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This page was generated on 2025-04-02 19:32 -0400 (Wed, 02 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4449
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (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 781/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRutils 1.4.10  (landing page)
Arkadiusz Gladki
Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025)
git_url: https://git.bioconductor.org/packages/gDRutils
git_branch: RELEASE_3_20
git_last_commit: 18d3e76
git_last_commit_date: 2025-02-11 06:44:03 -0400 (Tue, 11 Feb 2025)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for gDRutils on merida1

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.

raw results


Summary

Package: gDRutils
Version: 1.4.10
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gDRutils_1.4.10.tar.gz
StartedAt: 2025-04-01 03:18:01 -0400 (Tue, 01 Apr 2025)
EndedAt: 2025-04-01 03:25:05 -0400 (Tue, 01 Apr 2025)
EllapsedTime: 424.4 seconds
RetCode: 0
Status:   OK  
CheckDir: gDRutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gDRutils_1.4.10.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/gDRutils.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* 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 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


Installation output

gDRutils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gDRutils
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)

Tests output

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: x86_64-apple-darwin20

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 
 81.586   2.819  93.787 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply1.2850.1341.452
SE_metadata0.0610.0080.069
addClass0.0030.0010.004
aggregate_assay1.8220.0872.149
apply_bumpy_function3.5430.1843.800
assert_choices0.0010.0010.000
average_biological_replicates_dt0.1030.0030.106
calc_sd0.0010.0010.002
capVals0.5890.0230.614
cap_assay_infinities0.5150.0100.529
cap_xc500.0010.0010.001
convert_colData_to_json0.1390.0020.141
convert_combo_data_to_dt0.6090.0340.647
convert_combo_field_to_assay0.0040.0010.004
convert_mae_assay_to_dt0.1330.0080.142
convert_mae_to_json0.0290.0010.031
convert_metadata_to_json0.0190.0010.021
convert_rowData_to_json0.0050.0010.006
convert_se_assay_to_custom_dt1.5580.1181.692
convert_se_assay_to_dt0.1400.0100.151
convert_se_to_json0.0290.0020.030
define_matrix_grid_positions0.1120.0020.114
demote_fields0.8330.0180.855
df_to_bm_assay0.3140.0140.330
dot-set_invalid_fit_params0.0010.0010.001
extend_normalization_type_name0.0000.0010.000
fit_curves0.2980.0290.331
flatten0.0170.0020.018
gen_synthetic_data0.0130.0030.017
geometric_mean0.0000.0000.001
get_MAE_identifiers0.0120.0020.015
get_additional_variables0.0160.0020.018
get_assay_dt_duplicated_rows0.2150.0040.220
get_assay_names0.0010.0000.001
get_assay_req_uniq_cols0.1670.0030.172
get_combo_assay_names0.0010.0000.002
get_combo_base_assay_names0.0020.0010.003
get_combo_excess_field_names0.0030.0010.003
get_combo_score_assay_names0.0010.0010.002
get_combo_score_field_names0.0020.0000.002
get_default_identifiers0.0010.0020.004
get_duplicated_rows0.0060.0010.006
get_env_assay_names0.0010.0000.001
get_env_var000
get_expect_one_identifiers0.0010.0010.002
get_experiment_groups0.0000.0000.001
get_identifiers_dt0.0110.0080.020
get_idfs_synonyms0.0010.0000.000
get_isobologram_columns0.0750.0030.081
get_non_empty_assays0.1010.0020.103
get_required_identifiers0.0010.0000.001
get_settings_from_json0.0010.0010.003
get_supported_experiments0.0000.0010.001
get_synthetic_data0.0190.0020.021
get_testdata0.1970.0610.265
get_testdata_codilution0.1770.0140.192
get_testdata_combo0.4210.0500.479
has_assay_dt_duplicated_rows0.1660.0030.169
has_dt_duplicated_rows0.0020.0000.002
has_single_codrug_data0.1700.0020.173
has_valid_codrug_data0.1630.0020.165
headers0.0280.0240.053
identifiers0.0000.0000.001
identify_unique_se_metadata_fields0.0120.0010.012
is_any_exp_empty0.1010.0010.104
is_combo_data0.2370.0230.262
is_exp_empty0.0990.0010.101
is_mae_empty0.1010.0010.102
logisticFit0.0560.0010.058
loop0.0000.0010.000
mcolData0.0260.0030.028
merge_SE3.5520.0443.674
merge_assay0.7410.0440.799
merge_metadata0.0120.0010.015
modifyData0.2270.0030.230
mrowData0.0290.0020.032
predict_conc_from_efficacy0.0010.0000.001
predict_efficacy_from_conc0.0000.0000.001
prettify_flat_metrics0.0500.0010.051
promote_fields0.4220.0060.450
refine_coldata0.0180.0020.026
refine_rowdata0.0990.0030.113
remove_codrug_data0.0760.0020.080
remove_drug_batch0.0030.0020.005
rename_DFrame0.0190.0030.021
rename_bumpy0.0660.0020.103
round_concentration0.0000.0000.001
set_constant_fit_params0.0010.0010.002
set_unique_cl_names0.1110.0010.114
set_unique_cl_names_dt0.0490.0010.051
set_unique_drug_names0.1690.0020.173
set_unique_drug_names_dt0.0870.0010.091
set_unique_identifiers0.6870.0050.741
set_unique_names_dt0.0430.0010.047
shorten_normalization_type_name0.0010.0000.001
split_SE_components0.1310.0070.161
standardize_mae0.2770.0040.301
standardize_se0.0720.0030.080
throw_msg_if_duplicates0.1690.0040.192
update_env_idfs_from_mae0.0030.0000.004
update_idfs_synonyms0.0010.0010.001
validate_MAE0.1850.0030.196
validate_SE0.0540.0010.057
validate_identifiers0.0150.0030.018
validate_json0.0010.0010.001
validate_mae_with_schema0.6220.0790.835
validate_se_assay_name0.0070.0000.009