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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 765/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRutils 1.3.1  (landing page)
Arkadiusz Gladki
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/gDRutils
git_branch: devel
git_last_commit: 342ee40
git_last_commit_date: 2024-05-29 06:18:27 -0400 (Wed, 29 May 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows 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: 1.3.1
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_1.3.1.tar.gz
StartedAt: 2024-06-10 03:52:30 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 04:00:19 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 469.5 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_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/gDRutils.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 ‘1.3.1’
* 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 ... OK
* 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: OK


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 Patched (2024-04-24 r86482) -- "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 624 ]
> 
> proc.time()
   user  system elapsed 
 82.890   3.435 106.162 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply1.2240.0831.393
SE_metadata0.0760.0080.091
addClass0.0040.0010.004
aggregate_assay1.9160.0782.206
apply_bumpy_function3.7920.2594.544
assert_choices0.0010.0010.001
average_biological_replicates_dt0.7080.0230.734
capVals0.1550.0110.168
cap_xc500.0010.0010.001
convert_colData_to_json0.1500.0020.153
convert_combo_data_to_dt0.5030.0250.529
convert_combo_field_to_assay0.0030.0010.004
convert_mae_assay_to_dt0.1390.0090.151
convert_mae_to_json0.0340.0010.038
convert_metadata_to_json0.0200.0010.021
convert_rowData_to_json0.0060.0010.007
convert_se_assay_to_custom_dt0.9550.0891.154
convert_se_assay_to_dt0.1440.0080.164
convert_se_to_json0.0310.0010.033
define_matrix_grid_positions0.1220.0040.134
demote_fields1.5810.0361.913
df_to_bm_assay0.3080.0030.389
dot-set_invalid_fit_params0.0010.0000.001
extend_normalization_type_name0.0000.0000.004
fit_curves0.3070.0310.420
flatten0.0170.0010.021
gen_synthetic_data0.0160.0030.027
geometric_mean0.0000.0000.001
get_MAE_identifiers0.0150.0040.022
get_additional_variables0.4000.0090.487
get_assay_names0.0000.0010.001
get_combo_assay_names0.0020.0010.002
get_combo_base_assay_names0.0010.0010.004
get_combo_col_settings0.0050.0000.006
get_combo_excess_field_names0.0040.0010.007
get_combo_score_assay_names0.0020.0010.002
get_combo_score_field_names0.0020.0000.002
get_default_identifiers0.0010.0010.003
get_duplicated_rows0.0040.0010.006
get_env_assay_names0.0000.0010.001
get_expect_one_identifiers0.0010.0010.002
get_experiment_groups0.0000.0000.001
get_identifiers_dt0.0110.0080.023
get_idfs_synonyms0.0010.0000.001
get_iso_colors0.0040.0010.005
get_isobologram_columns0.0830.0040.104
get_non_empty_assays0.1140.0040.148
get_required_identifiers0.0000.0000.001
get_settings_from_json0.0020.0010.002
get_supported_experiments0.0000.0000.005
get_synthetic_data0.0220.0020.031
get_testdata0.2100.0630.346
get_testdata_codilution0.2200.0160.278
get_testdata_combo0.4140.0520.584
has_single_codrug_data0.1870.0020.230
has_valid_codrug_data0.1830.0030.227
headers0.0270.0160.057
identifiers0.0010.0000.003
identify_unique_se_metadata_fields0.0150.0020.020
is_any_exp_empty0.1180.0020.144
is_combo_data0.2240.0250.315
is_exp_empty0.1040.0020.127
is_mae_empty0.1050.0020.129
logisticFit0.0610.0010.072
loop0.0010.0000.000
mcolData0.0310.0030.043
merge_SE3.9320.0404.756
merge_assay0.8150.0241.018
merge_metadata0.0140.0020.021
modifyData0.2430.0120.299
mrowData0.0300.0020.036
predict_conc_from_efficacy0.0000.0000.001
predict_efficacy_from_conc0.0010.0000.001
prettify_flat_metrics0.0500.0020.060
promote_fields0.4290.0040.488
refine_coldata0.0210.0020.027
refine_rowdata0.1090.0030.134
remove_codrug_data0.0820.0020.100
rename_DFrame0.0210.0020.027
rename_bumpy0.0720.0020.091
round_concentration0.0010.0000.001
set_constant_fit_params0.0010.0010.001
shorten_normalization_type_name000
split_SE_components0.1420.0040.174
standardize_mae0.3850.0080.478
standardize_se0.0870.0030.104
update_env_idfs_from_mae0.0030.0010.004
update_idfs_synonyms0.0010.0010.001
validate_MAE0.2100.0030.266
validate_SE0.0610.0010.076
validate_identifiers0.0170.0030.026
validate_json0.0010.0000.000
validate_mae_with_schema0.6590.0941.048
validate_se_assay_name0.0100.0010.014