Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-08-02 12:05 -0400 (Sat, 02 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4535
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4517
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 790/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRutils 1.7.14  (landing page)
Arkadiusz Gladki
Snapshot Date: 2025-08-01 13:25 -0400 (Fri, 01 Aug 2025)
git_url: https://git.bioconductor.org/packages/gDRutils
git_branch: devel
git_last_commit: 51d6463
git_last_commit_date: 2025-07-31 05:03:35 -0400 (Thu, 31 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.1 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 nebbiolo2

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: 1.7.14
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings gDRutils_1.7.14.tar.gz
StartedAt: 2025-08-01 22:38:06 -0400 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 22:42:46 -0400 (Fri, 01 Aug 2025)
EllapsedTime: 279.3 seconds
RetCode: 0
Status:   OK  
CheckDir: gDRutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings gDRutils_1.7.14.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘gDRutils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRutils’ version ‘1.7.14’
* 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
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
merge_MAE 4.359  0.672   3.603
* 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-3.22-bioc/meat/gDRutils.Rcheck/00check.log’
for details.


Installation output

gDRutils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL gDRutils
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘gDRutils’ ...
** this is package ‘gDRutils’ version ‘1.7.14’
** 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 826 ]
> 
> proc.time()
   user  system elapsed 
 99.224   2.105  98.870 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.3930.0530.446
SE_metadata0.0340.0000.033
addClass0.0020.0000.002
aggregate_assay0.5450.0170.557
apply_bumpy_function2.0810.0212.102
assert_choices0.0010.0000.000
average_biological_replicates_dt0.3430.0750.417
calc_sd0.0000.0010.000
capVals0.1860.0320.218
cap_assay_infinities0.2920.0040.252
cap_xc50000
convert_colData_to_json0.0480.0000.048
convert_combo_data_to_dt0.3100.0070.285
convert_combo_field_to_assay0.0020.0000.002
convert_mae_assay_to_dt0.0600.0010.061
convert_mae_to_json0.0160.0000.018
convert_metadata_to_json0.010.000.01
convert_rowData_to_json0.0030.0000.003
convert_se_assay_to_custom_dt0.5170.0070.486
convert_se_assay_to_dt0.0570.0000.058
convert_se_to_json0.0140.0000.014
define_matrix_grid_positions0.0660.0000.051
demote_fields0.4470.0000.353
df_to_bm_assay0.1220.0000.122
dot-set_invalid_fit_params0.0010.0000.000
dot-standardize_conc000
extend_normalization_type_name0.0000.0000.001
fit_curves0.1380.0080.146
flatten0.0070.0000.008
gen_synthetic_data0.0040.0000.005
geometric_mean0.0000.0000.001
get_MAE_identifiers0.0060.0010.007
get_additional_variables0.0120.0010.012
get_assay_dt_duplicated_rows0.1690.0020.170
get_assay_names0.0010.0000.000
get_assay_req_uniq_cols0.1310.0000.131
get_combo_assay_names0.0000.0000.001
get_combo_base_assay_names0.0010.0000.001
get_combo_excess_field_names0.0010.0000.001
get_combo_score_assay_names0.0000.0000.001
get_combo_score_field_names0.0000.0000.001
get_default_identifiers0.0000.0000.001
get_duplicated_rows0.0030.0000.003
get_env_assay_names0.0010.0000.000
get_env_var000
get_expect_one_identifiers0.0010.0000.000
get_experiment_groups000
get_gDR_session_info0.0530.0120.061
get_identifiers_dt0.0070.0010.006
get_idfs_synonyms000
get_isobologram_columns0.0620.0010.062
get_non_empty_assays0.0550.0000.044
get_required_identifiers000
get_settings_from_json0.0020.0000.001
get_supported_experiments0.0010.0000.000
get_synthetic_data0.0110.0000.010
get_testdata0.0860.0050.081
get_testdata_codilution0.0920.0000.078
get_testdata_combo0.2620.0200.264
has_assay_dt_duplicated_rows0.1060.0060.112
has_dt_duplicated_rows000
has_single_codrug_data0.1580.0050.163
has_valid_codrug_data0.1310.0020.133
headers0.0190.0010.020
identifiers000
identify_unique_se_metadata_fields0.0070.0010.007
is_any_exp_empty0.0530.0000.043
is_combo_data0.1470.0030.144
is_exp_empty0.0500.0010.044
is_mae_empty0.0510.0000.042
logisticFit0.0280.0000.026
loop2.9190.1334.213
map_conc_to_standardized_conc0.0040.0010.005
mcolData0.0160.0020.018
merge_MAE4.3590.6723.603
merge_SE1.5770.0641.428
merge_assay0.3070.0060.283
merge_metadata0.0070.0000.008
modifyData0.2760.0060.283
mrowData0.0160.0000.017
predict_conc_from_efficacy0.0000.0000.001
predict_efficacy_from_conc0.0000.0010.000
prettify_flat_metrics0.0390.0010.039
process_batch0.7570.0820.838
promote_fields0.1980.0000.177
refine_coldata0.0090.0010.010
refine_rowdata0.040.000.04
remove_codrug_data0.0570.0000.057
remove_drug_batch0.0010.0000.001
rename_DFrame0.0090.0010.010
rename_bumpy0.0280.0000.028
round_concentration0.0010.0000.001
set_constant_fit_params000
set_unique_cl_names0.0470.0000.048
set_unique_cl_names_dt0.0180.0000.018
set_unique_drug_names0.050.000.05
set_unique_drug_names_dt0.0330.0000.034
set_unique_identifiers0.2280.0000.229
set_unique_names_dt0.0180.0000.018
shorten_normalization_type_name000
split_SE_components0.0910.0000.091
split_big_table_for_xlsx0.0040.0000.004
standardize_mae0.1110.0040.115
standardize_se0.0330.0000.033
throw_msg_if_duplicates0.1280.0150.143
update_env_idfs_from_mae0.0010.0000.001
update_idfs_synonyms0.0010.0000.001
validate_MAE0.0800.0020.082
validate_SE0.0260.0000.026
validate_identifiers0.0070.0000.007
validate_json0.0000.0000.001
validate_mae_with_schema0.4220.0360.461
validate_se_assay_name0.0070.0000.007