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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

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: 2024-12-19 13:00 -0500 (Thu, 19 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 kjohnson1

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: /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_1.4.0.tar.gz
StartedAt: 2024-12-20 20:07:36 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 20:11:20 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 223.7 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_1.4.0.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: aarch64-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 Ventura 13.7.1
* 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 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-arm64/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: aarch64-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 687 ]
> 
> proc.time()
   user  system elapsed 
 47.342   2.158  46.492 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.7460.0600.806
SE_metadata0.0530.0050.059
addClass0.0030.0010.004
aggregate_assay1.3230.0451.268
apply_bumpy_function1.5250.0671.510
assert_choices000
average_biological_replicates_dt0.0480.0010.050
calc_sd0.0000.0010.001
capVals0.2810.0220.303
cap_xc500.0010.0010.000
convert_colData_to_json0.0510.0030.054
convert_combo_data_to_dt0.4680.0440.314
convert_combo_field_to_assay0.0040.0000.002
convert_mae_assay_to_dt0.1130.0100.066
convert_mae_to_json0.0400.0040.022
convert_metadata_to_json0.0160.0020.010
convert_rowData_to_json0.0050.0010.003
convert_se_assay_to_custom_dt0.5450.0420.500
convert_se_assay_to_dt0.1170.0100.068
convert_se_to_json0.0260.0020.015
define_matrix_grid_positions1.0620.0510.870
demote_fields0.7100.0500.429
df_to_bm_assay0.2440.0160.145
dot-set_invalid_fit_params0.0000.0010.000
extend_normalization_type_name0.0010.0000.001
fit_curves0.1630.0290.193
flatten0.0080.0010.009
gen_synthetic_data0.0050.0010.006
geometric_mean0.0010.0000.001
get_MAE_identifiers0.0110.0020.013
get_additional_variables0.0060.0010.007
get_assay_dt_duplicated_rows0.1130.0090.123
get_assay_names0.0010.0000.001
get_assay_req_uniq_cols0.0780.0020.087
get_combo_assay_names0.0010.0000.001
get_combo_base_assay_names0.0010.0010.001
get_combo_excess_field_names0.0020.0000.002
get_combo_score_assay_names0.0010.0010.001
get_combo_score_field_names0.0010.0000.001
get_default_identifiers0.0010.0010.001
get_duplicated_rows0.0030.0010.003
get_env_assay_names0.0000.0000.001
get_expect_one_identifiers0.0000.0010.001
get_experiment_groups0.0010.0000.001
get_identifiers_dt0.0080.0040.012
get_idfs_synonyms000
get_isobologram_columns0.0340.0020.036
get_non_empty_assays0.0540.0020.051
get_required_identifiers0.0010.0000.000
get_settings_from_json0.0030.0010.002
get_supported_experiments0.0000.0010.000
get_synthetic_data0.0290.0030.017
get_testdata0.1770.0310.111
get_testdata_codilution0.1390.0140.081
get_testdata_combo0.4150.0490.242
has_assay_dt_duplicated_rows0.1320.0090.075
has_dt_duplicated_rows0.0010.0000.001
has_single_codrug_data0.1250.0090.070
has_valid_codrug_data0.0930.0030.086
headers0.0110.0060.017
identifiers0.0000.0000.001
identify_unique_se_metadata_fields0.0110.0000.012
is_any_exp_empty0.0520.0010.049
is_combo_data0.3580.0410.224
is_exp_empty0.0540.0020.051
is_mae_empty0.0940.0070.052
logisticFit0.0440.0030.025
loop000
mcolData0.0330.0040.018
merge_SE2.3330.1261.571
merge_assay0.4860.0310.328
merge_metadata0.0130.0010.013
modifyData0.1040.0010.104
mrowData0.0180.0020.020
predict_conc_from_efficacy000
predict_efficacy_from_conc000
prettify_flat_metrics0.0190.0010.019
promote_fields0.3190.0220.200
refine_coldata0.0300.0040.018
refine_rowdata0.0890.0060.063
remove_codrug_data0.0310.0000.031
rename_DFrame0.0150.0010.015
rename_bumpy0.0350.0010.036
round_concentration0.0010.0000.000
set_constant_fit_params0.0000.0010.001
set_unique_cl_names0.1170.0030.121
set_unique_cl_names_dt0.0220.0000.023
set_unique_drug_names0.0520.0010.053
set_unique_drug_names_dt0.0300.0000.031
set_unique_identifiers0.3260.0030.329
shorten_normalization_type_name000
split_SE_components0.0560.0010.058
standardize_mae0.1180.0020.119
standardize_se0.0340.0010.035
throw_msg_if_duplicates0.0720.0020.074
update_env_idfs_from_mae0.0020.0000.001
update_idfs_synonyms000
validate_MAE0.0750.0030.079
validate_SE0.0270.0010.028
validate_identifiers0.0070.0010.008
validate_json000
validate_mae_with_schema0.4390.0880.510
validate_se_assay_name0.0100.0020.011