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This page was generated on 2025-09-23 12:06 -0400 (Tue, 23 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4816
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4605
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4549
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4560
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 797/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRutils 1.7.17  (landing page)
Arkadiusz Gladki
Snapshot Date: 2025-09-22 13:45 -0400 (Mon, 22 Sep 2025)
git_url: https://git.bioconductor.org/packages/gDRutils
git_branch: devel
git_last_commit: 7911c11
git_last_commit_date: 2025-08-27 05:07:29 -0400 (Wed, 27 Aug 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 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 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: 1.7.17
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_1.7.17.tar.gz
StartedAt: 2025-09-22 19:32:25 -0400 (Mon, 22 Sep 2025)
EndedAt: 2025-09-22 19:34:10 -0400 (Mon, 22 Sep 2025)
EllapsedTime: 105.3 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_1.7.17.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/gDRutils.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gDRutils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRutils’ version ‘1.7.17’
* 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 ‘1.7.17’
** 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 (2025-09-10 r88807) -- "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 832 ]
> 
> proc.time()
   user  system elapsed 
 35.780   2.001  37.890 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.1870.0110.199
SE_metadata0.0140.0020.016
addClass0.0010.0000.001
aggregate_assay0.1690.0100.179
apply_bumpy_function0.3940.0140.409
assert_choices000
average_biological_replicates_dt0.1370.0050.142
calc_sd000
capVals0.0660.0030.089
cap_assay_infinities0.3520.0070.370
cap_xc50000
convert_colData_to_json0.0150.0000.015
convert_combo_data_to_dt0.0850.0040.117
convert_combo_field_to_assay0.0010.0000.000
convert_mae_assay_to_dt0.0190.0010.021
convert_mae_to_json0.0060.0000.006
convert_metadata_to_json0.0030.0000.003
convert_rowData_to_json0.0010.0000.001
convert_se_assay_to_custom_dt0.1880.0240.221
convert_se_assay_to_dt0.0180.0010.020
convert_se_to_json0.0040.0010.004
define_matrix_grid_positions0.0180.0010.020
demote_fields0.1160.0030.118
df_to_bm_assay0.0360.0000.037
dot-set_invalid_fit_params000
dot-standardize_conc000
extend_normalization_type_name000
fit_curves0.0470.0070.054
flatten0.0020.0000.002
gen_synthetic_data0.0010.0000.002
geometric_mean0.0000.0010.000
get_MAE_identifiers0.0030.0000.004
get_additional_variables0.0040.0010.007
get_assay_dt_duplicated_rows0.0520.0020.058
get_assay_names000
get_assay_req_uniq_cols0.0400.0010.041
get_combo_assay_names0.0000.0000.001
get_combo_base_assay_names000
get_combo_excess_field_names0.0000.0000.001
get_combo_score_assay_names0.0010.0000.000
get_combo_score_field_names000
get_default_identifiers0.0000.0010.001
get_duplicated_rows0.0010.0000.001
get_env_assay_names000
get_env_var000
get_expect_one_identifiers0.0000.0000.001
get_experiment_groups000
get_gDR_session_info0.4390.2160.685
get_identifiers_dt0.0020.0010.004
get_idfs_synonyms000
get_isobologram_columns0.0180.0010.018
get_non_empty_assays0.0140.0010.017
get_required_identifiers0.0010.0000.000
get_settings_from_json000
get_supported_experiments000
get_synthetic_data0.0040.0000.003
get_testdata0.0250.0060.031
get_testdata_codilution0.0220.0020.024
get_testdata_combo0.0730.0080.110
has_assay_dt_duplicated_rows0.0330.0010.034
has_dt_duplicated_rows000
has_single_codrug_data0.0700.0030.076
has_valid_codrug_data0.0400.0000.041
headers0.0070.0030.010
identifiers000
identify_unique_se_metadata_fields0.0030.0010.003
is_any_exp_empty0.0140.0000.015
is_combo_data0.0660.0050.079
is_exp_empty0.0250.0030.029
is_mae_empty0.0150.0010.015
logisticFit0.0090.0000.013
loop1.1290.0191.636
map_conc_to_standardized_conc0.0010.0040.006
mcolData0.0060.0070.012
merge_MAE1.0180.0831.114
merge_SE0.4060.0140.422
merge_assay0.0820.0030.086
merge_metadata0.0030.0000.004
modifyData0.0760.0010.079
mrowData0.0050.0010.006
predict_conc_from_efficacy0.0000.0010.000
predict_efficacy_from_conc000
prettify_flat_metrics0.010.000.01
process_batch0.3500.0390.388
promote_fields0.0540.0010.056
refine_coldata0.0040.0000.005
refine_rowdata0.0150.0010.015
remove_codrug_data0.0170.0010.018
remove_drug_batch000
rename_DFrame0.0040.0000.005
rename_bumpy0.010.000.01
round_concentration000
set_constant_fit_params0.0000.0000.001
set_unique_cl_names0.0160.0010.016
set_unique_cl_names_dt0.0050.0000.006
set_unique_drug_names0.0140.0000.014
set_unique_drug_names_dt0.010.000.01
set_unique_identifiers0.0730.0010.076
set_unique_names_dt0.0050.0000.005
shorten_normalization_type_name0.0000.0000.001
split_SE_components0.0260.0010.026
split_big_table_for_xlsx0.0020.0010.002
standardize_mae0.0390.0010.040
standardize_se0.010.000.01
throw_msg_if_duplicates0.0320.0010.033
update_env_idfs_from_mae0.0000.0000.001
update_idfs_synonyms000
validate_MAE0.0210.0000.022
validate_SE0.0080.0000.008
validate_identifiers0.0020.0010.002
validate_json000
validate_mae_with_schema0.1370.0130.146
validate_se_assay_name0.0030.0010.004