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This page was generated on 2025-03-06 12:08 -0500 (Thu, 06 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4769
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4504
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4527
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4480
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4416
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: 2025-03-03 13:00 -0500 (Mon, 03 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 -0500 (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 merida1

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gDRutils_1.4.10.tar.gz
StartedAt: 2025-03-04 03:31:23 -0500 (Tue, 04 Mar 2025)
EndedAt: 2025-03-04 03:38:35 -0500 (Tue, 04 Mar 2025)
EllapsedTime: 432.5 seconds
RetCode: 0
Status:   OK  
CheckDir: gDRutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gDRutils_1.4.10.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/gDRutils.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gDRutils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRutils’ version ‘1.4.10’
* 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 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

gDRutils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gDRutils
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
 82.468   2.901  94.148 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply1.2920.1351.438
SE_metadata0.0620.0090.071
addClass0.0030.0010.005
aggregate_assay1.8060.0861.962
apply_bumpy_function3.5120.1773.737
assert_choices0.0010.0000.001
average_biological_replicates_dt0.1060.0030.110
calc_sd0.0010.0010.002
capVals0.6410.0250.673
cap_assay_infinities0.5000.0090.512
cap_xc500.0010.0010.001
convert_colData_to_json0.1300.0020.132
convert_combo_data_to_dt0.6070.0310.641
convert_combo_field_to_assay0.0030.0000.004
convert_mae_assay_to_dt0.1320.0070.139
convert_mae_to_json0.0290.0010.031
convert_metadata_to_json0.0190.0000.020
convert_rowData_to_json0.0050.0010.006
convert_se_assay_to_custom_dt1.5370.1211.668
convert_se_assay_to_dt0.1330.0080.143
convert_se_to_json0.0300.0010.031
define_matrix_grid_positions0.1090.0020.112
demote_fields0.8480.0220.878
df_to_bm_assay0.3090.0100.323
dot-set_invalid_fit_params0.0010.0010.001
extend_normalization_type_name0.0000.0000.001
fit_curves0.3020.0300.336
flatten0.0170.0010.023
gen_synthetic_data0.0120.0030.016
geometric_mean0.0010.0000.001
get_MAE_identifiers0.0120.0030.016
get_additional_variables0.0160.0020.018
get_assay_dt_duplicated_rows0.2060.0040.210
get_assay_names0.0000.0000.001
get_assay_req_uniq_cols0.1590.0030.161
get_combo_assay_names0.0010.0000.002
get_combo_base_assay_names0.0020.0000.002
get_combo_excess_field_names0.0030.0010.004
get_combo_score_assay_names0.0020.0000.003
get_combo_score_field_names0.0020.0000.002
get_default_identifiers0.0010.0020.004
get_duplicated_rows0.0070.0010.008
get_env_assay_names0.0010.0010.002
get_env_var0.0000.0010.000
get_expect_one_identifiers0.0010.0000.002
get_experiment_groups0.0000.0010.001
get_identifiers_dt0.0120.0080.020
get_idfs_synonyms0.0000.0000.001
get_isobologram_columns0.0790.0030.083
get_non_empty_assays0.1020.0020.105
get_required_identifiers0.0000.0010.001
get_settings_from_json0.0020.0010.003
get_supported_experiments0.0000.0010.001
get_synthetic_data0.0200.0020.022
get_testdata0.2010.0570.259
get_testdata_codilution0.1820.0120.195
get_testdata_combo0.4050.0510.457
has_assay_dt_duplicated_rows0.1590.0020.163
has_dt_duplicated_rows0.0020.0000.002
has_single_codrug_data0.1570.0020.159
has_valid_codrug_data0.1680.0020.170
headers0.0290.0230.053
identifiers0.0000.0010.000
identify_unique_se_metadata_fields0.0120.0020.014
is_any_exp_empty0.0950.0010.096
is_combo_data0.2120.0200.231
is_exp_empty0.0810.0010.082
is_mae_empty0.0900.0010.092
logisticFit0.0520.0010.054
loop0.0000.0010.001
mcolData0.0230.0020.026
merge_SE3.5110.0423.577
merge_assay0.7750.0380.928
merge_metadata0.0120.0020.014
modifyData0.2290.0030.242
mrowData0.0270.0020.029
predict_conc_from_efficacy0.0000.0010.001
predict_efficacy_from_conc0.0010.0010.001
prettify_flat_metrics0.0480.0010.050
promote_fields0.4180.0050.428
refine_coldata0.0180.0020.021
refine_rowdata0.0960.0030.101
remove_codrug_data0.0770.0020.081
remove_drug_batch0.0040.0010.005
rename_DFrame0.0170.0020.020
rename_bumpy0.0640.0030.067
round_concentration0.0010.0010.001
set_constant_fit_params0.0010.0010.002
set_unique_cl_names0.1310.0010.135
set_unique_cl_names_dt0.0470.0010.050
set_unique_drug_names0.1470.0010.151
set_unique_drug_names_dt0.0870.0000.088
set_unique_identifiers0.6870.0040.698
set_unique_names_dt0.0430.0010.043
shorten_normalization_type_name0.0000.0010.000
split_SE_components0.1360.0040.140
standardize_mae0.2830.0020.287
standardize_se0.0730.0020.076
throw_msg_if_duplicates0.1670.0030.175
update_env_idfs_from_mae0.0030.0010.004
update_idfs_synonyms0.0010.0010.001
validate_MAE0.1910.0020.196
validate_SE0.0660.0020.069
validate_identifiers0.0190.0020.021
validate_json000
validate_mae_with_schema0.6360.0850.838
validate_se_assay_name0.0080.0020.021