Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-08 11:41:34 -0400 (Wed, 08 May 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" | 4707 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
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 1.14.0 (landing page) Luke Zappia
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: zellkonverter |
Version: 1.14.0 |
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings zellkonverter_1.14.0.tar.gz |
StartedAt: 2024-05-08 13:11:35 -0000 (Wed, 08 May 2024) |
EndedAt: 2024-05-08 13:23:33 -0000 (Wed, 08 May 2024) |
EllapsedTime: 718.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: zellkonverter.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:zellkonverter.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings zellkonverter_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/zellkonverter.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘zellkonverter/DESCRIPTION’ ... OK * this is package ‘zellkonverter’ version ‘1.14.0’ * 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/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 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 ... 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 30.083 1.544 32.631 writeH5AD 5.891 0.347 6.257 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ── Error ('test-write.R:133:5'): writeH5AD works as expected with version 0.7.6 ── Error: one or more Python packages failed to install [error code 1] Backtrace: ▆ 1. └─zellkonverter::writeH5AD(sce, temp, version = "0.7.6") at test-write.R:133:5 2. └─basilisk::basiliskRun(...) 3. └─basilisk::basiliskStart(...) 4. └─basilisk::obtainEnvironmentPath(env) 5. └─basilisk::setupBasiliskEnv(...) 6. └─reticulate::conda_install(...) 7. └─reticulate:::stopf(fmt, result) [ FAIL 2 | WARN 29 | SKIP 3 | PASS 134 ] Error: Test failures Execution halted * 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 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/zellkonverter.Rcheck/00check.log’ for details.
zellkonverter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL zellkonverter ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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 beta (2024-04-15 r86425) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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. > if (requireNamespace("spelling", quietly = TRUE)) { + spelling::spell_check_test( + vignettes = TRUE, + error = FALSE, + skip_on_cran = TRUE + ) + } NULL > > proc.time() user system elapsed 0.170 0.051 0.206
zellkonverter.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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: /home/biocbuild/.cache/R/basilisk/1.16.0/zellkonverter/1.14.0/zellkonverterAnnDataEnv-0.7.6 added / updated specs: - python=3.7.10 The following NEW packages will be INSTALLED: _openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu ca-certificates conda-forge/linux-aarch64::ca-certificates-2024.2.2-hcefe29a_0 ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.40-hba4e955_0 libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5 libgcc-ng conda-forge/linux-aarch64::libgcc-ng-13.2.0-he277a41_7 libgomp conda-forge/linux-aarch64::libgomp-13.2.0-he277a41_7 libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0 libsqlite conda-forge/linux-aarch64::libsqlite-3.45.3-h194ca79_0 libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-13.2.0-h3f4de04_7 libzlib conda-forge/linux-aarch64::libzlib-1.2.13-h31becfc_5 ncurses conda-forge/linux-aarch64::ncurses-6.4.20240210-h0425590_0 openssl conda-forge/linux-aarch64::openssl-3.3.0-h31becfc_0 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 python conda-forge/linux-aarch64::python-3.7.10-h47f6e27_104_cpython readline conda-forge/linux-aarch64::readline-8.2-h8fc344f_1 setuptools conda-forge/noarch::setuptools-69.0.3-pyhd8ed1ab_0 sqlite conda-forge/linux-aarch64::sqlite-3.45.3-h3b3482f_0 tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0 wheel conda-forge/noarch::wheel-0.42.0-pyhd8ed1ab_0 xz conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_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: 24.4.0 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... failed with initial frozen solve. Retrying with flexible solve. PackagesNotFoundError: The following packages are not available from current channels: - anndata=0.7.6 Current channels: - https://conda.anaconda.org/conda-forge/linux-aarch64 - https://conda.anaconda.org/conda-forge/noarch - https://repo.anaconda.com/pkgs/main/linux-aarch64 - https://repo.anaconda.com/pkgs/main/noarch - https://repo.anaconda.com/pkgs/r/linux-aarch64 - https://repo.anaconda.com/pkgs/r/noarch To search for alternate channels that may provide the conda package you're looking for, navigate to https://anaconda.org and use the search bar at the top of the page. /home/biocbuild/.cache/R/basilisk/1.16.0/zellkonverter/1.14.0/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( /home/biocbuild/.cache/R/basilisk/1.16.0/zellkonverter/1.14.0/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( /home/biocbuild/.cache/R/basilisk/1.16.0/zellkonverter/1.14.0/zellkonverterAnnDataEnv-0.10.2/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024. warnings.warn( 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: /home/biocbuild/.cache/R/basilisk/1.16.0/zellkonverter/1.14.0/zellkonverterAnnDataEnv-0.7.6 added / updated specs: - python=3.7.10 The following NEW packages will be INSTALLED: _openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu ca-certificates conda-forge/linux-aarch64::ca-certificates-2024.2.2-hcefe29a_0 ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.40-hba4e955_0 libffi conda-forge/linux-aarch64::libffi-3.4.2-h3557bc0_5 libgcc-ng conda-forge/linux-aarch64::libgcc-ng-13.2.0-he277a41_7 libgomp conda-forge/linux-aarch64::libgomp-13.2.0-he277a41_7 libnsl conda-forge/linux-aarch64::libnsl-2.0.1-h31becfc_0 libsqlite conda-forge/linux-aarch64::libsqlite-3.45.3-h194ca79_0 libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-13.2.0-h3f4de04_7 libzlib conda-forge/linux-aarch64::libzlib-1.2.13-h31becfc_5 ncurses conda-forge/linux-aarch64::ncurses-6.4.20240210-h0425590_0 openssl conda-forge/linux-aarch64::openssl-3.3.0-h31becfc_0 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 python conda-forge/linux-aarch64::python-3.7.10-h47f6e27_104_cpython readline conda-forge/linux-aarch64::readline-8.2-h8fc344f_1 setuptools conda-forge/noarch::setuptools-69.0.3-pyhd8ed1ab_0 sqlite conda-forge/linux-aarch64::sqlite-3.45.3-h3b3482f_0 tk conda-forge/linux-aarch64::tk-8.6.13-h194ca79_0 wheel conda-forge/noarch::wheel-0.42.0-pyhd8ed1ab_0 xz conda-forge/linux-aarch64::xz-5.2.6-h9cdd2b7_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: 24.4.0 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... failed with initial frozen solve. Retrying with flexible solve. PackagesNotFoundError: The following packages are not available from current channels: - anndata=0.7.6 Current channels: - https://conda.anaconda.org/conda-forge/linux-aarch64 - https://conda.anaconda.org/conda-forge/noarch - https://repo.anaconda.com/pkgs/main/linux-aarch64 - https://repo.anaconda.com/pkgs/main/noarch - https://repo.anaconda.com/pkgs/r/linux-aarch64 - https://repo.anaconda.com/pkgs/r/noarch To search for alternate channels that may provide the conda package you're looking for, navigate to https://anaconda.org and use the search bar at the top of the page. /home/biocbuild/.cache/R/basilisk/1.16.0/zellkonverter/1.14.0/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( /home/biocbuild/.cache/R/basilisk/1.16.0/zellkonverter/1.14.0/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( /home/biocbuild/.cache/R/basilisk/1.16.0/zellkonverter/1.14.0/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( /home/biocbuild/.cache/R/basilisk/1.16.0/zellkonverter/1.14.0/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( /home/biocbuild/.cache/R/basilisk/1.16.0/zellkonverter/1.14.0/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( /home/biocbuild/.cache/R/basilisk/1.16.0/zellkonverter/1.14.0/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( /home/biocbuild/.cache/R/basilisk/1.16.0/zellkonverter/1.14.0/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( /home/biocbuild/.cache/R/basilisk/1.16.0/zellkonverter/1.14.0/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( /home/biocbuild/.cache/R/basilisk/1.16.0/zellkonverter/1.14.0/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( /home/biocbuild/.cache/R/basilisk/1.16.0/zellkonverter/1.14.0/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( /home/biocbuild/.cache/R/basilisk/1.16.0/zellkonverter/1.14.0/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( /home/biocbuild/.cache/R/basilisk/1.16.0/zellkonverter/1.14.0/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( /home/biocbuild/.cache/R/basilisk/1.16.0/zellkonverter/1.14.0/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( /home/biocbuild/.cache/R/basilisk/1.16.0/zellkonverter/1.14.0/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 2 | WARN 29 | SKIP 3 | PASS 134 ] ══ Skipped tests (3) ═══════════════════════════════════════════════════════════ • On CRAN (3): 'test-read.R:155:5', 'test-zzz-anndata.R:6:5', 'test-zzz-anndata.R:54:5' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-read.R:39:5'): Reading H5AD works with version 0.7.6 ─────────── Error: one or more Python packages failed to install [error code 1] Backtrace: ▆ 1. └─zellkonverter::readH5AD(file, version = "0.7.6") at test-read.R:39:5 2. └─basilisk::basiliskRun(...) 3. └─basilisk::basiliskStart(...) 4. └─basilisk::obtainEnvironmentPath(env) 5. └─basilisk::setupBasiliskEnv(...) 6. └─reticulate::conda_install(...) 7. └─reticulate:::stopf(fmt, result) ── Error ('test-write.R:133:5'): writeH5AD works as expected with version 0.7.6 ── Error: one or more Python packages failed to install [error code 1] Backtrace: ▆ 1. └─zellkonverter::writeH5AD(sce, temp, version = "0.7.6") at test-write.R:133:5 2. └─basilisk::basiliskRun(...) 3. └─basilisk::basiliskStart(...) 4. └─basilisk::obtainEnvironmentPath(env) 5. └─basilisk::setupBasiliskEnv(...) 6. └─reticulate::conda_install(...) 7. └─reticulate:::stopf(fmt, result) [ FAIL 2 | WARN 29 | SKIP 3 | PASS 134 ] Error: Test failures Execution halted
zellkonverter.Rcheck/zellkonverter-Ex.timings
name | user | system | elapsed | |
AnnData-Conversion | 30.083 | 1.544 | 32.631 | |
AnnData-Environment | 0.007 | 0.000 | 0.008 | |
readH5AD | 1.319 | 0.032 | 1.363 | |
setZellkonverterVerbose | 0 | 0 | 0 | |
writeH5AD | 5.891 | 0.347 | 6.257 | |