Aaron Lun
| Snapshot Date: 2025-07-18 13:25 -0400 (Fri, 18 Jul 2025) |
| git_url: https://git.bioconductor.org/packages/basilisk.utils |
| git_branch: devel |
| git_last_commit: f0a06f8 |
| git_last_commit_date: 2025-05-17 00:49:01 -0400 (Sat, 17 May 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-07-19 12:11 -0400 (Sat, 19 Jul 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4791 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4529 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4572 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4513 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4510 |
| 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 140/2311 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| basilisk.utils 1.21.2 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 24.04.2 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 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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: 2025-07-18 04:32:01 -0000 (Fri, 18 Jul 2025) |
| EndedAt: 2025-07-18 04:33:52 -0000 (Fri, 18 Jul 2025) |
| EllapsedTime: 111.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: basilisk.utils.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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’
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: OK
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
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")
Channels:
- conda-forge
Platform: linux-aarch64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/biocbuild/tmp/RtmpPAhhlp/file13f1822bb71b74/foo/biocconda/more-test-env
added / updated specs:
- pandas
The following packages will be downloaded:
package | build
---------------------------|-----------------
libexpat-2.7.1 | hfae3067_0 73 KB conda-forge
numpy-2.3.1 | py313h11e5ff7_1 7.3 MB conda-forge
python_abi-3.13 | 8_cp313 7 KB conda-forge
------------------------------------------------------------
Total: 7.4 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-h68df207_7
ca-certificates conda-forge/noarch::ca-certificates-2025.7.14-hbd8a1cb_0
icu conda-forge/linux-aarch64::icu-75.1-hf9b3779_0
ld_impl_linux-aar~ conda-forge/linux-aarch64::ld_impl_linux-aarch64-2.44-h5e2c951_1
libblas conda-forge/linux-aarch64::libblas-3.9.0-32_h1a9f1db_openblas
libcblas conda-forge/linux-aarch64::libcblas-3.9.0-32_hab92f65_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-15.1.0-he277a41_3
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-15.1.0-he9431aa_3
libgfortran conda-forge/linux-aarch64::libgfortran-15.1.0-he9431aa_3
libgfortran5 conda-forge/linux-aarch64::libgfortran5-15.1.0-hbc25352_3
libgomp conda-forge/linux-aarch64::libgomp-15.1.0-he277a41_3
liblapack conda-forge/linux-aarch64::liblapack-3.9.0-32_h411afd4_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_0
libsqlite conda-forge/linux-aarch64::libsqlite-3.50.2-hdbb6186_2
libstdcxx conda-forge/linux-aarch64::libstdcxx-15.1.0-h3f4de04_3
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-15.1.0-hf1166c9_3
libuuid conda-forge/linux-aarch64::libuuid-2.38.1-hb4cce97_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-2.3.1-py313h11e5ff7_1
openssl conda-forge/linux-aarch64::openssl-3.5.1-hd08dc88_0
pandas conda-forge/linux-aarch64::pandas-2.3.1-py313h9de0199_0
pip conda-forge/noarch::pip-25.1.1-pyh145f28c_0
python conda-forge/linux-aarch64::python-3.13.5-h2382df9_102_cp313
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-3.13-8_cp313
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-pyhd8ed1ab_0
tk conda-forge/linux-aarch64::tk-8.6.13-noxft_h5688188_102
tzdata conda-forge/noarch::tzdata-2025b-h78e105d_0
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/RtmpPAhhlp/file13f1822bb71b74/foo/biocconda/test-env
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-2025.7.14-hbd8a1cb_0
hdf5 conda-forge/linux-aarch64::hdf5-1.14.6-nompi_h587839b_102
keyutils conda-forge/linux-aarch64::keyutils-1.6.1-h4e544f5_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-15.1.0-he277a41_3
