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This page was generated on 2025-08-06 13:56 -0400 (Wed, 06 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4813
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4550
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4592
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4534
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 790/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRutils 1.7.15  (landing page)
Arkadiusz Gladki
Snapshot Date: 2025-08-05 13:25 -0400 (Tue, 05 Aug 2025)
git_url: https://git.bioconductor.org/packages/gDRutils
git_branch: devel
git_last_commit: cbc994d
git_last_commit_date: 2025-08-05 07:48:19 -0400 (Tue, 05 Aug 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  YES
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  YES


CHECK results for gDRutils on kjohnson3

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: 1.7.15
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_1.7.15.tar.gz
StartedAt: 2025-08-05 19:28:20 -0400 (Tue, 05 Aug 2025)
EndedAt: 2025-08-05 19:30:08 -0400 (Tue, 05 Aug 2025)
EllapsedTime: 108.3 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_1.7.15.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/gDRutils.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gDRutils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRutils’ version ‘1.7.15’
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SE_metadata.Rd: SummarizedExperiment-class
  convert_mae_assay_to_dt.Rd: SummarizedExperiment-class,
    MultiAssayExperiment-class
  convert_se_assay_to_dt.Rd: SummarizedExperiment-class
  is_exp_empty.Rd: SummarizedExperiment-class
  split_SE_components.Rd: SummarizedExperiment-class
  validate_se_assay_name.Rd: SummarizedExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/gDRutils.Rcheck/00check.log’
for details.


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/4.5-arm64/Resources/library’
* installing *source* package ‘gDRutils’ ...
** this is package ‘gDRutils’ version ‘1.7.15’
** 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 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 829 ]
> 
> proc.time()
   user  system elapsed 
 36.449   2.272  39.109 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.1890.0110.200
SE_metadata0.0140.0010.015
addClass0.0010.0000.001
aggregate_assay0.1750.0090.184
apply_bumpy_function0.3960.0150.412
assert_choices0.0000.0000.001
average_biological_replicates_dt0.1420.0060.147
calc_sd0.0000.0000.001
capVals0.0610.0030.065
cap_assay_infinities0.3340.0080.341
cap_xc500.0000.0010.000
convert_colData_to_json0.0150.0000.015
convert_combo_data_to_dt0.0830.0040.087
convert_combo_field_to_assay0.0010.0000.000
convert_mae_assay_to_dt0.0180.0010.019
convert_mae_to_json0.0050.0000.007
convert_metadata_to_json0.0030.0000.003
convert_rowData_to_json0.0010.0000.001
convert_se_assay_to_custom_dt0.1490.0180.175
convert_se_assay_to_dt0.0190.0010.020
convert_se_to_json0.0040.0000.004
define_matrix_grid_positions0.0180.0020.019
demote_fields0.1210.0030.120
df_to_bm_assay0.0370.0000.038
dot-set_invalid_fit_params0.0000.0010.000
dot-standardize_conc000
extend_normalization_type_name000
fit_curves0.0480.0070.056
flatten0.0030.0010.003
gen_synthetic_data0.0010.0000.002
geometric_mean000
get_MAE_identifiers0.0030.0010.004
get_additional_variables0.0040.0000.004
get_assay_dt_duplicated_rows0.0520.0030.055
get_assay_names000
get_assay_req_uniq_cols0.0340.0010.036
get_combo_assay_names0.0000.0000.001
get_combo_base_assay_names000
get_combo_excess_field_names0.0010.0000.001
get_combo_score_assay_names000
get_combo_score_field_names000
get_default_identifiers000
get_duplicated_rows0.0010.0000.001
get_env_assay_names000
get_env_var000
get_expect_one_identifiers000
get_experiment_groups000
get_gDR_session_info0.4540.2090.664
get_identifiers_dt0.0020.0010.003
get_idfs_synonyms000
get_isobologram_columns0.0180.0010.019
get_non_empty_assays0.0160.0010.018
get_required_identifiers000
get_settings_from_json0.0010.0000.001
get_supported_experiments000
get_synthetic_data0.0040.0000.005
get_testdata0.0270.0060.032
get_testdata_codilution0.0230.0010.025
get_testdata_combo0.0770.0080.087
has_assay_dt_duplicated_rows0.0330.0010.035
has_dt_duplicated_rows000
has_single_codrug_data0.0410.0000.045
has_valid_codrug_data0.0600.0040.063
headers0.0060.0020.009
identifiers000
identify_unique_se_metadata_fields0.0030.0000.004
is_any_exp_empty0.0130.0010.014
is_combo_data0.0650.0050.069
is_exp_empty0.0150.0000.015
is_mae_empty0.0220.0030.025
logisticFit0.0090.0000.010
loop1.1430.0161.672
map_conc_to_standardized_conc0.2900.2270.013
mcolData0.0060.0090.015
merge_MAE1.0110.0941.119
merge_SE0.4190.0180.445
merge_assay0.0860.0030.089
merge_metadata0.0030.0000.003
modifyData0.0790.0010.081
mrowData0.0050.0010.005
predict_conc_from_efficacy000
predict_efficacy_from_conc000
prettify_flat_metrics0.010.000.01
process_batch0.2990.0410.340
promote_fields0.0550.0020.057
refine_coldata0.0040.0010.005
refine_rowdata0.0140.0000.015
remove_codrug_data0.0170.0010.018
remove_drug_batch0.0010.0000.001
rename_DFrame0.0040.0000.004
rename_bumpy0.0090.0010.010
round_concentration000
set_constant_fit_params0.0000.0000.001
set_unique_cl_names0.0160.0000.016
set_unique_cl_names_dt0.0060.0000.005
set_unique_drug_names0.0150.0000.015
set_unique_drug_names_dt0.010.000.01
set_unique_identifiers0.0710.0050.076
set_unique_names_dt0.0050.0010.006
shorten_normalization_type_name000
split_SE_components0.0280.0040.032
split_big_table_for_xlsx0.0020.0010.002
standardize_mae0.0430.0030.046
standardize_se0.0100.0000.011
throw_msg_if_duplicates0.0320.0010.033
update_env_idfs_from_mae0.0010.0000.001
update_idfs_synonyms000
validate_MAE0.0220.0010.022
validate_SE0.0070.0000.007
validate_identifiers0.0010.0000.002
validate_json000
validate_mae_with_schema0.1430.0160.152
validate_se_assay_name0.0040.0010.003