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This page was generated on 2025-04-02 19:28 -0400 (Wed, 02 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4449
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4426
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 781/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRutils 1.4.10  (landing page)
Arkadiusz Gladki
Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025)
git_url: https://git.bioconductor.org/packages/gDRutils
git_branch: RELEASE_3_20
git_last_commit: 18d3e76
git_last_commit_date: 2025-02-11 06:44:03 -0400 (Tue, 11 Feb 2025)
nebbiolo2Linux (Ubuntu 24.04.1 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
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
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: 1.4.10
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings gDRutils_1.4.10.tar.gz
StartedAt: 2025-03-31 22:20:58 -0400 (Mon, 31 Mar 2025)
EndedAt: 2025-03-31 22:24:31 -0400 (Mon, 31 Mar 2025)
EllapsedTime: 213.3 seconds
RetCode: 0
Status:   OK  
CheckDir: gDRutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings gDRutils_1.4.10.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/gDRutils.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 ‘1.4.10’
* 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 ... OK
* 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: OK


Installation output

gDRutils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL gDRutils
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘gDRutils’ ...
** 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 4.4.3 (2025-02-28) -- "Trophy Case"
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 727 ]
> 
> proc.time()
   user  system elapsed 
 46.839   1.449  47.252 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.5250.0480.574
SE_metadata0.0350.0000.035
addClass0.0030.0000.002
aggregate_assay1.5540.0101.558
apply_bumpy_function1.4100.1351.545
assert_choices000
average_biological_replicates_dt0.0440.0000.044
calc_sd000
capVals0.2430.0000.242
cap_assay_infinities0.2610.0030.233
cap_xc500.0000.0000.001
convert_colData_to_json0.050.000.05
convert_combo_data_to_dt0.3210.0070.297
convert_combo_field_to_assay0.0020.0000.001
convert_mae_assay_to_dt0.0610.0020.063
convert_mae_to_json0.0170.0000.017
convert_metadata_to_json0.0090.0000.009
convert_rowData_to_json0.0030.0000.002
convert_se_assay_to_custom_dt1.3620.0051.345
convert_se_assay_to_dt0.0570.0000.057
convert_se_to_json0.0140.0000.014
define_matrix_grid_positions0.0620.0000.053
demote_fields0.4500.0000.396
df_to_bm_assay0.1470.0000.147
dot-set_invalid_fit_params000
extend_normalization_type_name000
fit_curves0.1360.0030.138
flatten0.0080.0000.008
gen_synthetic_data0.0040.0000.005
geometric_mean000
get_MAE_identifiers0.0070.0010.008
get_additional_variables0.0080.0000.007
get_assay_dt_duplicated_rows0.0880.0000.088
get_assay_names0.0000.0000.001
get_assay_req_uniq_cols0.0720.0000.072
get_combo_assay_names0.0000.0000.001
get_combo_base_assay_names0.0010.0000.000
get_combo_excess_field_names0.0010.0000.001
get_combo_score_assay_names0.0010.0000.000
get_combo_score_field_names0.0010.0000.000
get_default_identifiers000
get_duplicated_rows0.0020.0000.003
get_env_assay_names000
get_env_var0.0010.0000.000
get_expect_one_identifiers000
get_experiment_groups000
get_identifiers_dt0.0060.0020.007
get_idfs_synonyms000
get_isobologram_columns0.0370.0010.038
get_non_empty_assays0.0590.0010.051
get_required_identifiers000
get_settings_from_json0.0020.0000.001
get_supported_experiments000
get_synthetic_data0.0110.0000.011
get_testdata0.0890.0030.086
get_testdata_codilution0.0880.0000.083
get_testdata_combo0.2220.0110.216
has_assay_dt_duplicated_rows0.0690.0030.072
has_dt_duplicated_rows000
has_single_codrug_data0.0670.0000.067
has_valid_codrug_data0.070.000.07
headers0.0100.0010.011
identifiers000
identify_unique_se_metadata_fields0.0090.0000.009
is_any_exp_empty0.0640.0000.053
is_combo_data0.1560.0080.162
is_exp_empty0.0590.0000.049
is_mae_empty0.0630.0010.049
logisticFit0.0260.0000.024
loop000
mcolData0.0160.0000.015
merge_SE1.7810.0021.609
merge_assay0.3380.0010.323
merge_metadata0.0080.0000.008
modifyData0.1190.0030.121
mrowData0.0140.0020.015
predict_conc_from_efficacy000
predict_efficacy_from_conc0.0000.0000.001
prettify_flat_metrics0.020.000.02
promote_fields0.2010.0010.190
refine_coldata0.0090.0020.011
refine_rowdata0.0560.0000.056
remove_codrug_data0.0330.0000.032
remove_drug_batch0.0010.0000.002
rename_DFrame0.010.000.01
rename_bumpy0.0310.0010.032
round_concentration000
set_constant_fit_params0.0010.0000.000
set_unique_cl_names0.0560.0000.056
set_unique_cl_names_dt0.0200.0000.019
set_unique_drug_names0.0790.0000.079
set_unique_drug_names_dt0.0390.0000.038
set_unique_identifiers0.3180.0000.317
set_unique_names_dt0.0180.0010.019
shorten_normalization_type_name0.0000.0000.001
split_SE_components0.0540.0010.055
standardize_mae0.1190.0010.119
standardize_se0.0320.0000.031
throw_msg_if_duplicates0.0760.0000.076
update_env_idfs_from_mae0.0000.0010.001
update_idfs_synonyms000
validate_MAE0.0800.0010.081
validate_SE0.0280.0000.028
validate_identifiers0.0060.0000.006
validate_json0.0010.0000.000
validate_mae_with_schema0.4260.0240.391
validate_se_assay_name0.0070.0000.007