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This page was generated on 2025-10-16 11:39 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 796/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRutils 1.6.0  (landing page)
Arkadiusz Gladki
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/gDRutils
git_branch: RELEASE_3_21
git_last_commit: c9fd3fb
git_last_commit_date: 2025-04-15 13:16:41 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (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: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2025-10-14 04:06:03 -0400 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 04:13:44 -0400 (Tue, 14 Oct 2025)
EllapsedTime: 461.8 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/gDRutils.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘1.6.0’
* 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 ... 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-3.21-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 ‘1.6.0’
** 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 RC (2025-06-05 r88288) -- "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 778 ]
> 
> proc.time()
   user  system elapsed 
 88.860   4.332 105.173 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply1.0450.0471.243
SE_metadata0.0690.0100.086
addClass0.0030.0000.004
aggregate_assay1.8010.1322.244
apply_bumpy_function3.6990.2064.492
assert_choices0.0010.0010.001
average_biological_replicates_dt0.1080.0030.131
calc_sd0.0010.0000.002
capVals0.9820.0291.141
cap_assay_infinities0.6020.0110.706
cap_xc500.0010.0010.001
convert_colData_to_json0.1330.0010.153
convert_combo_data_to_dt1.3610.0621.649
convert_combo_field_to_assay0.0040.0000.003
convert_mae_assay_to_dt0.1420.0090.174
convert_mae_to_json0.0300.0020.042
convert_metadata_to_json0.0210.0010.024
convert_rowData_to_json0.0050.0000.006
convert_se_assay_to_custom_dt0.9280.0901.190
convert_se_assay_to_dt0.1540.0110.199
convert_se_to_json0.0310.0010.039
define_matrix_grid_positions0.1190.0050.139
demote_fields0.8590.0161.041
df_to_bm_assay0.2720.0030.330
dot-set_invalid_fit_params0.0000.0010.001
dot-standardize_conc0.0010.0010.002
extend_normalization_type_name0.0010.0000.000
fit_curves0.3310.0330.416
flatten0.0170.0010.021
gen_synthetic_data0.0130.0020.018
geometric_mean0.0000.0010.001
get_MAE_identifiers0.0130.0030.019
get_additional_variables0.0150.0010.018
get_assay_dt_duplicated_rows0.2810.0080.330
get_assay_names0.0000.0010.001
get_assay_req_uniq_cols0.1980.0050.239
get_combo_assay_names0.0020.0000.002
get_combo_base_assay_names0.0020.0000.002
get_combo_excess_field_names0.0040.0010.004
get_combo_score_assay_names0.0020.0000.004
get_combo_score_field_names0.0020.0000.003
get_default_identifiers0.0010.0020.004
get_duplicated_rows0.0060.0010.008
get_env_assay_names0.0010.0010.002
get_env_var0.0000.0000.001
get_expect_one_identifiers0.0010.0020.002
get_experiment_groups0.0000.0010.001
get_gDR_session_info2.7031.1564.606
get_identifiers_dt0.0100.0070.019
get_idfs_synonyms0.0000.0000.001
get_isobologram_columns0.0820.0030.092
get_non_empty_assays0.1120.0020.130
get_required_identifiers0.0000.0010.001
get_settings_from_json0.0020.0010.003
get_supported_experiments0.0000.0000.001
get_synthetic_data0.0210.0020.026
get_testdata0.2020.0570.290
get_testdata_codilution0.2010.0200.265
get_testdata_combo0.4240.0780.595
has_assay_dt_duplicated_rows0.1880.0050.198
has_dt_duplicated_rows0.0020.0000.002
has_single_codrug_data0.2300.0050.246
has_valid_codrug_data0.1770.0020.189
headers0.0280.0270.058
identifiers0.0010.0010.001
identify_unique_se_metadata_fields0.0120.0020.014
is_any_exp_empty0.0990.0020.104
is_combo_data0.2170.0170.244
is_exp_empty0.1020.0010.105
is_mae_empty0.0990.0020.103
logisticFit0.0560.0020.060
loop000
map_conc_to_standardized_conc0.0070.0010.009
mcolData0.0240.0020.026
merge_SE3.5000.0333.654
merge_assay0.7580.0350.831
merge_metadata0.0130.0010.016
modifyData0.2320.0030.241
mrowData0.0270.0030.033
predict_conc_from_efficacy0.0000.0010.001
predict_efficacy_from_conc0.0010.0010.002
prettify_flat_metrics0.0490.0010.055
promote_fields0.4040.0040.475
refine_coldata0.0200.0040.030
refine_rowdata0.0890.0040.108
remove_codrug_data0.0730.0030.089
remove_drug_batch0.0030.0020.008
rename_DFrame0.0170.0030.022
rename_bumpy0.0660.0030.080
round_concentration0.0000.0010.002
set_constant_fit_params0.0010.0010.002
set_unique_cl_names0.1130.0010.131
set_unique_cl_names_dt0.0450.0010.053
set_unique_drug_names0.1260.0010.152
set_unique_drug_names_dt0.1180.0030.142
set_unique_identifiers0.6850.0040.822
set_unique_names_dt0.0460.0010.054
shorten_normalization_type_name0.0010.0010.002
split_SE_components0.1280.0060.153
split_big_table_for_xlsx0.0100.0050.017
standardize_mae0.2760.0030.320
standardize_se0.0720.0020.090
throw_msg_if_duplicates0.1980.0050.236
update_env_idfs_from_mae0.0030.0010.005
update_idfs_synonyms0.0010.0010.002
validate_MAE0.1770.0020.217
validate_SE0.0570.0020.067
validate_identifiers0.0160.0040.024
validate_json0.0010.0000.001
validate_mae_with_schema0.6200.0861.013
validate_se_assay_name0.0090.0000.012