Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-11 12:06 -0400 (Sat, 11 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4864 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4586 |
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 142/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
basilisk.utils 1.21.2 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the basilisk.utils package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/basilisk.utils.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: basilisk.utils |
Version: 1.21.2 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:basilisk.utils.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings basilisk.utils_1.21.2.tar.gz |
StartedAt: 2025-10-10 05:41:53 -0000 (Fri, 10 Oct 2025) |
EndedAt: 2025-10-10 05:45:43 -0000 (Fri, 10 Oct 2025) |
EllapsedTime: 230.1 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: basilisk.utils.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:basilisk.utils.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings basilisk.utils_1.21.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/basilisk.utils.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘basilisk.utils/DESCRIPTION’ ... OK * this is package ‘basilisk.utils’ version ‘1.21.2’ * 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 ‘basilisk.utils’ can be installed ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: env.loc, status)) } success <- TRUE })(env.loc = "/home/biocbuild/tmp/RtmpP50gWA/filecdd04d2e51c9/foo/biocconda/more-test-env", packages = "pandas", conda = NULL, channels = "conda-forge", override.channels = TRUE, extra = "--quiet")`: failed to create conda environment at '/home/biocbuild/tmp/RtmpP50gWA/filecdd04d2e51c9/foo/biocconda/more-test-env' (returned 1) Backtrace: ▆ 1. └─basilisk.utils::configureEnvironments(ext) at test-configureEnvironments.R:45:5 2. ├─base::do.call(.create_environment, cur.args) 3. └─basilisk.utils (local) `<fn>`(...) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ] 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 See ‘/home/biocbuild/bbs-3.22-bioc/meat/basilisk.utils.Rcheck/00check.log’ for details.
basilisk.utils.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL basilisk.utils ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘basilisk.utils’ ... ** this is package ‘basilisk.utils’ version ‘1.21.2’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (basilisk.utils)
basilisk.utils.Rcheck/tests/testthat.Rout.fail
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 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(basilisk.utils) Attaching package: 'basilisk.utils' The following object is masked from 'package:utils': find > test_check("basilisk.utils") Retrieving notices: ...working... done Channels: - conda-forge Platform: linux-aarch64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-15.2.0-he277a41_7.conda> Elapsed: - An HTTP error occurred when trying to retrieve this URL. HTTP errors are often intermittent, and a simple retry will get you on your way. CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-15.2.0-he277a41_7.conda> Elapsed: - An HTTP error occurred when trying to retrieve this URL. HTTP errors are often intermittent, and a simple retry will get you on your way. ## Package Plan ## environment location: /home/biocbuild/tmp/RtmpP50gWA/filecdd04d2e51c9/foo/biocconda/more-test-env added / updated specs: - pandas The