| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-04-02 19:35 -0400 (Wed, 02 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4426 |
| 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 781/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gDRutils 1.4.10 (landing page) Arkadiusz Gladki
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / 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: 1.4.10 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gDRutils_1.4.10.tar.gz |
| StartedAt: 2025-04-01 06:41:09 -0000 (Tue, 01 Apr 2025) |
| EndedAt: 2025-04-01 06:45:25 -0000 (Tue, 01 Apr 2025) |
| EllapsedTime: 256.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gDRutils.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gDRutils_1.4.10.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/gDRutils.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 ‘gDRutils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRutils’ version ‘1.4.10’
* 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 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
gDRutils.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL gDRutils ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.3/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 4.4.3 (2025-02-28) -- "Trophy Case"
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("gDRutils")
> library("testthat")
>
> test_check("gDRutils")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 727 ]
>
> proc.time()
user system elapsed
63.956 2.117 65.791
gDRutils.Rcheck/gDRutils-Ex.timings
| name | user | system | elapsed | |
| MAEpply | 0.730 | 0.032 | 0.763 | |
| SE_metadata | 0.043 | 0.000 | 0.043 | |
| addClass | 0.003 | 0.000 | 0.003 | |
| aggregate_assay | 1.145 | 0.008 | 1.154 | |
| apply_bumpy_function | 1.918 | 0.112 | 2.033 | |
| assert_choices | 0.001 | 0.000 | 0.000 | |
| average_biological_replicates_dt | 0.055 | 0.008 | 0.062 | |
| calc_sd | 0.000 | 0.001 | 0.000 | |
| capVals | 0.319 | 0.011 | 0.330 | |
| cap_assay_infinities | 0.300 | 0.008 | 0.304 | |
| cap_xc50 | 0.001 | 0.000 | 0.001 | |
| convert_colData_to_json | 0.104 | 0.019 | 0.124 | |
| convert_combo_data_to_dt | 0.431 | 0.192 | 0.621 | |
| convert_combo_field_to_assay | 0.003 | 0.000 | 0.003 | |
| convert_mae_assay_to_dt | 0.098 | 0.008 | 0.106 | |
| convert_mae_to_json | 0.020 | 0.004 | 0.024 | |
| convert_metadata_to_json | 0.014 | 0.000 | 0.014 | |
| convert_rowData_to_json | 0.004 | 0.000 | 0.004 | |
| convert_se_assay_to_custom_dt | 1.057 | 0.810 | 1.869 | |
| convert_se_assay_to_dt | 0.085 | 0.003 | 0.088 | |
| convert_se_to_json | 0.019 | 0.001 | 0.019 | |
| define_matrix_grid_positions | 0.071 | 0.003 | 0.074 | |
| demote_fields | 0.511 | 0.004 | 0.508 | |
| df_to_bm_assay | 0.187 | 0.000 | 0.188 | |
| dot-set_invalid_fit_params | 0.001 | 0.000 | 0.001 | |
| extend_normalization_type_name | 0 | 0 | 0 | |
| fit_curves | 0.177 | 0.000 | 0.177 | |
| flatten | 0.009 | 0.000 | 0.009 | |
| gen_synthetic_data | 0.007 | 0.000 | 0.007 | |
| geometric_mean | 0.001 | 0.000 | 0.000 | |
| get_MAE_identifiers | 0.009 | 0.000 | 0.010 | |
| get_additional_variables | 0.009 | 0.000 | 0.009 | |
| get_assay_dt_duplicated_rows | 0.12 | 0.00 | 0.12 | |
| get_assay_names | 0.001 | 0.000 | 0.000 | |
| get_assay_req_uniq_cols | 0.09 | 0.00 | 0.09 | |
| get_combo_assay_names | 0 | 0 | 0 | |
