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This page was generated on 2024-05-30 11:35:35 -0400 (Thu, 30 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4753
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4518
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: 2024-05-29 14:00:10 -0400 (Wed, 29 May 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

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: 1.2.0
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: 2024-05-29 20:57:19 -0400 (Wed, 29 May 2024)
EndedAt: 2024-05-29 21:01:30 -0400 (Wed, 29 May 2024)
EllapsedTime: 251.2 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gDRutils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRutils’ version ‘1.2.0’
* 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 
 50.921   2.081  53.610 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.7070.0610.778
SE_metadata0.0460.0050.051
addClass0.0020.0010.003
aggregate_assay1.1990.0421.253
apply_bumpy_function2.0320.1282.195
assert_choices000
average_biological_replicates_dt0.3810.0250.417
cap_xc500.0010.0000.001
convert_colData_to_json0.0760.0020.080
convert_combo_data_to_dt0.3090.0160.328
convert_combo_field_to_assay0.0030.0000.003
convert_mae_assay_to_dt0.0800.0060.091
convert_mae_to_json0.0230.0020.024
convert_metadata_to_json0.0130.0000.013
convert_rowData_to_json0.0040.0000.005
convert_se_assay_to_dt0.0730.0040.078
convert_se_to_json0.0170.0010.017
demote_fields0.5380.0150.564
df_to_bm_assay0.8440.0260.883
dot-set_invalid_fit_params0.0010.0000.000
extend_normalization_type_name0.0010.0000.000
fit_curves0.2360.0340.274
flatten0.0130.0010.014
gen_synthetic_data0.0070.0010.009
geometric_mean0.0000.0000.001
get_MAE_identifiers0.0090.0020.012
get_assay_names0.0000.0010.001
get_combo_assay_names0.0010.0000.001
get_combo_base_assay_names0.0010.0000.002
get_combo_col_settings0.0030.0000.003
get_combo_excess_field_names0.0020.0010.003
get_combo_score_assay_names0.0010.0000.001
get_combo_score_field_names0.0010.0000.001
get_default_identifiers0.0010.0010.001
get_duplicated_rows0.0030.0000.003
get_env_assay_names0.0000.0000.001
get_expect_one_identifiers0.0000.0010.001
get_experiment_groups0.0000.0010.000
get_identifiers_dt0.0070.0040.011
get_idfs_synonyms0.0000.0000.001
get_iso_colors0.0020.0000.003
get_non_empty_assays0.0670.0020.069
get_required_identifiers0.0000.0000.001
get_synthetic_data0.0140.0010.015
get_testdata0.1000.0230.123
get_testdata_codilution0.0930.0080.105
get_testdata_combo0.2130.0270.243
headers0.0140.0080.022
identifiers0.0000.0000.001
identify_unique_se_metadata_fields0.0070.0020.009
is_any_exp_empty0.0660.0020.068
is_exp_empty0.0640.0030.068
is_mae_empty0.0850.0060.092
logisticFit0.0300.0000.031
loop0.0000.0000.001
mcolData0.0210.0010.023
merge_SE1.9960.0462.077
merge_assay0.3960.0070.408
merge_metadata0.0110.0020.012
modifyData0.1320.0030.136
mrowData0.0200.0020.022
predict_conc_from_efficacy0.0010.0000.001
predict_efficacy_from_conc0.0000.0010.000
prettify_flat_metrics0.0230.0000.024
promote_fields0.2700.0040.276
refine_coldata0.0120.0020.014
refine_rowdata0.0610.0020.064
rename_DFrame0.0310.0020.033
rename_bumpy0.0400.0010.042
set_constant_fit_params0.0010.0010.001
shorten_normalization_type_name000
split_SE_components0.0770.0030.083
standardize_mae0.1760.0040.181
standardize_se0.0390.0020.041
update_env_idfs_from_mae0.0020.0000.002
update_idfs_synonyms0.0010.0000.000
validate_MAE0.0890.0020.091
validate_SE0.0280.0010.030
validate_identifiers0.0090.0010.010
validate_json000
validate_mae_with_schema0.4350.0720.530
validate_se_assay_name0.0080.0010.009