conda-forge/osx-64::numpy-1.20.2-py37h84c02c4_0 packaging conda-forge/noarch::packaging-20.9-pyh44b312d_0 pandas pkgs/main/osx-64::pandas-1.2.4-py37h23ab428_0 pyparsing conda-forge/noarch::pyparsing-3.1.2-pyhd8ed1ab_0 python-dateutil conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0 python_abi conda-forge/osx-64::python_abi-3.7-4_cp37m pytz conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0 scipy conda-forge/osx-64::scipy-1.6.3-py37h866764c_0 six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 typing_extensions conda-forge/noarch::typing_extensions-4.7.1-pyha770c72_0 zipp conda-forge/noarch::zipp-3.15.0-pyhd8ed1ab_0 zlib conda-forge/osx-64::zlib-1.2.13-h87427d6_6 The following packages will be DOWNGRADED: libffi 3.4.2-h0d85af4_5 --> 3.3-h046ec9c_2 libzlib 1.3.1-h87427d6_1 --> 1.2.13-h87427d6_6 openssl 3.3.1-h87427d6_0 --> 1.1.1w-h8a1eda9_0 python 3.7.10-hf3644f1_104_cpython --> 3.7.10-h7728216_100_cpython sqlite 3.46.0-h28673e1_0 --> 3.35.5-h44b9ce1_0 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done /private/var/cache/basilisk/1.16.0/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(
zellkonverter.Rcheck/zellkonverter-Ex.timings
name | user | system | elapsed | |
AnnData-Conversion | 40.540 | 5.087 | 60.991 | |
AnnData-Environment | 0.011 | 0.004 | 0.015 | |
readH5AD | 2.106 | 0.153 | 2.275 | |
setZellkonverterVerbose | 0.001 | 0.001 | 0.002 | |
writeH5AD | 6.649 | 0.685 | 7.738 | |