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This page was generated on 2024-05-13 11:32:04 -0400 (Mon, 13 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4378
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Package 762/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRutils 1.3.0  (landing page)
Arkadiusz Gladki
Snapshot Date: 2024-05-11 09:00:03 -0400 (Sat, 11 May 2024)
git_url: https://git.bioconductor.org/packages/gDRutils
git_branch: devel
git_last_commit: 29cb67a
git_last_commit_date: 2024-04-30 11:49:57 -0400 (Tue, 30 Apr 2024)
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:
- 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: 1.3.0
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_1.3.0.tar.gz
StartedAt: 2024-05-12 14:12:52 -0400 (Sun, 12 May 2024)
EndedAt: 2024-05-12 14:16:40 -0400 (Sun, 12 May 2024)
EllapsedTime: 227.8 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_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/gDRutils.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 ‘1.3.0’
* 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-3.20-bioc-mac-arm64/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
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 
 44.115   1.342  45.504 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.6810.0400.725
SE_metadata0.0610.0050.067
addClass0.0030.0000.004
aggregate_assay1.2950.0291.329
apply_bumpy_function1.5720.0751.651
assert_choices0.0010.0010.000
average_biological_replicates_dt0.3190.0150.335
cap_xc500.0000.0010.001
convert_colData_to_json0.0530.0010.053
convert_combo_data_to_dt0.2580.0100.269
convert_combo_field_to_assay0.0020.0010.002
convert_mae_assay_to_dt0.0650.0030.069
convert_mae_to_json0.0230.0010.024
convert_metadata_to_json0.0100.0000.009
convert_rowData_to_json0.0030.0000.003
convert_se_assay_to_dt0.0620.0040.066
convert_se_to_json0.0150.0010.016
demote_fields0.4400.0070.450
df_to_bm_assay0.9390.0110.952
dot-set_invalid_fit_params0.0000.0010.001
extend_normalization_type_name0.0000.0000.001
fit_curves0.2340.0250.259
flatten0.0100.0000.011
gen_synthetic_data0.0050.0000.006
geometric_mean0.0000.0000.001
get_MAE_identifiers0.0130.0020.015
get_assay_names000
get_combo_assay_names0.0010.0000.001
get_combo_base_assay_names0.0010.0000.000
get_combo_col_settings0.0020.0010.002
get_combo_excess_field_names0.0020.0000.002
get_combo_score_assay_names0.0010.0010.001
get_combo_score_field_names0.0010.0000.001
get_default_identifiers0.0000.0010.001
get_duplicated_rows0.0020.0000.003
get_env_assay_names0.0010.0000.001
get_expect_one_identifiers0.0000.0000.001
get_experiment_groups000
get_identifiers_dt0.0070.0030.010
get_idfs_synonyms000
get_iso_colors0.0020.0000.002
get_non_empty_assays0.0610.0010.062
get_required_identifiers0.0010.0000.001
get_synthetic_data0.0160.0010.016
get_testdata0.0900.0180.107
get_testdata_codilution0.0750.0050.082
get_testdata_combo0.2170.0240.243
headers0.0120.0050.017
identifiers0.0000.0000.001
identify_unique_se_metadata_fields0.0120.0010.013
is_any_exp_empty0.0490.0010.050
is_exp_empty0.0530.0020.053
is_mae_empty0.0830.0040.086
logisticFit0.0270.0000.027
loop000
mcolData0.0210.0010.022
merge_SE1.6650.0221.697
merge_assay0.3370.0060.356
merge_metadata0.0140.0010.015
modifyData0.1060.0010.108
mrowData0.0200.0010.022
predict_conc_from_efficacy0.0000.0000.001
predict_efficacy_from_conc000
prettify_flat_metrics0.0200.0010.020
promote_fields0.2070.0030.210
refine_coldata0.0160.0010.018
refine_rowdata0.0610.0010.063
rename_DFrame0.0300.0020.031
rename_bumpy0.0390.0010.041
set_constant_fit_params0.0000.0000.001
shorten_normalization_type_name000
split_SE_components0.0550.0010.056
standardize_mae0.1550.0030.158
standardize_se0.0410.0010.041
update_env_idfs_from_mae0.0010.0010.002
update_idfs_synonyms000
validate_MAE0.0800.0010.082
validate_SE0.0330.0010.035
validate_identifiers0.0070.0010.007
validate_json0.0000.0000.001
validate_mae_with_schema0.4750.0360.478
validate_se_assay_name0.0150.0010.016