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This page was generated on 2025-01-16 12:08 -0500 (Thu, 16 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4746
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4489
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4517
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4469
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4387
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 1.4.0  (landing page)
Arkadiusz Gladki
Snapshot Date: 2025-01-13 13:00 -0500 (Mon, 13 Jan 2025)
git_url: https://git.bioconductor.org/packages/gDRutils
git_branch: RELEASE_3_20
git_last_commit: 1433886
git_last_commit_date: 2024-10-29 11:21:35 -0500 (Tue, 29 Oct 2024)
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    NA  


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: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2025-01-14 03:39:07 -0500 (Tue, 14 Jan 2025)
EndedAt: 2025-01-14 03:46:22 -0500 (Tue, 14 Jan 2025)
EllapsedTime: 434.7 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/gDRutils.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 ‘1.4.0’
* 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 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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 687 ]
> 
> proc.time()
   user  system elapsed 
 80.908   3.111  93.545 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply1.2310.0791.529
SE_metadata0.1660.0110.208
addClass0.0040.0000.005
aggregate_assay1.9370.0692.345
apply_bumpy_function3.8200.2824.756
assert_choices0.0010.0010.001
average_biological_replicates_dt0.0990.0030.122
calc_sd0.0010.0000.001
capVals0.6620.0270.804
cap_xc500.0010.0010.002
convert_colData_to_json0.1470.0030.172
convert_combo_data_to_dt0.6290.0350.799
convert_combo_field_to_assay0.0030.0000.005
convert_mae_assay_to_dt0.1560.0090.198
convert_mae_to_json0.0350.0020.044
convert_metadata_to_json0.0240.0010.033
convert_rowData_to_json0.0060.0010.007
convert_se_assay_to_custom_dt0.9830.0931.168
convert_se_assay_to_dt0.1480.0080.155
convert_se_to_json0.0310.0020.033
define_matrix_grid_positions0.1140.0120.139
demote_fields1.6030.0521.716
df_to_bm_assay0.2950.0030.313
dot-set_invalid_fit_params0.0010.0010.001
extend_normalization_type_name0.0000.0010.001
fit_curves0.3080.0320.354
flatten0.0160.0020.018
gen_synthetic_data0.0120.0030.015
geometric_mean0.0000.0000.001
get_MAE_identifiers0.0120.0030.016
get_additional_variables0.0130.0010.013
get_assay_dt_duplicated_rows0.2140.0060.223
get_assay_names0.0000.0010.001
get_assay_req_uniq_cols0.1630.0100.177
get_combo_assay_names0.0020.0010.002
get_combo_base_assay_names0.0020.0010.003
get_combo_excess_field_names0.0030.0010.004
get_combo_score_assay_names0.0020.0010.003
get_combo_score_field_names0.0020.0000.002
get_default_identifiers0.0010.0020.003
get_duplicated_rows0.0060.0010.006
get_env_assay_names0.0000.0010.002
get_expect_one_identifiers0.0000.0000.001
get_experiment_groups0.0010.0000.001
get_identifiers_dt0.0110.0080.018
get_idfs_synonyms0.0010.0010.001
get_isobologram_columns0.0810.0090.092
get_non_empty_assays0.1110.0040.105
get_required_identifiers0.0010.0000.001
get_settings_from_json0.0040.0010.003
get_supported_experiments0.0010.0010.001
get_synthetic_data0.0340.0030.021
get_testdata0.2820.0760.281
get_testdata_codilution0.2260.0280.236
get_testdata_combo0.5200.1050.458
has_assay_dt_duplicated_rows0.1830.0150.163
has_dt_duplicated_rows0.0010.0000.002
has_single_codrug_data0.1760.0020.178
has_valid_codrug_data0.1730.0020.177
headers0.0280.0200.048
identifiers0.0000.0010.000
identify_unique_se_metadata_fields0.0120.0020.014
is_any_exp_empty0.1060.0030.101
is_combo_data0.3520.0340.236
is_exp_empty0.1050.0030.101
is_mae_empty0.1840.0080.111
logisticFit0.0990.0070.060
loop0.0010.0010.001
mcolData0.0350.0080.028
merge_SE3.8130.0824.121
merge_assay0.7610.0120.885
merge_metadata0.0130.0010.015
modifyData0.2380.0030.262
mrowData0.0290.0030.034
predict_conc_from_efficacy0.0000.0000.001
predict_efficacy_from_conc0.0010.0010.001
prettify_flat_metrics0.0520.0010.059
promote_fields0.4330.0070.534
refine_coldata0.0180.0020.023
refine_rowdata0.1010.0040.114
remove_codrug_data0.0790.0020.091
rename_DFrame0.0180.0020.022
rename_bumpy0.0880.0040.107
round_concentration0.0010.0000.001
set_constant_fit_params0.0010.0010.002
set_unique_cl_names0.1130.0010.137
set_unique_cl_names_dt0.0520.0010.062
set_unique_drug_names0.1170.0020.131
set_unique_drug_names_dt0.0800.0010.093
set_unique_identifiers0.7300.0060.814
shorten_normalization_type_name0.0000.0000.001
split_SE_components0.1370.0040.153
standardize_mae0.2880.0030.315
standardize_se0.0740.0020.088
throw_msg_if_duplicates0.1730.0040.198
update_env_idfs_from_mae0.0030.0000.004
update_idfs_synonyms0.0010.0000.002
validate_MAE0.1870.0020.204
validate_SE0.0600.0020.068
validate_identifiers0.0160.0020.019
validate_json000
validate_mae_with_schema0.6490.0901.013
validate_se_assay_name0.0080.0010.014