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This page was generated on 2024-08-06 17:41 -0400 (Tue, 06 Aug 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4756
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4490
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4519
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4468
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 791/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRutils 1.2.0  (landing page)
Arkadiusz Gladki
Snapshot Date: 2024-08-04 14:00 -0400 (Sun, 04 Aug 2024)
git_url: https://git.bioconductor.org/packages/gDRutils
git_branch: RELEASE_3_19
git_last_commit: d1f7215
git_last_commit_date: 2024-04-30 11:49:57 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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 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: 1.2.0
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_1.2.0.tar.gz
StartedAt: 2024-08-05 05:17:29 -0400 (Mon, 05 Aug 2024)
EndedAt: 2024-08-05 05:25:31 -0400 (Mon, 05 Aug 2024)
EllapsedTime: 481.9 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/gDRutils.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gDRutils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRutils’ version ‘1.2.0’
* 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 ... NOTE
checkRd: (-1) split_SE_components.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) split_SE_components.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) split_SE_components.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) split_SE_components.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) split_SE_components.Rd:35: Lost braces in \itemize; meant \describe ?
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/gDRutils.Rcheck/00check.log’
for details.


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 (2024-06-14) -- "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 496 ]
> 
> proc.time()
   user  system elapsed 
 70.322   3.116  96.190 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply1.1960.0731.469
SE_metadata0.0740.0070.090
addClass0.0030.0000.004
aggregate_assay1.8660.0872.313
apply_bumpy_function3.7620.2494.801
assert_choices0.0000.0000.001
average_biological_replicates_dt0.7270.0360.899
cap_xc500.0010.0010.001
convert_colData_to_json0.1340.0010.158
convert_combo_data_to_dt0.5200.0230.633
convert_combo_field_to_assay0.0030.0010.004
convert_mae_assay_to_dt0.1430.0090.172
convert_mae_to_json0.0350.0020.040
convert_metadata_to_json0.0210.0010.026
convert_rowData_to_json0.0060.0010.008
convert_se_assay_to_dt0.1420.0090.182
convert_se_to_json0.0310.0020.041
demote_fields1.5730.0331.844
df_to_bm_assay0.2810.0020.325
dot-set_invalid_fit_params0.0000.0010.001
extend_normalization_type_name0.0000.0010.001
fit_curves0.4250.0340.509
flatten0.0200.0020.026
gen_synthetic_data0.0150.0040.021
geometric_mean0.0000.0000.001
get_MAE_identifiers0.0140.0030.019
get_assay_names0.0000.0000.001
get_combo_assay_names0.0020.0000.001
get_combo_base_assay_names0.0020.0010.003
get_combo_col_settings0.0050.0010.007
get_combo_excess_field_names0.0040.0000.006
get_combo_score_assay_names0.0020.0010.002
get_combo_score_field_names0.0020.0010.002
get_default_identifiers0.0010.0010.003
get_duplicated_rows0.0040.0010.004
get_env_assay_names0.0000.0000.001
get_expect_one_identifiers0.0010.0010.002
get_experiment_groups0.0000.0000.001
get_identifiers_dt0.0110.0070.022
get_idfs_synonyms0.0000.0010.001
get_iso_colors0.0040.0010.005
get_non_empty_assays0.1120.0020.134
get_required_identifiers0.0000.0010.001
get_synthetic_data0.0210.0020.026
get_testdata0.1900.0570.289
get_testdata_codilution0.1800.0150.224
get_testdata_combo0.4020.0570.540
headers0.0270.0180.048
identifiers0.0000.0010.001
identify_unique_se_metadata_fields0.0150.0010.020
is_any_exp_empty0.1310.0060.149
is_exp_empty0.0990.0020.110
is_mae_empty0.1000.0020.112
logisticFit0.0590.0010.066
loop0.0000.0000.001
mcolData0.0300.0020.036
merge_SE3.6110.0404.103
merge_assay0.7550.0130.865
merge_metadata0.0150.0030.019
modifyData0.2180.0060.253
mrowData0.0310.0030.040
predict_conc_from_efficacy0.0000.0010.001
predict_efficacy_from_conc0.0010.0010.003
prettify_flat_metrics0.0500.0010.060
promote_fields0.4490.0130.526
refine_coldata0.0210.0030.027
refine_rowdata0.1040.0040.126
rename_DFrame0.0210.0020.027
rename_bumpy0.0690.0020.084
set_constant_fit_params0.0010.0010.002
shorten_normalization_type_name0.0000.0000.001
split_SE_components0.1360.0030.158
standardize_mae0.3440.0050.394
standardize_se0.0730.0030.084
update_env_idfs_from_mae0.0030.0000.005
update_idfs_synonyms0.0010.0000.001
validate_MAE0.1760.0030.212
validate_SE0.0620.0020.077
validate_identifiers0.0150.0020.019
validate_json0.0010.0000.000
validate_mae_with_schema0.6350.0582.317
validate_se_assay_name0.0110.0010.015