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This page was generated on 2025-03-10 12:07 -0400 (Mon, 10 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4670
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4355
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4446
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4439
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4306
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: 2025-03-06 13:00 -0500 (Thu, 06 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 palomino8

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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gDRutils.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings gDRutils_1.4.10.tar.gz
StartedAt: 2025-03-07 01:57:30 -0500 (Fri, 07 Mar 2025)
EndedAt: 2025-03-07 02:02:05 -0500 (Fri, 07 Mar 2025)
EllapsedTime: 275.0 seconds
RetCode: 0
Status:   OK  
CheckDir: gDRutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gDRutils.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings gDRutils_1.4.10.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/gDRutils.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL gDRutils
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 ucrt) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
  62.23    2.10   77.81 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.690.050.74
SE_metadata0.160.000.16
addClass0.020.000.02
aggregate_assay1.310.031.34
apply_bumpy_function2.080.142.22
assert_choices000
average_biological_replicates_dt0.060.000.06
calc_sd000
capVals0.300.030.35
cap_assay_infinities0.260.020.33
cap_xc50000
convert_colData_to_json0.050.000.04
convert_combo_data_to_dt0.380.000.38
convert_combo_field_to_assay000
convert_mae_assay_to_dt0.070.000.08
convert_mae_to_json0.020.000.01
convert_metadata_to_json0.010.000.02
convert_rowData_to_json000
convert_se_assay_to_custom_dt1.240.031.26
convert_se_assay_to_dt0.080.000.08
convert_se_to_json0.010.000.02
define_matrix_grid_positions0.070.000.06
demote_fields0.510.000.51
df_to_bm_assay0.200.000.21
dot-set_invalid_fit_params000
extend_normalization_type_name000
fit_curves0.250.000.25
flatten0.020.000.01
gen_synthetic_data000
geometric_mean000
get_MAE_identifiers000
get_additional_variables0.010.000.01
get_assay_dt_duplicated_rows0.140.010.16
get_assay_names000
get_assay_req_uniq_cols0.110.000.11
get_combo_assay_names000
get_combo_base_assay_names000
get_combo_excess_field_names000
get_combo_score_assay_names000
get_combo_score_field_names000
get_default_identifiers000
get_duplicated_rows0.010.000.01
get_env_assay_names000
get_env_var000
get_expect_one_identifiers000
get_experiment_groups000
get_identifiers_dt0.000.020.02
get_idfs_synonyms000
get_isobologram_columns0.060.000.06
get_non_empty_assays0.070.010.08
get_required_identifiers000
get_settings_from_json000
get_supported_experiments000
get_synthetic_data0.010.000.01
get_testdata0.110.000.11
get_testdata_codilution0.100.000.11
get_testdata_combo0.200.020.28
has_assay_dt_duplicated_rows0.120.000.13
has_dt_duplicated_rows000
has_single_codrug_data0.160.000.15
has_valid_codrug_data0.130.000.13
headers0.030.000.03
identifiers000
identify_unique_se_metadata_fields000
is_any_exp_empty0.060.000.06
is_combo_data0.160.000.16
is_exp_empty0.060.000.06
is_mae_empty0.080.000.08
logisticFit0.010.000.02
loop000
mcolData0.000.020.02
merge_SE1.950.011.95
merge_assay0.360.030.39
merge_metadata0.020.000.02
modifyData0.140.000.14
mrowData0.010.000.01
predict_conc_from_efficacy000
predict_efficacy_from_conc000
prettify_flat_metrics0.030.000.04
promote_fields0.270.000.27
refine_coldata0.000.020.02
refine_rowdata0.070.000.06
remove_codrug_data0.070.000.08
remove_drug_batch0.020.000.01
rename_DFrame0.020.000.02
rename_bumpy0.040.000.05
round_concentration000
set_constant_fit_params000
set_unique_cl_names0.070.000.06
set_unique_cl_names_dt0.030.000.03
set_unique_drug_names0.060.000.06
set_unique_drug_names_dt0.030.000.03
set_unique_identifiers0.420.000.43
set_unique_names_dt0.020.000.01
shorten_normalization_type_name000
split_SE_components0.090.000.10
standardize_mae0.140.000.14
standardize_se0.030.000.03
throw_msg_if_duplicates0.110.000.11
update_env_idfs_from_mae000
update_idfs_synonyms000
validate_MAE0.110.000.11
validate_SE0.030.000.03
validate_identifiers0.020.000.01
validate_json000
validate_mae_with_schema0.230.031.19
validate_se_assay_name0.020.000.02