following packages will be downloaded: package | build ---------------------------|----------------- libgcc-15.2.0 | he277a41_7 499 KB conda-forge libgfortran-15.2.0 | he9431aa_7 29 KB conda-forge libgfortran5-15.2.0 | h87db57e_7 1.1 MB conda-forge libgomp-15.2.0 | he277a41_7 440 KB conda-forge libstdcxx-15.2.0 | h3f4de04_7 3.7 MB conda-forge numpy-2.3.3 | py314h488ef0c_0 7.4 MB conda-forge pandas-2.3.3 | py314h91eeaa4_1 14.4 MB conda-forge python-3.14.0 |ha9132a3_100_cp314 35.4 MB conda-forge python_abi-3.14 | 8_cp314 7 KB conda-forge ------------------------------------------------------------ Total: 62.9 MB The following NEW packages will be INSTALLED: _openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu bzip2 conda-forge/linux-aarch64::bzip2-1.0.8-h4777abc_8 ca-certificates conda-forge/noarch::ca-certificates-2025.10.5-hbd8a1cb_0 ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.44-h9df1782_2 libblas conda-forge/linux-aarch64::libblas-3.9.0-36_haddc8a3_openblas libcblas conda-forge/linux-aarch64::libcblas-3.9.0-36_hd72aa62_openblas libexpat conda-forge/linux-aarch64::libexpat-2.7.1-hfae3067_0 libffi conda-forge/linux-aarch64::libffi-3.4.6-he21f813_1 libgcc conda-forge/linux-aarch64::libgcc-15.2.0-he277a41_7 libgfortran conda-forge/linux-aarch64::libgfortran-15.2.0-he9431aa_7 libgfortran5 conda-forge/linux-aarch64::libgfortran5-15.2.0-h87db57e_7 libgomp conda-forge/linux-aarch64::libgomp-15.2.0-he277a41_7 liblapack conda-forge/linux-aarch64::liblapack-3.9.0-36_h88aeb00_openblas liblzma conda-forge/linux-aarch64::liblzma-5.8.1-h86ecc28_2 libmpdec conda-forge/linux-aarch64::libmpdec-4.0.0-h86ecc28_0 libopenblas conda-forge/linux-aarch64::libopenblas-0.3.30-pthreads_h9d3fd7e_2 libsqlite conda-forge/linux-aarch64::libsqlite-3.50.4-h022381a_0 libstdcxx conda-forge/linux-aarch64::libstdcxx-15.2.0-h3f4de04_7 libuuid conda-forge/linux-aarch64::libuuid-2.41.2-h3e4203c_0 libzlib conda-forge/linux-aarch64::libzlib-1.3.1-h86ecc28_2 ncurses conda-forge/linux-aarch64::ncurses-6.5-ha32ae93_3 numpy conda-forge/linux-aarch64::numpy-2.3.3-py314h488ef0c_0 openssl conda-forge/linux-aarch64::openssl-3.5.4-h8e36d6e_0 pandas conda-forge/linux-aarch64::pandas-2.3.3-py314h91eeaa4_1 pip conda-forge/noarch::pip-25.2-pyh145f28c_0 python conda-forge/linux-aarch64::python-3.14.0-ha9132a3_100_cp314 python-dateutil conda-forge/noarch::python-dateutil-2.9.0.post0-pyhe01879c_2 python-tzdata conda-forge/noarch::python-tzdata-2025.2-pyhd8ed1ab_0 python_abi conda-forge/noarch::python_abi-3.14-8_cp314 pytz conda-forge/noarch::pytz-2025.2-pyhd8ed1ab_0 readline conda-forge/linux-aarch64::readline-8.2-h8382b9d_2 six conda-forge/noarch::six-1.17.0-pyhe01879c_1 tk conda-forge/linux-aarch64::tk-8.6.13-noxft_h5688188_102 tzdata conda-forge/noarch::tzdata-2025b-h78e105d_0 zstd conda-forge/linux-aarch64::zstd-1.5.7-hbcf94c1_2 Channels: - conda-forge Platform: linux-aarch64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/biocbuild/tmp/RtmpP50gWA/filecdd06a72d538/test_env/1.0.0 added / updated specs: - hdf5 The following packages will be downloaded: package | build ---------------------------|----------------- libgcc-15.2.0 | he277a41_7 499 KB conda-forge libgcc-ng-15.2.0 | he9431aa_7 29 KB conda-forge libstdcxx-ng-15.2.0 | hf1166c9_7 29 KB conda-forge ------------------------------------------------------------ Total: 556 KB The following NEW packages will be INSTALLED: _openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu c-ares conda-forge/linux-aarch64::c-ares-1.34.5-h86ecc28_0 ca-certificates conda-forge/noarch::ca-certificates-2025.10.5-hbd8a1cb_0 hdf5 conda-forge/linux-aarch64::hdf5-1.14.6-nompi_h587839b_103 keyutils conda-forge/linux-aarch64::keyutils-1.6.3-h86ecc28_0 krb5 conda-forge/linux-aarch64::krb5-1.21.3-h50a48e9_0 libaec conda-forge/linux-aarch64::libaec-1.1.4-h1e66f74_0 libcurl conda-forge/linux-aarch64::libcurl-8.14.1-h6702fde_0 libedit conda-forge/linux-aarch64::libedit-3.1.20250104-pl5321h976ea20_0 libev conda-forge/linux-aarch64::libev-4.33-h31becfc_2 libgcc conda-forge/linux-aarch64::libgcc-15.2.0-he277a41_7 libgcc-ng conda-forge/linux-aarch64::libgcc-ng-15.2.0-he9431aa_7 libgfortran conda-forge/linux-aarch64::libgfortran-15.2.0-he9431aa_7 libgfortran5 conda-forge/linux-aarch64::libgfortran5-15.2.0-h87db57e_7 libgomp conda-forge/linux-aarch64::libgomp-15.2.0-he277a41_7 libnghttp2 conda-forge/linux-aarch64::libnghttp2-1.67.0-ha888d0e_0 libssh2 conda-forge/linux-aarch64::libssh2-1.11.1-h18c354c_0 libstdcxx conda-forge/linux-aarch64::libstdcxx-15.2.0-h3f4de04_7 libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-15.2.0-hf1166c9_7 libzlib conda-forge/linux-aarch64::libzlib-1.3.1-h86ecc28_2 ncurses conda-forge/linux-aarch64::ncurses-6.5-ha32ae93_3 openssl conda-forge/linux-aarch64::openssl-3.5.4-h8e36d6e_0 zstd conda-forge/linux-aarch64::zstd-1.5.7-hbcf94c1_2 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Channels: - conda-forge Platform: linux-aarch64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/biocbuild/tmp/RtmpP50gWA/filecdd06a72d538/test_env/1.0.1 added / updated specs: - hdf5 The following NEW packages will be INSTALLED: _openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu c-ares conda-forge/linux-aarch64::c-ares-1.34.5-h86ecc28_0 ca-certificates conda-forge/noarch::ca-certificates-2025.10.5-hbd8a1cb_0 hdf5 conda-forge/linux-aarch64::hdf5-1.14.6-nompi_h587839b_103 keyutils conda-forge/linux-aarch64::keyutils-1.6.3-h86ecc28_0 krb5 conda-forge/linux-aarch64::krb5-1.21.3-h50a48e9_0 libaec conda-forge/linux-aarch64::libaec-1.1.4-h1e66f74_0 libcurl conda-forge/linux-aarch64::libcurl-8.14.1-h6702fde_0 libedit conda-forge/linux-aarch64::libedit-3.1.20250104-pl5321h976ea20_0 libev conda-forge/linux-aarch64::libev-4.33-h31becfc_2 libgcc conda-forge/linux-aarch64::libgcc-15.2.0-he277a41_7 libgcc-ng conda-forge/linux-aarch64::libgcc-ng-15.2.0-he9431aa_7 libgfortran conda-forge/linux-aarch64::libgfortran-15.2.0-he9431aa_7 libgfortran5 conda-forge/linux-aarch64::libgfortran5-15.2.0-h87db57e_7 libgomp conda-forge/linux-aarch64::libgomp-15.2.0-he277a41_7 libnghttp2 conda-forge/linux-aarch64::libnghttp2-1.67.0-ha888d0e_0 libssh2 conda-forge/linux-aarch64::libssh2-1.11.1-h18c354c_0 libstdcxx conda-forge/linux-aarch64::libstdcxx-15.2.0-h3f4de04_7 libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-15.2.0-hf1166c9_7 libzlib conda-forge/linux-aarch64::libzlib-1.3.1-h86ecc28_2 ncurses conda-forge/linux-aarch64::ncurses-6.5-ha32ae93_3 openssl conda-forge/linux-aarch64::openssl-3.5.4-h8e36d6e_0 zstd conda-forge/linux-aarch64::zstd-1.5.7-hbcf94c1_2 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Channels: - conda-forge Platform: linux-aarch64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/biocbuild/tmp/RtmpP50gWA/filecdd06a72d538/test_env/1.0.0 added / updated specs: - hdf5 The following NEW packages will be INSTALLED: _openmp_mutex