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This page was generated on 2025-01-02 12:04 -0500 (Thu, 02 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1.4.0  (landing page)
Arkadiusz Gladki
Snapshot Date: 2024-12-30 13:00 -0500 (Mon, 30 Dec 2024)
git_url: https://git.bioconductor.org/packages/gDRutils
git_branch: RELEASE_3_20
git_last_commit: 1433886
git_last_commit_date: 2024-10-29 11:21:35 -0500 (Tue, 29 Oct 2024)
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


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: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2024-12-31 01:38:19 -0500 (Tue, 31 Dec 2024)
EndedAt: 2024-12-31 01:42:56 -0500 (Tue, 31 Dec 2024)
EllapsedTime: 276.9 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/gDRutils.Rcheck'
* using R version 4.4.2 (2024-10-31 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 '1.4.0'
* 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 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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 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 687 ]
> 
> proc.time()
   user  system elapsed 
  62.25    1.84   77.67 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply1.260.061.33
SE_metadata0.060.000.06
addClass000
aggregate_assay0.670.080.75
apply_bumpy_function1.790.041.85
assert_choices000
average_biological_replicates_dt0.050.020.06
calc_sd000
capVals0.410.060.47
cap_xc50000
convert_colData_to_json0.080.000.08
convert_combo_data_to_dt0.920.020.95
convert_combo_field_to_assay000
convert_mae_assay_to_dt0.050.000.05
convert_mae_to_json0.020.000.01
convert_metadata_to_json000
convert_rowData_to_json000
convert_se_assay_to_custom_dt0.460.060.53
convert_se_assay_to_dt0.080.000.08
convert_se_to_json0.020.000.01
define_matrix_grid_positions0.040.000.05
demote_fields0.440.000.43
df_to_bm_assay0.160.000.16
dot-set_invalid_fit_params000
extend_normalization_type_name0.010.000.01
fit_curves0.180.050.22
flatten0.010.000.02
gen_synthetic_data0.000.020.01
geometric_mean000
get_MAE_identifiers000
get_additional_variables000
get_assay_dt_duplicated_rows0.130.000.13
get_assay_names000
get_assay_req_uniq_cols0.090.000.09
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_rows0.020.000.01
get_env_assay_names000
get_expect_one_identifiers000
get_experiment_groups000
get_identifiers_dt000
get_idfs_synonyms000
get_isobologram_columns0.030.000.03
get_non_empty_assays0.070.000.06
get_required_identifiers0.010.000.02
get_settings_from_json000
get_supported_experiments000
get_synthetic_data0.020.000.02
get_testdata0.110.030.14
get_testdata_codilution0.120.000.14
get_testdata_combo0.280.040.32
has_assay_dt_duplicated_rows0.130.000.13
has_dt_duplicated_rows000
has_single_codrug_data0.140.000.14
has_valid_codrug_data0.120.000.13
headers0.030.000.03
identifiers000
identify_unique_se_metadata_fields0.020.000.01
is_any_exp_empty0.060.000.06
is_combo_data0.170.010.19
is_exp_empty0.100.020.11
is_mae_empty0.040.000.05
logisticFit0.040.000.03
loop000
mcolData0.010.000.02
merge_SE1.720.011.71
merge_assay0.420.000.43
merge_metadata000
modifyData0.110.000.11
mrowData0.030.000.03
predict_conc_from_efficacy000
predict_efficacy_from_conc000
prettify_flat_metrics0.030.000.03
promote_fields0.300.020.31
refine_coldata0.020.000.02
refine_rowdata0.070.000.07
remove_codrug_data0.070.000.07
rename_DFrame0.010.000.01
rename_bumpy0.050.000.05
round_concentration000
set_constant_fit_params000
set_unique_cl_names0.110.000.11
set_unique_cl_names_dt0.030.000.03
set_unique_drug_names0.090.000.09
set_unique_drug_names_dt0.050.000.05
set_unique_identifiers0.420.000.42
shorten_normalization_type_name000
split_SE_components0.050.010.06
standardize_mae0.090.000.10
standardize_se0.030.020.05
throw_msg_if_duplicates0.100.000.09
update_env_idfs_from_mae000
update_idfs_synonyms000
validate_MAE0.090.000.09
validate_SE0.020.000.02
validate_identifiers0.010.000.01
validate_json000
validate_mae_with_schema0.390.050.94
validate_se_assay_name000