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This page was generated on 2025-08-07 12:07 -0400 (Thu, 07 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4815
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 1.7.16  (landing page)
Arkadiusz Gladki
Snapshot Date: 2025-08-06 14:04 -0400 (Wed, 06 Aug 2025)
git_url: https://git.bioconductor.org/packages/gDRutils
git_branch: devel
git_last_commit: 23526b4
git_last_commit_date: 2025-08-06 04:19:21 -0400 (Wed, 06 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 lconway

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: 1.7.16
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_1.7.16.tar.gz
StartedAt: 2025-08-06 21:18:12 -0400 (Wed, 06 Aug 2025)
EndedAt: 2025-08-06 21:23:48 -0400 (Wed, 06 Aug 2025)
EllapsedTime: 336.5 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_1.7.16.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/gDRutils.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* 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 ‘1.7.16’
* 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-x86_64/Resources/library’
* installing *source* package ‘gDRutils’ ...
** this is package ‘gDRutils’ version ‘1.7.16’
** 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 (2025-06-13) -- "Great Square Root"
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 832 ]
> 
> proc.time()
   user  system elapsed 
118.952   4.537 124.777 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.6480.0590.717
SE_metadata0.0380.0060.046
addClass0.0010.0000.002
aggregate_assay0.6530.0490.713
apply_bumpy_function2.0920.0992.213
assert_choices0.0000.0000.001
average_biological_replicates_dt0.5780.0270.612
calc_sd0.0010.0000.002
capVals0.2680.0160.286
cap_assay_infinities0.9650.0170.993
cap_xc50000
convert_colData_to_json0.0660.0010.067
convert_combo_data_to_dt0.3730.0140.389
convert_combo_field_to_assay0.0020.0010.003
convert_mae_assay_to_dt0.0790.0040.083
convert_mae_to_json0.0200.0010.022
convert_metadata_to_json0.0130.0010.015
convert_rowData_to_json0.0040.0010.004
convert_se_assay_to_custom_dt0.7830.0740.864
convert_se_assay_to_dt0.0760.0030.081
convert_se_to_json0.0170.0010.017
define_matrix_grid_positions0.0650.0020.069
demote_fields0.4760.0080.490
df_to_bm_assay0.1710.0020.174
dot-set_invalid_fit_params0.0000.0000.001
dot-standardize_conc0.0000.0000.001
extend_normalization_type_name000
fit_curves0.1820.0270.211
flatten0.0100.0010.011
gen_synthetic_data0.0070.0010.009
geometric_mean000
get_MAE_identifiers0.0070.0020.009
get_additional_variables0.0170.0010.018
get_assay_dt_duplicated_rows0.2310.0090.242
get_assay_names0.0000.0000.001
get_assay_req_uniq_cols0.1700.0060.180
get_combo_assay_names0.0010.0000.001
get_combo_base_assay_names0.0010.0000.001
get_combo_excess_field_names0.0030.0000.002
get_combo_score_assay_names0.0010.0010.001
get_combo_score_field_names0.0010.0000.001
get_default_identifiers0.0000.0010.001
get_duplicated_rows0.0030.0010.004
get_env_assay_names0.0000.0000.001
get_env_var000
get_expect_one_identifiers0.0000.0000.001
get_experiment_groups0.0000.0000.001
get_gDR_session_info1.7641.1092.906
get_identifiers_dt0.0060.0050.011
get_idfs_synonyms0.0000.0010.000
get_isobologram_columns0.0850.0020.088
get_non_empty_assays0.0560.0010.058
get_required_identifiers000
get_settings_from_json0.0010.0010.001
get_supported_experiments0.0010.0000.000
get_synthetic_data0.0110.0010.012
get_testdata0.1080.0230.131
get_testdata_codilution0.1000.0080.110
get_testdata_combo0.2520.0250.282
has_assay_dt_duplicated_rows0.1450.0050.151
has_dt_duplicated_rows0.0010.0000.001
has_single_codrug_data0.2590.0070.268
has_valid_codrug_data0.1750.0020.179
headers0.0290.0130.042
identifiers0.0000.0000.001
identify_unique_se_metadata_fields0.0070.0010.008
is_any_exp_empty0.0560.0020.059
is_combo_data0.1340.0120.148
is_exp_empty0.0850.0040.089
is_mae_empty0.0590.0020.062
logisticFit0.0430.0010.045
loop2.7660.0624.541
map_conc_to_standardized_conc0.0060.0100.016
mcolData0.8560.9850.094
merge_MAE4.1980.1674.410
merge_SE1.7180.0361.773
merge_assay0.3570.0090.371
merge_metadata0.0070.0010.008
modifyData0.3390.0050.346
mrowData0.0150.0010.016
predict_conc_from_efficacy0.0000.0000.001
predict_efficacy_from_conc0.0010.0010.000
prettify_flat_metrics0.0500.0010.051
process_batch0.7850.1030.897
promote_fields0.2090.0030.216
refine_coldata0.0090.0010.010
refine_rowdata0.0430.0020.044
remove_codrug_data0.0760.0020.078
remove_drug_batch0.0020.0010.002
rename_DFrame0.0100.0010.011
rename_bumpy0.0370.0010.039
round_concentration000
set_constant_fit_params0.0010.0000.000
set_unique_cl_names0.0610.0010.063
set_unique_cl_names_dt0.0260.0010.026
set_unique_drug_names0.0710.0010.072
set_unique_drug_names_dt0.0400.0010.041
set_unique_identifiers0.3490.0090.365
set_unique_names_dt0.0220.0000.023
shorten_normalization_type_name0.0010.0000.001
split_SE_components0.1180.0030.121
split_big_table_for_xlsx0.0050.0010.007
standardize_mae0.1600.0030.164
standardize_se0.0380.0020.039
throw_msg_if_duplicates0.1480.0040.153
update_env_idfs_from_mae0.0010.0000.001
update_idfs_synonyms0.0000.0000.001
validate_MAE0.0930.0020.099
validate_SE0.0290.0010.030
validate_identifiers0.0100.0010.010
validate_json0.0000.0000.001
validate_mae_with_schema0.4160.0650.503
validate_se_assay_name0.0070.0010.008