| get_combo_base_assay_names | 0.001 | 0.000 | 0.001 | |
| get_combo_excess_field_names | 0.002 | 0.000 | 0.002 | |
| get_combo_score_assay_names | 0.001 | 0.000 | 0.001 | |
| get_combo_score_field_names | 0.001 | 0.000 | 0.001 | |
| get_default_identifiers | 0 | 0 | 0 | |
| get_duplicated_rows | 0.003 | 0.000 | 0.003 | |
| get_env_assay_names | 0.001 | 0.000 | 0.001 | |
| get_env_var | 0 | 0 | 0 | |
| get_expect_one_identifiers | 0 | 0 | 0 | |
| get_experiment_groups | 0 | 0 | 0 | |
| get_identifiers_dt | 0.007 | 0.000 | 0.007 | |
| get_idfs_synonyms | 0 | 0 | 0 | |
| get_isobologram_columns | 0.043 | 0.000 | 0.042 | |
| get_non_empty_assays | 0.060 | 0.000 | 0.059 | |
| get_required_identifiers | 0 | 0 | 0 | |
| get_settings_from_json | 0.001 | 0.000 | 0.001 | |
| get_supported_experiments | 0 | 0 | 0 | |
| get_synthetic_data | 0.012 | 0.000 | 0.012 | |
| get_testdata | 0.095 | 0.007 | 0.102 | |
| get_testdata_codilution | 0.100 | 0.007 | 0.109 | |
| get_testdata_combo | 0.252 | 0.020 | 0.288 | |
| has_assay_dt_duplicated_rows | 0.091 | 0.000 | 0.092 | |
| has_dt_duplicated_rows | 0.001 | 0.000 | 0.001 | |
| has_single_codrug_data | 0.098 | 0.000 | 0.098 | |
| has_valid_codrug_data | 0.092 | 0.004 | 0.096 | |
| headers | 0.015 | 0.000 | 0.015 | |
| identifiers | 0 | 0 | 0 | |
| identify_unique_se_metadata_fields | 0.009 | 0.000 | 0.009 | |
| is_any_exp_empty | 0.059 | 0.000 | 0.058 | |
| is_combo_data | 0.197 | 0.016 | 0.214 | |
| is_exp_empty | 0.062 | 0.000 | 0.061 | |
| is_mae_empty | 0.060 | 0.000 | 0.058 | |
| logisticFit | 0.027 | 0.003 | 0.031 | |
| loop | 0.000 | 0.000 | 0.001 | |
| mcolData | 0.014 | 0.003 | 0.017 | |
| merge_SE | 2.059 | 0.064 | 2.119 | |
| merge_assay | 0.402 | 0.024 | 0.425 | |
| merge_metadata | 0.01 | 0.00 | 0.01 | |
| modifyData | 0.152 | 0.000 | 0.153 | |
| mrowData | 0.015 | 0.004 | 0.019 | |
| predict_conc_from_efficacy | 0 | 0 | 0 | |
| predict_efficacy_from_conc | 0 | 0 | 0 | |
| prettify_flat_metrics | 0.028 | 0.000 | 0.027 | |
| promote_fields | 0.232 | 0.004 | 0.236 | |
| refine_coldata | 0.013 | 0.000 | 0.013 | |
| refine_rowdata | 0.062 | 0.000 | 0.062 | |
| remove_codrug_data | 0.043 | 0.000 | 0.042 | |
| remove_drug_batch | 0.002 | 0.000 | 0.002 | |
| rename_DFrame | 0.012 | 0.000 | 0.013 | |
| rename_bumpy | 0.038 | 0.000 | 0.039 | |
| round_concentration | 0.000 | 0.000 | 0.001 | |
| set_constant_fit_params | 0.000 | 0.001 | 0.000 | |
| set_unique_cl_names | 0.059 | 0.003 | 0.063 | |
| set_unique_cl_names_dt | 0.024 | 0.000 | 0.025 | |
| set_unique_drug_names | 0.071 | 0.000 | 0.071 | |
| set_unique_drug_names_dt | 0.05 | 0.00 | 0.05 | |
| set_unique_identifiers | 0.436 | 0.000 | 0.437 | |
| set_unique_names_dt | 0.025 | 0.000 | 0.025 | |
| shorten_normalization_type_name | 0.000 | 0.000 | 0.001 | |
| split_SE_components | 0.074 | 0.000 | 0.074 | |
| standardize_mae | 0.148 | 0.000 | 0.148 | |
| standardize_se | 0.041 | 0.000 | 0.041 | |
| throw_msg_if_duplicates | 0.094 | 0.000 | 0.094 | |
| update_env_idfs_from_mae | 0.002 | 0.000 | 0.002 | |
| update_idfs_synonyms | 0.001 | 0.000 | 0.001 | |
| validate_MAE | 0.099 | 0.000 | 0.099 | |
| validate_SE | 0.034 | 0.000 | 0.034 | |
| validate_identifiers | 0.009 | 0.000 | 0.008 | |
| validate_json | 0 | 0 | 0 | |
| validate_mae_with_schema | 0.699 | 0.041 | 0.886 | |
| validate_se_assay_name | 0.008 | 0.000 | 0.008 | |