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

This page was generated on 2025-09-02 12:04 -0400 (Tue, 02 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 792/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRutils 1.7.17  (landing page)
Arkadiusz Gladki
Snapshot Date: 2025-09-01 13:45 -0400 (Mon, 01 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    NA  
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 taishan

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: 1.7.17
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_1.7.17.tar.gz
StartedAt: 2025-09-02 06:54:24 -0000 (Tue, 02 Sep 2025)
EndedAt: 2025-09-02 07:00:09 -0000 (Tue, 02 Sep 2025)
EllapsedTime: 344.3 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_1.7.17.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/gDRutils.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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)
* 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 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 5.676  0.883    5.42
* 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-3.22-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-4.5.0/site-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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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 832 ]
> 
> proc.time()
   user  system elapsed 
131.207   3.706 134.356 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.5100.0440.556
SE_metadata0.0420.0000.043
addClass0.0030.0000.002
aggregate_assay0.7030.0080.713
apply_bumpy_function2.7530.0602.823
assert_choices0.0000.0000.001
average_biological_replicates_dt0.5490.0630.615
calc_sd0.0010.0000.001
capVals0.2930.0280.324
cap_assay_infinities0.3300.0400.365
cap_xc500.0010.0000.001
convert_colData_to_json0.0770.0000.077
convert_combo_data_to_dt0.3950.0160.410
convert_combo_field_to_assay0.0020.0000.002
convert_mae_assay_to_dt0.0840.0000.084
convert_mae_to_json0.020.000.02
convert_metadata_to_json0.0120.0000.012
convert_rowData_to_json0.0030.0000.004
convert_se_assay_to_custom_dt0.8250.0200.844
convert_se_assay_to_dt0.0870.0000.088
convert_se_to_json0.0170.0000.018
define_matrix_grid_positions0.0670.0040.069
demote_fields0.4990.0040.497
df_to_bm_assay0.1790.0000.179
dot-set_invalid_fit_params0.0010.0000.000
dot-standardize_conc0.0010.0000.000
extend_normalization_type_name000
fit_curves0.1850.0080.194
flatten0.010.000.01
gen_synthetic_data0.0080.0000.008
geometric_mean0.0010.0000.000
get_MAE_identifiers0.0080.0000.009
get_additional_variables0.0170.0000.017
get_assay_dt_duplicated_rows0.2720.0040.278
get_assay_names0.0000.0000.001
get_assay_req_uniq_cols0.1540.0000.154
get_combo_assay_names0.0010.0000.001
get_combo_base_assay_names0.0010.0000.002
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_identifiers0.0010.0000.000
get_duplicated_rows0.0040.0000.003
get_env_assay_names0.0010.0000.000
get_env_var000
get_expect_one_identifiers000
get_experiment_groups0.0010.0000.000
get_gDR_session_info0.0710.0040.075
get_identifiers_dt0.0030.0040.008
get_idfs_synonyms0.0000.0000.001
get_isobologram_columns0.0950.0040.099
get_non_empty_assays0.0680.0000.067
get_required_identifiers000
get_settings_from_json0.0010.0000.001
get_supported_experiments000
get_synthetic_data0.0070.0070.013
get_testdata0.1170.0040.122
get_testdata_codilution0.1160.0040.122
get_testdata_combo0.3470.0280.396
has_assay_dt_duplicated_rows0.1540.0000.154
has_dt_duplicated_rows0.0010.0000.001
has_single_codrug_data0.7790.0160.798
has_valid_codrug_data0.190.000.19
headers0.0290.0000.029
identifiers000
identify_unique_se_metadata_fields0.0080.0000.009
is_any_exp_empty0.0580.0000.057
is_combo_data0.1490.0040.154
is_exp_empty0.0610.0000.061
is_mae_empty0.0620.0000.061
logisticFit0.040.000.04
loop2.6080.0643.734
map_conc_to_standardized_conc0.0070.0000.006
mcolData0.0150.0080.024
merge_MAE5.6760.8835.420
merge_SE1.9890.0522.024
merge_assay0.4350.0000.434
merge_metadata0.0090.0000.009
modifyData0.3920.0120.405
mrowData0.0170.0000.017
predict_conc_from_efficacy0.0000.0000.001
predict_efficacy_from_conc000
prettify_flat_metrics0.0530.0040.056
process_batch0.6940.1440.841
promote_fields0.2370.0000.237
refine_coldata0.0120.0000.012
refine_rowdata0.0530.0000.053
remove_codrug_data0.0850.0000.085
remove_drug_batch0.0020.0000.001
rename_DFrame0.0120.0000.012
rename_bumpy0.0390.0000.040
round_concentration0.0000.0010.001
set_constant_fit_params000
set_unique_cl_names0.0620.0020.064
set_unique_cl_names_dt0.0250.0000.025
set_unique_drug_names0.0710.0000.071
set_unique_drug_names_dt0.0490.0000.049
set_unique_identifiers0.3640.0120.377
set_unique_names_dt0.0270.0000.027
shorten_normalization_type_name000
split_SE_components0.1490.0000.149
split_big_table_for_xlsx0.0070.0000.006
standardize_mae0.1660.0000.167
standardize_se0.0690.0000.070
throw_msg_if_duplicates0.1770.0000.178
update_env_idfs_from_mae0.0000.0020.002
update_idfs_synonyms0.0000.0010.000
validate_MAE0.1290.0150.145
validate_SE0.0310.0080.039
validate_identifiers0.010.000.01
validate_json0.0010.0000.000
validate_mae_with_schema0.6800.0530.879
validate_se_assay_name0.0090.0000.009