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This page was generated on 2024-04-18 11:32:10 -0400 (Thu, 18 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4388
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Package 781/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRutils 1.0.0  (landing page)
Arkadiusz Gladki
Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024)
git_url: https://git.bioconductor.org/packages/gDRutils
git_branch: RELEASE_3_18
git_last_commit: b8a1d96
git_last_commit_date: 2023-10-24 11:49:34 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 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:
- 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: 1.0.0
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_1.0.0.tar.gz
StartedAt: 2024-04-17 14:23:36 -0400 (Wed, 17 Apr 2024)
EndedAt: 2024-04-17 14:27:26 -0400 (Wed, 17 Apr 2024)
EllapsedTime: 229.4 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/gDRutils.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gDRutils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRutils’ version ‘1.0.0’
* 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 R 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 in ‘inst/doc’ ... 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/4.3-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

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 461 ]
> 
> proc.time()
   user  system elapsed 
 45.106   1.289  46.772 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply1.4760.0531.542
SE_metadata0.0520.0040.057
aggregate_assay0.6390.0350.680
apply_bumpy_function1.5160.0791.611
assert_choices0.0010.0000.000
cap_xc500.0010.0000.001
convert_combo_data_to_dt0.7600.0640.834
convert_mae_assay_to_dt0.0630.0040.067
convert_mae_to_json0.8470.0280.887
convert_se_assay_to_dt0.0570.0030.060
convert_se_to_json0.0180.0000.019
demote_fields0.3690.0060.387
df_to_bm_assay0.1070.0020.111
dot-convert_colData_to_json0.0030.0010.003
dot-convert_metadata_to_json0.0040.0000.004
dot-convert_rowData_to_json0.0030.0000.003
dot-set_constant_fit_params0.0000.0010.001
dot-set_invalid_fit_params0.0000.0000.001
extend_normalization_type_name0.0010.0010.001
fit_curves0.2420.0330.278
flatten0.0120.0010.013
gen_synthetic_data0.0070.0010.007
get_MAE_identifiers0.0320.0030.037
get_assay_names0.0010.0000.001
get_combo_assay_names0.0010.0000.001
get_combo_base_assay_names0.0010.0010.001
get_combo_col_settings0.0030.0000.003
get_combo_score_assay_names0.0000.0000.001
get_default_identifiers0.0000.0010.001
get_env_assay_names0.0010.0000.000
get_expect_one_identifiers000
get_experiment_groups000
get_identifiers_dt0.0080.0030.011
get_idfs_synonyms0.0000.0010.000
get_iso_colors0.0010.0000.002
get_non_empty_assays0.0580.0010.059
get_required_identifiers0.0000.0000.001
get_synthetic_data0.0150.0010.016
get_testdata0.0850.0210.106
headers0.0050.0050.011
identifiers000
identify_unique_se_metadata_fields0.0120.0000.012
is_any_exp_empty0.0470.0000.048
is_exp_empty0.0480.0010.049
is_mae_empty0.0510.0010.052
logisticFit0.0230.0000.024
loop000
mcolData0.0180.0020.021
merge_SE1.6690.0321.725
merge_assay0.3330.0060.342
merge_metadata0.0120.0010.014
mrowData0.0200.0010.020
predict_conc_from_efficacy0.0000.0000.001
predict_efficacy_from_conc0.0000.0010.001
prettify_flat_metrics0.0050.0000.006
promote_fields0.2440.0130.265
refine_coldata0.0140.0020.016
refine_rowdata0.0750.0030.079
rename_DFrame0.0140.0010.015
rename_bumpy0.0320.0010.033
shorten_normalization_type_name0.0010.0000.000
split_SE_components0.0320.0010.035
standardize_mae0.1600.0030.166
standardize_se0.0330.0020.034
update_env_idfs_from_mae0.0010.0010.002
update_idfs_synonyms0.0000.0000.001
validate_MAE0.0760.0020.077
validate_SE0.0300.0010.033
validate_identifiers0.0080.0000.008
validate_json000
validate_mae_with_schema0.4640.0610.528
validate_se_assay_name0.0100.0010.012