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This page was generated on 2024-06-27 11:38 -0400 (Thu, 27 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4691
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4405
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4354
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 766/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRutils 1.3.2  (landing page)
Arkadiusz Gladki
Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 Jun 2024)
git_url: https://git.bioconductor.org/packages/gDRutils
git_branch: devel
git_last_commit: a926756
git_last_commit_date: 2024-06-24 19:48:06 -0400 (Mon, 24 Jun 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for gDRutils on lconway

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: 1.3.2
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_1.3.2.tar.gz
StartedAt: 2024-06-26 20:25:34 -0400 (Wed, 26 Jun 2024)
EndedAt: 2024-06-26 20:29:45 -0400 (Wed, 26 Jun 2024)
EllapsedTime: 251.0 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_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/gDRutils.Rcheck’
* using R version 4.4.1 RC (2024-06-06 r86719)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gDRutils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRutils’ version ‘1.3.2’
* 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 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life"
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 624 ]
> 
> proc.time()
   user  system elapsed 
 56.750   1.982  59.167 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.7830.0680.868
SE_metadata0.1510.0100.161
addClass0.0030.0000.002
aggregate_assay1.3510.0451.416
apply_bumpy_function2.1340.1312.298
assert_choices000
average_biological_replicates_dt0.3690.0200.394
capVals0.0860.0080.095
cap_xc500.0000.0000.001
convert_colData_to_json0.0670.0010.069
convert_combo_data_to_dt0.2910.0150.310
convert_combo_field_to_assay0.0020.0010.002
convert_mae_assay_to_dt0.0700.0030.074
convert_mae_to_json0.0200.0010.021
convert_metadata_to_json0.0100.0010.010
convert_rowData_to_json0.0030.0000.003
convert_se_assay_to_custom_dt0.5180.0410.565
convert_se_assay_to_dt0.0720.0040.075
convert_se_to_json0.0150.0010.017
define_matrix_grid_positions0.0580.0030.062
demote_fields1.1890.0121.211
df_to_bm_assay0.1460.0010.148
dot-set_invalid_fit_params000
extend_normalization_type_name0.0000.0000.001
fit_curves0.1510.0220.175
flatten0.0080.0010.009
gen_synthetic_data0.0040.0010.005
geometric_mean000
get_MAE_identifiers0.0100.0010.010
get_additional_variables0.2030.0020.211
get_assay_names0.0000.0000.001
get_combo_assay_names0.0010.0000.001
get_combo_base_assay_names0.0010.0010.002
get_combo_col_settings0.0030.0000.003
get_combo_excess_field_names0.0020.0000.003
get_combo_score_assay_names0.0000.0010.001
get_combo_score_field_names0.0010.0000.001
get_default_identifiers0.0010.0010.002
get_duplicated_rows0.0020.0000.003
get_env_assay_names0.0000.0000.001
get_expect_one_identifiers000
get_experiment_groups0.0000.0010.000
get_identifiers_dt0.0070.0040.010
get_idfs_synonyms0.0000.0010.000
get_iso_colors0.0020.0010.002
get_isobologram_columns0.0440.0030.048
get_non_empty_assays0.0580.0020.061
get_required_identifiers0.0000.0000.001
get_settings_from_json0.0010.0010.003
get_supported_experiments0.0000.0000.001
get_synthetic_data0.0150.0010.015
get_testdata0.0990.0260.126
get_testdata_codilution0.0830.0070.092
get_testdata_combo0.2150.0230.240
has_single_codrug_data0.0940.0030.103
has_valid_codrug_data0.0880.0010.089
headers0.0110.0070.019
identifiers0.0000.0010.000
identify_unique_se_metadata_fields0.0090.0010.011
is_any_exp_empty0.0510.0020.052
is_combo_data0.1340.0130.149
is_exp_empty0.0890.0060.095
is_mae_empty0.0540.0020.055
logisticFit0.0270.0010.028
loop000
mcolData0.0170.0010.018
merge_SE1.8220.0271.868
merge_assay0.3940.0190.416
merge_metadata0.0090.0010.010
modifyData0.1090.0020.111
mrowData0.0150.0010.017
predict_conc_from_efficacy000
predict_efficacy_from_conc0.0000.0000.001
prettify_flat_metrics0.0290.0020.034
promote_fields0.2230.0030.227
refine_coldata0.0120.0010.013
refine_rowdata0.0660.0010.067
remove_codrug_data0.0400.0010.041
rename_DFrame0.0130.0010.013
rename_bumpy0.0370.0010.039
round_concentration000
set_constant_fit_params0.0000.0000.001
shorten_normalization_type_name0.0010.0000.000
split_SE_components0.0750.0020.079
standardize_mae0.1800.0040.185
standardize_se0.0370.0020.039
update_env_idfs_from_mae0.0010.0000.001
update_idfs_synonyms0.0010.0000.000
validate_MAE0.0860.0030.093
validate_SE0.0330.0010.034
validate_identifiers0.0090.0010.010
validate_json0.0010.0000.000
validate_mae_with_schema0.4160.0570.500
validate_se_assay_name0.0110.0010.013