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This page was generated on 2024-03-29 11:37:45 -0400 (Fri, 29 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4669
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4404
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4427
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 781/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRutils 1.0.0  (landing page)
Arkadiusz Gladki
Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 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)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for gDRutils on merida1


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: 1.0.0
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: 2024-03-28 03:04:28 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 03:11:24 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 415.8 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/meat/gDRutils.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-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 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 ‘1.0.0’
* 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-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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 
 68.184   2.779  84.015 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply1.8350.0912.009
SE_metadata0.0610.0080.071
aggregate_assay1.2750.1061.593
apply_bumpy_function3.4880.2253.974
assert_choices0.0000.0000.001
cap_xc500.0010.0000.002
convert_combo_data_to_dt1.5300.0751.692
convert_mae_assay_to_dt0.1350.0080.146
convert_mae_to_json0.8290.0210.892
convert_se_assay_to_dt0.1270.0070.141
convert_se_to_json0.0380.0010.040
demote_fields0.7240.0060.766
df_to_bm_assay0.1970.0020.210
dot-convert_colData_to_json0.0050.0010.006
dot-convert_metadata_to_json0.0090.0010.010
dot-convert_rowData_to_json0.0060.0010.007
dot-set_constant_fit_params0.0010.0010.003
dot-set_invalid_fit_params0.0010.0000.001
extend_normalization_type_name0.0000.0000.001
fit_curves0.4140.0410.475
flatten0.0180.0010.020
gen_synthetic_data0.0130.0030.018
get_MAE_identifiers0.0360.0030.042
get_assay_names0.0010.0010.002
get_combo_assay_names0.0020.0000.003
get_combo_base_assay_names0.0020.0000.003
get_combo_col_settings0.0070.0010.009
get_combo_score_assay_names0.0020.0000.003
get_default_identifiers0.0010.0010.003
get_env_assay_names0.0010.0010.001
get_expect_one_identifiers0.0000.0010.002
get_experiment_groups0.0010.0010.001
get_identifiers_dt0.0100.0080.020
get_idfs_synonyms000
get_iso_colors0.0040.0010.006
get_non_empty_assays0.1050.0020.114
get_required_identifiers0.0000.0000.001
get_synthetic_data0.0190.0010.021
get_testdata0.1800.0550.249
headers0.0130.0140.027
identifiers0.0000.0000.001
identify_unique_se_metadata_fields0.0120.0010.015
is_any_exp_empty0.0990.0010.104
is_exp_empty0.0940.0020.100
is_mae_empty0.0930.0010.099
logisticFit0.0470.0010.049
loop0.0000.0000.001
mcolData0.0250.0020.028
merge_SE3.3100.0363.535
merge_assay0.6930.0180.779
merge_metadata0.0120.0020.015
mrowData0.0270.0020.031
predict_conc_from_efficacy0.0010.0000.001
predict_efficacy_from_conc0.0000.0010.001
prettify_flat_metrics0.0110.0020.015
promote_fields0.4460.0170.509
refine_coldata0.0170.0020.021
refine_rowdata0.0930.0030.100
rename_DFrame0.0160.0020.020
rename_bumpy0.0630.0020.070
shorten_normalization_type_name0.0010.0010.001
split_SE_components0.0630.0040.071
standardize_mae0.3270.0050.368
standardize_se0.0670.0020.075
update_env_idfs_from_mae0.0030.0000.003
update_idfs_synonyms0.0010.0000.001
validate_MAE0.1640.0010.176
validate_SE0.0520.0010.057
validate_identifiers0.0150.0020.019
validate_json0.0010.0000.000
validate_mae_with_schema0.6210.0850.943
validate_se_assay_name0.0070.0010.010