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This page was generated on 2025-09-22 11:41 -0400 (Mon, 22 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4581
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: 2025-09-18 13:40 -0400 (Thu, 18 Sep 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 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 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 kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: gDRutils
Version: 1.6.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gDRutils_1.6.0.tar.gz
StartedAt: 2025-09-19 10:00:47 -0000 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 10:05:37 -0000 (Fri, 19 Sep 2025)
EllapsedTime: 289.3 seconds
RetCode: 0
Status:   OK  
CheckDir: gDRutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gDRutils_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/gDRutils.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* 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 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* 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/R/R/bin/R CMD INSTALL gDRutils
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
 74.326   2.629  76.515 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.5410.0400.582
SE_metadata0.050.000.05
addClass0.0020.0000.002
aggregate_assay0.7510.0200.772
apply_bumpy_function2.9770.0203.002
assert_choices0.0000.0010.001
average_biological_replicates_dt0.0550.0110.065
calc_sd0.0010.0000.001
capVals0.3380.0360.375
cap_assay_infinities0.3600.0230.377
cap_xc500.0010.0000.001
convert_colData_to_json0.0720.0080.080
convert_combo_data_to_dt0.4010.0040.402
convert_combo_field_to_assay0.0030.0000.002
convert_mae_assay_to_dt0.0910.0000.091
convert_mae_to_json0.0220.0000.022
convert_metadata_to_json0.0130.0000.014
convert_rowData_to_json0.0040.0000.004
convert_se_assay_to_custom_dt0.5670.0080.574
convert_se_assay_to_dt0.0810.0000.082
convert_se_to_json0.0170.0000.018
define_matrix_grid_positions0.0740.0000.072
demote_fields0.5590.0080.578
df_to_bm_assay0.1720.0000.172
dot-set_invalid_fit_params000
dot-standardize_conc0.0010.0000.001
extend_normalization_type_name0.0000.0000.001
fit_curves0.1800.0030.185
flatten0.0090.0000.010
gen_synthetic_data0.0040.0030.007
geometric_mean0.0010.0000.000
get_MAE_identifiers0.0090.0000.009
get_additional_variables0.0090.0000.009
get_assay_dt_duplicated_rows0.1600.0040.164
get_assay_names000
get_assay_req_uniq_cols0.1380.0000.138
get_combo_assay_names0.0000.0000.001
get_combo_base_assay_names0.0010.0000.001
get_combo_excess_field_names0.0020.0000.002
get_combo_score_assay_names0.0010.0000.001
get_combo_score_field_names0.0010.0000.001
get_default_identifiers0.0000.0000.001
get_duplicated_rows0.0030.0000.004
get_env_assay_names000
get_env_var000
get_expect_one_identifiers0.0000.0000.001
get_experiment_groups000
get_gDR_session_info0.0680.0120.080
get_identifiers_dt0.0030.0040.007
get_idfs_synonyms0.0010.0000.000
get_isobologram_columns0.0470.0000.047
get_non_empty_assays0.0610.0040.063
get_required_identifiers000
get_settings_from_json0.0010.0000.001
get_supported_experiments000
get_synthetic_data0.0100.0040.014
get_testdata0.1050.0040.109
get_testdata_codilution0.1020.0080.112
get_testdata_combo0.2820.0090.310
has_assay_dt_duplicated_rows0.1210.0000.122
has_dt_duplicated_rows0.0010.0000.001
has_single_codrug_data0.0990.0080.106
has_valid_codrug_data0.1780.0000.178
headers0.0150.0000.015
identifiers000
identify_unique_se_metadata_fields0.0110.0000.011
is_any_exp_empty0.0630.0000.062
is_combo_data0.1730.0200.193
is_exp_empty0.0670.0000.066
is_mae_empty0.0880.0000.087
logisticFit0.0330.0000.034
loop000
map_conc_to_standardized_conc0.0040.0000.005
mcolData0.0180.0000.019
merge_SE2.2560.0002.251
merge_assay0.4410.0270.468
merge_metadata0.0110.0000.011
modifyData0.1420.0080.151
mrowData0.0160.0040.020
predict_conc_from_efficacy000
predict_efficacy_from_conc0.0000.0000.001
prettify_flat_metrics0.0270.0040.031
promote_fields1.0590.0601.119
refine_coldata0.0140.0000.014
refine_rowdata0.0640.0000.064
remove_codrug_data0.0460.0000.046
remove_drug_batch0.0020.0000.002
rename_DFrame0.0130.0000.013
rename_bumpy0.0420.0000.042
round_concentration0.0000.0000.001
set_constant_fit_params0.0010.0000.000
set_unique_cl_names0.0670.0000.067
set_unique_cl_names_dt0.0270.0000.027
set_unique_drug_names0.0740.0000.074
set_unique_drug_names_dt0.0520.0000.052
set_unique_identifiers0.4430.0080.453
set_unique_names_dt0.0370.0000.037
shorten_normalization_type_name0.0010.0000.000
split_SE_components0.0940.0160.109
split_big_table_for_xlsx0.0050.0040.009
standardize_mae0.1840.0360.220
standardize_se0.0410.0160.058
throw_msg_if_duplicates0.1340.0240.158
update_env_idfs_from_mae0.0020.0000.002
update_idfs_synonyms0.0010.0000.000
validate_MAE0.140.000.14
validate_SE0.0400.0000.039
validate_identifiers0.0100.0000.011
validate_json000
validate_mae_with_schema0.6910.0600.720
validate_se_assay_name0.0050.0080.013