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This page was generated on 2025-10-16 11:38 -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 nebbiolo1

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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings gDRutils_1.6.0.tar.gz
StartedAt: 2025-10-15 23:26:37 -0400 (Wed, 15 Oct 2025)
EndedAt: 2025-10-15 23:30:21 -0400 (Wed, 15 Oct 2025)
EllapsedTime: 223.3 seconds
RetCode: 0
Status:   OK  
CheckDir: gDRutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings gDRutils_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/gDRutils.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/gDRutils.Rcheck/00check.log’
for details.


Installation output

gDRutils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL gDRutils
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
 53.542   1.936  54.047 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.3730.0510.424
SE_metadata0.0330.0030.037
addClass0.0020.0000.002
aggregate_assay0.5080.0140.516
apply_bumpy_function1.9870.0252.013
assert_choices000
average_biological_replicates_dt0.0420.0000.042
calc_sd0.0000.0000.001
capVals0.340.010.35
cap_assay_infinities0.2810.0050.226
cap_xc500.0010.0010.001
convert_colData_to_json0.0590.0040.059
convert_combo_data_to_dt0.2760.0100.229
convert_combo_field_to_assay0.0020.0000.002
convert_mae_assay_to_dt0.0540.0060.060
convert_mae_to_json0.0140.0010.015
convert_metadata_to_json0.0080.0000.008
convert_rowData_to_json0.0020.0000.003
convert_se_assay_to_custom_dt0.4170.0270.402
convert_se_assay_to_dt0.0560.0030.059
convert_se_to_json0.0110.0020.013
define_matrix_grid_positions0.0660.0020.051
demote_fields0.4340.0020.348
df_to_bm_assay0.1110.0000.111
dot-set_invalid_fit_params000
dot-standardize_conc000
extend_normalization_type_name000
fit_curves0.1260.0050.131
flatten0.0070.0010.007
gen_synthetic_data0.0050.0000.005
geometric_mean000
get_MAE_identifiers0.0070.0010.008
get_additional_variables0.0060.0020.007
get_assay_dt_duplicated_rows0.1140.0030.117
get_assay_names000
get_assay_req_uniq_cols0.0800.0030.083
get_combo_assay_names0.0000.0010.000
get_combo_base_assay_names0.0010.0000.001
get_combo_excess_field_names0.0010.0000.002
get_combo_score_assay_names0.0000.0010.001
get_combo_score_field_names0.0010.0000.001
get_default_identifiers0.0010.0000.001
get_duplicated_rows0.0180.0000.018
get_env_assay_names0.0000.0010.001
get_env_var0.0010.0000.000
get_expect_one_identifiers0.0000.0010.000
get_experiment_groups000
get_gDR_session_info0.0530.0050.058
get_identifiers_dt0.0050.0020.007
get_idfs_synonyms000
get_isobologram_columns0.0310.0000.031
get_non_empty_assays0.0570.0020.044
get_required_identifiers0.0000.0000.001
get_settings_from_json0.0010.0010.001
get_supported_experiments000
get_synthetic_data0.0110.0000.011
get_testdata0.0880.0240.099
get_testdata_codilution0.0850.0050.076
get_testdata_combo0.2390.0320.245
has_assay_dt_duplicated_rows0.0800.0000.081
has_dt_duplicated_rows0.0000.0000.001
has_single_codrug_data0.0630.0010.064
has_valid_codrug_data0.0670.0000.066
headers0.0090.0110.020
identifiers000
identify_unique_se_metadata_fields0.0090.0010.009
is_any_exp_empty0.7190.0020.706
is_combo_data0.1270.0080.125
is_exp_empty0.0640.0010.046
is_mae_empty0.0740.0010.046
logisticFit0.0320.0000.021
loop000
map_conc_to_standardized_conc0.0040.0000.003
mcolData0.0120.0010.014
merge_SE1.5430.0681.487
merge_assay0.3200.0010.308
merge_metadata0.0090.0000.008
modifyData0.0990.0000.098
mrowData0.0140.0000.014
predict_conc_from_efficacy0.0010.0000.000
predict_efficacy_from_conc000
prettify_flat_metrics0.0210.0000.021
promote_fields0.2080.0110.192
refine_coldata0.0070.0050.013
refine_rowdata0.0410.0070.049
remove_codrug_data0.0270.0070.034
remove_drug_batch0.0010.0020.002
rename_DFrame0.0090.0020.012
rename_bumpy0.0250.0090.034
round_concentration000
set_constant_fit_params000
set_unique_cl_names0.0460.0080.054
set_unique_cl_names_dt0.0200.0020.022
set_unique_drug_names0.0620.0050.067
set_unique_drug_names_dt0.0340.0000.033
set_unique_identifiers0.2700.0000.269
set_unique_names_dt0.0190.0000.019
shorten_normalization_type_name000
split_SE_components0.0560.0010.057
split_big_table_for_xlsx0.0050.0010.006
standardize_mae0.1090.0010.109
standardize_se0.0330.0010.034
throw_msg_if_duplicates0.0830.0010.085
update_env_idfs_from_mae0.0010.0000.002
update_idfs_synonyms0.0000.0000.001
validate_MAE0.0730.0010.075
validate_SE0.0250.0020.027
validate_identifiers0.0070.0010.007
validate_json0.0010.0000.000
validate_mae_with_schema0.3730.0580.433
validate_se_assay_name0.0100.0000.009