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-15.1.0-he9431aa_3
libgfortran conda-forge/linux-aarch64::libgfortran-15.1.0-he9431aa_3
libgfortran5 conda-forge/linux-aarch64::libgfortran5-15.1.0-hbc25352_3
libgomp conda-forge/linux-aarch64::libgomp-15.1.0-he277a41_3
libnghttp2 conda-forge/linux-aarch64::libnghttp2-1.64.0-hc8609a4_0
libssh2 conda-forge/linux-aarch64::libssh2-1.11.1-h18c354c_0
libstdcxx conda-forge/linux-aarch64::libstdcxx-15.1.0-h3f4de04_3
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-15.1.0-hf1166c9_3
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-3.5.1-hd08dc88_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/RtmpPAhhlp/file13f182bfe2241/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-2025.7.14-hbd8a1cb_0
hdf5 conda-forge/linux-aarch64::hdf5-1.14.6-nompi_h587839b_102
keyutils conda-forge/linux-aarch64::keyutils-1.6.1-h4e544f5_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-15.1.0-he277a41_3
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-15.1.0-he9431aa_3
libgfortran conda-forge/linux-aarch64::libgfortran-15.1.0-he9431aa_3
libgfortran5 conda-forge/linux-aarch64::libgfortran5-15.1.0-hbc25352_3
libgomp conda-forge/linux-aarch64::libgomp-15.1.0-he277a41_3
libnghttp2 conda-forge/linux-aarch64::libnghttp2-1.64.0-hc8609a4_0
libssh2 conda-forge/linux-aarch64::libssh2-1.11.1-h18c354c_0
libstdcxx conda-forge/linux-aarch64::libstdcxx-15.1.0-h3f4de04_3
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-15.1.0-hf1166c9_3
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-3.5.1-hd08dc88_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/RtmpPAhhlp/file13f182bfe2241/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-2025.7.14-hbd8a1cb_0
hdf5 conda-forge/linux-aarch64::hdf5-1.14.6-nompi_h587839b_102
keyutils conda-forge/linux-aarch64::keyutils-1.6.1-h4e544f5_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-15.1.0-he277a41_3
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-15.1.0-he9431aa_3
libgfortran conda-forge/linux-aarch64::libgfortran-15.1.0-he9431aa_3
libgfortran5 conda-forge/linux-aarch64::libgfortran5-15.1.0-hbc25352_3
libgomp conda-forge/linux-aarch64::libgomp-15.1.0-he277a41_3
libnghttp2 conda-forge/linux-aarch64::libnghttp2-1.64.0-hc8609a4_0
libssh2 conda-forge/linux-aarch64::libssh2-1.11.1-h18c354c_0
libstdcxx conda-forge/linux-aarch64::libstdcxx-15.1.0-h3f4de04_3
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-15.1.0-hf1166c9_3
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-3.5.1-hd08dc88_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/RtmpPAhhlp/file13f182bfe2241/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-2025.7.14-hbd8a1cb_0
hdf5 conda-forge/linux-aarch64::hdf5-1.14.6-nompi_h587839b_102
keyutils conda-forge/linux-aarch64::keyutils-1.6.1-h4e544f5_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-15.1.0-he277a41_3
libgcc-ng conda-forge/linux-aarch64::libgcc-ng-15.1.0-he9431aa_3
libgfortran conda-forge/linux-aarch64::libgfortran-15.1.0-he9431aa_3
libgfortran5 conda-forge/linux-aarch64::libgfortran5-15.1.0-hbc25352_3
libgomp conda-forge/linux-aarch64::libgomp-15.1.0-he277a41_3
libnghttp2 conda-forge/linux-aarch64::libnghttp2-1.64.0-hc8609a4_0
libssh2 conda-forge/linux-aarch64::libssh2-1.11.1-h18c354c_0
libstdcxx conda-forge/linux-aarch64::libstdcxx-15.1.0-h3f4de04_3
libstdcxx-ng conda-forge/linux-aarch64::libstdcxx-ng-15.1.0-hf1166c9_3
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-3.5.1-hd08dc88_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 0 | WARN 0 | SKIP 0 | PASS 23 ]
>
> proc.time()
user system elapsed
48.630 5.436 92.045
basilisk.utils.Rcheck/basilisk.utils-Ex.timings
| name | user | system | elapsed | |
| binaryPath | 0 | 0 | 0 | |
| configureEnvironments | 0 | 0 | 0 | |
| createEnvironment | 0.003 | 0.000 | 0.003 | |
| defaults | 0.000 | 0.001 | 0.000 | |
| download | 0.000 | 0.005 | 0.008 | |
| find | 0.546 | 0.126 | 1.406 | |