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This page was generated on 2024-06-25 17:42 -0400 (Tue, 25 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
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: 2024-06-23 14:00 -0400 (Sun, 23 Jun 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
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 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: 2024-06-24 04:50:28 -0400 (Mon, 24 Jun 2024)
EndedAt: 2024-06-24 04:58:33 -0400 (Mon, 24 Jun 2024)
EllapsedTime: 484.5 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 4.4.0 (2024-04-24)
* 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 12.7.4
* 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 4.4.0 (2024-04-24) -- "Puppy Cup"
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 
 75.236   3.326 100.727 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply1.2600.0921.466
SE_metadata0.0780.0100.091
addClass0.0030.0010.005
aggregate_assay1.9860.0782.295
apply_bumpy_function3.9250.2684.719
assert_choices0.0000.0000.002
average_biological_replicates_dt0.7410.0260.839
cap_xc500.0010.0000.001
convert_colData_to_json0.1450.0030.165
convert_combo_data_to_dt0.5520.0290.654
convert_combo_field_to_assay0.0030.0000.004
convert_mae_assay_to_dt0.1470.0080.168
convert_mae_to_json0.0320.0020.036
convert_metadata_to_json0.0210.0010.025
convert_rowData_to_json0.0060.0010.006
convert_se_assay_to_dt0.1420.0080.174
convert_se_to_json0.0320.0020.037
demote_fields0.9220.0111.048
df_to_bm_assay0.9950.0181.125
dot-set_invalid_fit_params0.0000.0010.002
extend_normalization_type_name0.0010.0010.001
fit_curves0.4300.0370.530
flatten0.0200.0020.023
gen_synthetic_data0.0140.0020.017
geometric_mean0.0010.0000.001
get_MAE_identifiers0.0140.0030.017
get_assay_names0.0010.0010.001
get_combo_assay_names0.0010.0000.003
get_combo_base_assay_names0.0020.0000.003
get_combo_col_settings0.0050.0010.006
get_combo_excess_field_names0.0040.0000.006
get_combo_score_assay_names0.0020.0000.002
get_combo_score_field_names0.0010.0000.002
get_default_identifiers0.0010.0020.002
get_duplicated_rows0.0040.0010.005
get_env_assay_names0.0000.0000.001
get_expect_one_identifiers0.0010.0010.002
get_experiment_groups000
get_identifiers_dt0.0100.0060.018
get_idfs_synonyms0.0010.0010.001
get_iso_colors0.0030.0000.004
get_non_empty_assays0.1170.0020.131
get_required_identifiers0.0000.0010.002
get_synthetic_data0.0200.0020.023
get_testdata0.1980.0570.289
get_testdata_codilution0.1900.0150.237
get_testdata_combo0.4100.0550.541
headers0.0290.0170.051
identifiers0.0000.0010.001
identify_unique_se_metadata_fields0.0130.0010.016
is_any_exp_empty0.1070.0030.123
is_exp_empty0.1070.0050.126
is_mae_empty0.1430.0060.166
logisticFit0.0620.0020.069
loop0.0000.0010.001
mcolData0.0320.0020.040
merge_SE3.9210.0534.453
merge_assay0.8010.0150.880
merge_metadata0.0150.0020.035
modifyData0.2210.0030.234
mrowData0.0320.0040.040
predict_conc_from_efficacy0.0000.0010.002
predict_efficacy_from_conc0.0000.0010.001
prettify_flat_metrics0.0480.0010.051
promote_fields0.4510.0080.519
refine_coldata0.0190.0020.022
refine_rowdata0.1060.0040.135
rename_DFrame0.0440.0030.056
rename_bumpy0.0720.0030.087
set_constant_fit_params0.0010.0010.002
shorten_normalization_type_name0.0010.0010.001
split_SE_components0.1350.0040.154
standardize_mae0.3650.0060.410
standardize_se0.0740.0020.083
update_env_idfs_from_mae0.0030.0010.004
update_idfs_synonyms0.0000.0010.001
validate_MAE0.1830.0020.206
validate_SE0.0640.0030.076
validate_identifiers0.0160.0020.020
validate_json000
validate_mae_with_schema0.6470.0622.198
validate_se_assay_name0.0100.0010.011