Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-11-02 11:40:43 -0400 (Thu, 02 Nov 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
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 781/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
gDRutils 1.0.0 (landing page) Arkadiusz Gladki
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the gDRutils package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gDRutils.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: gDRutils |
Version: 1.0.0 |
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings gDRutils_1.0.0.tar.gz |
StartedAt: 2023-11-02 10:43:34 -0000 (Thu, 02 Nov 2023) |
EndedAt: 2023-11-02 10:48:00 -0000 (Thu, 02 Nov 2023) |
EllapsedTime: 265.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: gDRutils.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings gDRutils_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/gDRutils.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * 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 ‘gDRutils/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘gDRutils’ version ‘1.0.0’ * 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 ‘gDRutils’ 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 R 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 in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
gDRutils.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL gDRutils ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘gDRutils’ ... ** 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 (gDRutils)
gDRutils.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (64-bit) 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("gDRutils") > library("testthat") > > test_check("gDRutils") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 461 ] > > proc.time() user system elapsed 59.664 1.695 61.192
gDRutils.Rcheck/gDRutils-Ex.timings
name | user | system | elapsed | |
MAEpply | 1.336 | 0.040 | 1.396 | |
SE_metadata | 0.046 | 0.000 | 0.046 | |
aggregate_assay | 0.735 | 0.044 | 0.780 | |
apply_bumpy_function | 2.185 | 0.095 | 2.285 | |
assert_choices | 0 | 0 | 0 | |
cap_xc50 | 0 | 0 | 0 | |
convert_combo_data_to_dt | 1.623 | 0.076 | 1.704 | |
convert_mae_assay_to_dt | 0.076 | 0.000 | 0.076 | |
convert_mae_to_json | 0.103 | 0.011 | 0.115 | |
convert_se_assay_to_dt | 0.074 | 0.003 | 0.077 | |
convert_se_to_json | 0.024 | 0.000 | 0.024 | |
demote_fields | 0.469 | 0.020 | 0.481 | |
df_to_bm_assay | 0.144 | 0.004 | 0.148 | |
dot-convert_colData_to_json | 0.003 | 0.000 | 0.003 | |
dot-convert_metadata_to_json | 0.006 | 0.000 | 0.005 | |
dot-convert_rowData_to_json | 0.004 | 0.000 | 0.003 | |
dot-set_constant_fit_params | 0.001 | 0.000 | 0.001 | |
dot-set_invalid_fit_params | 0 | 0 | 0 | |
extend_normalization_type_name | 0.001 | 0.000 | 0.000 | |
fit_curves | 0.241 | 0.016 | 0.264 | |
flatten | 0.012 | 0.000 | 0.012 | |
gen_synthetic_data | 0.003 | 0.000 | 0.003 | |
get_MAE_identifiers | 0.006 | 0.004 | 0.009 | |
get_assay_names | 0.001 | 0.000 | 0.000 | |
get_combo_assay_names | 0.001 | 0.000 | 0.001 | |
get_combo_base_assay_names | 0.001 | 0.000 | 0.001 | |
get_combo_col_settings | 0.005 | 0.000 | 0.005 | |
get_combo_score_assay_names | 0.001 | 0.000 | 0.001 | |
get_default_identifiers | 0.001 | 0.000 | 0.000 | |
get_env_assay_names | 0 | 0 | 0 | |
get_expect_one_identifiers | 0 | 0 | 0 | |
get_experiment_groups | 0.000 | 0.000 | 0.001 | |
get_identifiers_dt | 0.007 | 0.000 | 0.007 | |
get_idfs_synonyms | 0 | 0 | 0 | |
get_iso_colors | 0.002 | 0.000 | 0.002 | |
get_non_empty_assays | 0.071 | 0.000 | 0.071 | |
get_required_identifiers | 0 | 0 | 0 | |
get_synthetic_data | 0.013 | 0.000 | 0.013 | |
get_testdata | 0.088 | 0.008 | 0.096 | |
headers | 0.007 | 0.000 | 0.007 | |
identifiers | 0 | 0 | 0 | |
identify_unique_se_metadata_fields | 0.008 | 0.000 | 0.008 | |
is_any_exp_empty | 0.064 | 0.000 | 0.062 | |
is_exp_empty | 0.064 | 0.000 | 0.063 | |
is_mae_empty | 0.064 | 0.000 | 0.062 | |
logisticFit | 0.025 | 0.000 | 0.025 | |
loop | 0 | 0 | 0 | |
mcolData | 0.017 | 0.000 | 0.017 | |
merge_SE | 2.262 | 0.012 | 2.266 | |
merge_assay | 0.434 | 0.004 | 0.439 | |
merge_metadata | 0.009 | 0.000 | 0.009 | |
mrowData | 0.017 | 0.000 | 0.017 | |
predict_conc_from_efficacy | 0 | 0 | 0 | |
predict_efficacy_from_conc | 0 | 0 | 0 | |
prettify_flat_metrics | 0.006 | 0.000 | 0.007 | |
promote_fields | 0.299 | 0.008 | 0.306 | |
refine_coldata | 0.011 | 0.000 | 0.012 | |
refine_rowdata | 0.06 | 0.00 | 0.06 | |
rename_DFrame | 0.011 | 0.000 | 0.012 | |
rename_bumpy | 0.036 | 0.004 | 0.041 | |
shorten_normalization_type_name | 0.000 | 0.000 | 0.001 | |
split_SE_components | 0.039 | 0.000 | 0.040 | |
standardize_mae | 0.199 | 0.000 | 0.204 | |
standardize_se | 0.041 | 0.000 | 0.042 | |
update_env_idfs_from_mae | 0.001 | 0.000 | 0.002 | |
update_idfs_synonyms | 0.000 | 0.000 | 0.001 | |
validate_MAE | 0.097 | 0.000 | 0.097 | |
validate_SE | 0.034 | 0.004 | 0.038 | |
validate_identifiers | 0.007 | 0.004 | 0.011 | |
validate_json | 0 | 0 | 0 | |
validate_mae_with_schema | 0.576 | 0.048 | 0.768 | |
validate_se_assay_name | 0.006 | 0.003 | 0.008 | |