conda-forge/linux-aarch64::_openmp_mutex-4.5-2_gnu c-ares conda-forge/linux-aarch64::c-ares-1.34.5-h86ecc28_0 ca-certificates conda-forge/noarch::ca-certificates-2025.10.5-hbd8a1cb_0 hdf5 conda-forge/linux-aarch64::hdf5-1.14.6-nompi_h587839b_103 keyutils conda-forge/linux-aarch64::keyutils-1.6.3-h86ecc28_0 krb5 conda-forge/linux-aarch64::krb5-1.21.3-h50a48e9_0 libaec conda-forge/linux-aarch64::libaec-1.1.4-h1e66f74_0 libcurl conda-forge/linux-aarch64::libcurl-8.14.1-h6702fde_0 libedit conda-forge/linux-aarch64::libedit-3.1.20250104-pl5321h976ea20_0 libev conda-forge/linux-aarch64::libev-4.33-h31becfc_2 libgcc conda-forge/linux-aarch64::libgcc-15.2.0-he277a41_7 libgcc-ng conda-forge/linux-aarch64::libgcc-ng-15.2.0-he9431aa_7 libgfortran conda-forge/linux-aarch64::libgfortran-15.2.0-he9431aa_7 libgfortran5 conda-forge/linux-aarch64::libgfortran5-15.2.0-h87db57e_7 libgomp conda-forge/linux-aarch64::libgomp-15.2.0-he277a41_7 libnghttp2 conda-forge/linux-aarch64::libnghttp2-1.67.0-ha888d0e_0 libssh2 conda-forge/linux-aarch64::libssh2-1.11.1-h18c354c_0 libstdcxx conda-forge/linux-aarch64::libstdcxx-15.2.0-h3f4de04_7 libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-15.2.0-hf1166c9_7 libzlib conda-forge/linux-aarch64::libzlib-1.3.1-h86ecc28_2 ncurses conda-forge/linux-aarch64::ncurses-6.5-ha32ae93_3 openssl conda-forge/linux-aarch64::openssl-3.5.4-h8e36d6e_0 zstd conda-forge/linux-aarch64::zstd-1.5.7-hbcf94c1_2 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Channels: - conda-forge Platform: linux-aarch64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... failed PackagesNotFoundError: The following packages are not available from current channels: - aaronrandompackageshouldntexist Current channels: - https://conda.anaconda.org/conda-forge 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. [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-configureEnvironments.R:45:5'): configureEnvironments works as expected ── Error in `(function (env.loc, conda, packages, channels, override.channels, extra) { success <- FALSE on.exit(if (!success) unlink2(env.loc), add = TRUE, after = FALSE) if (is.null(conda)) { conda <- find() } more.args <- character(0) for (ch in channels) { more.args <- c(more.args, "-c", ch) } if (override.channels) { more.args <- c(more.args, "--override-channels") } status <- system2(conda, c("create", "--prefix", env.loc, "--yes", packages, more.args, extra)) if (status != 0L) { stop(sprintf("failed to create conda environment at '%s' (returned %i)", env.loc, status)) } success <- TRUE })(env.loc = "/home/biocbuild/tmp/RtmpP50gWA/filecdd04d2e51c9/foo/biocconda/more-test-env", packages = "pandas", conda = NULL, channels = "conda-forge", override.channels = TRUE, extra = "--quiet")`: failed to create conda environment at '/home/biocbuild/tmp/RtmpP50gWA/filecdd04d2e51c9/foo/biocconda/more-test-env' (returned 1) Backtrace: ▆ 1. └─basilisk.utils::configureEnvironments(ext) at test-configureEnvironments.R:45:5 2. ├─base::do.call(.create_environment, cur.args) 3. └─basilisk.utils (local) `<fn>`(...) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 21 ] Error: Test failures Execution halted
basilisk.utils.Rcheck/basilisk.utils-Ex.timings
name | user | system | elapsed | |
binaryPath | 0 | 0 | 0 | |
configureEnvironments | 0 | 0 | 0 | |
createEnvironment | 0.003 | 0.000 | 0.004 | |
defaults | 0.000 | 0.000 | 0.001 | |
download | 0.002 | 0.004 | 0.009 | |
find | 0.598 | 0.118 | 1.493 | |