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This page was generated on 2024-10-18 20:42 -0400 (Fri, 18 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4500
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4530
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4480
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: 2024-10-16 14:00 -0400 (Wed, 16 Oct 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 kjohnson1

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: 2024-10-17 22:24:00 -0400 (Thu, 17 Oct 2024)
EndedAt: 2024-10-17 22:27:54 -0400 (Thu, 17 Oct 2024)
EllapsedTime: 233.6 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: aarch64-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 Ventura 13.6.6
* 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-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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 
 44.825   2.049  45.826 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.6640.0540.756
SE_metadata0.0660.0060.078
addClass0.0030.0000.004
aggregate_assay1.3230.0651.491
apply_bumpy_function1.6690.1041.896
assert_choices0.0010.0000.001
average_biological_replicates_dt0.3300.0260.367
cap_xc500.0010.0010.001
convert_colData_to_json0.0550.0040.060
convert_combo_data_to_dt0.2790.0170.304
convert_combo_field_to_assay0.0020.0000.002
convert_mae_assay_to_dt0.0750.0060.077
convert_mae_to_json0.0250.0030.024
convert_metadata_to_json0.0090.0010.010
convert_rowData_to_json0.0030.0010.003
convert_se_assay_to_dt0.0630.0050.065
convert_se_to_json0.0150.0010.018
demote_fields0.5730.0260.576
df_to_bm_assay0.9830.0230.937
dot-set_invalid_fit_params0.0010.0000.001
extend_normalization_type_name0.0000.0000.001
fit_curves0.2250.0270.268
flatten0.0090.0000.009
gen_synthetic_data0.0040.0010.006
geometric_mean000
get_MAE_identifiers0.0130.0020.019
get_assay_names000
get_combo_assay_names0.0010.0000.002
get_combo_base_assay_names0.0010.0000.001
get_combo_col_settings0.0030.0000.007
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_identifiers0.0000.0000.001
get_duplicated_rows0.0020.0000.003
get_env_assay_names0.0000.0000.001
get_expect_one_identifiers0.0000.0000.001
get_experiment_groups0.0000.0000.001
get_identifiers_dt0.0070.0040.011
get_idfs_synonyms0.0010.0000.001
get_iso_colors0.0010.0010.002
get_non_empty_assays0.0600.0020.057
get_required_identifiers0.0010.0000.000
get_synthetic_data0.0250.0020.016
get_testdata0.1670.0280.110
get_testdata_codilution0.1260.0130.090
get_testdata_combo0.3670.0470.256
headers0.0240.0060.018
identifiers0.0010.0000.001
identify_unique_se_metadata_fields0.0200.0020.014
is_any_exp_empty0.0920.0040.055
is_exp_empty0.0880.0080.055
is_mae_empty0.1180.0130.085
logisticFit0.0260.0020.024
loop0.0000.0000.001
mcolData0.0180.0020.020
merge_SE2.2500.1111.694
merge_assay0.4900.0210.355
merge_metadata0.0130.0010.014
modifyData0.0930.0010.096
mrowData0.0230.0010.026
predict_conc_from_efficacy000
predict_efficacy_from_conc0.0010.0000.001
prettify_flat_metrics0.0230.0000.024
promote_fields0.3280.0170.224
refine_coldata0.0320.0030.020
refine_rowdata0.0750.0030.065
rename_DFrame0.0320.0030.034
rename_bumpy0.0390.0010.042
set_constant_fit_params000
shorten_normalization_type_name0.0010.0000.000
split_SE_components0.0510.0010.053
standardize_mae0.1500.0030.154
standardize_se0.0380.0020.042
update_env_idfs_from_mae0.0010.0000.001
update_idfs_synonyms0.0010.0000.000
validate_MAE0.0700.0020.075
validate_SE0.0220.0010.023
validate_identifiers0.0070.0010.008
validate_json000
validate_mae_with_schema0.4470.0760.525
validate_se_assay_name0.0140.0020.016