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This page was generated on 2024-07-24 11:38 -0400 (Wed, 24 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4688
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4284
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4455
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4404
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 769/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRutils 1.3.6  (landing page)
Arkadiusz Gladki
Snapshot Date: 2024-07-23 14:00 -0400 (Tue, 23 Jul 2024)
git_url: https://git.bioconductor.org/packages/gDRutils
git_branch: devel
git_last_commit: 03cb476
git_last_commit_date: 2024-07-18 04:29:31 -0400 (Thu, 18 Jul 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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 / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for gDRutils on nebbiolo2

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: 1.3.6
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings gDRutils_1.3.6.tar.gz
StartedAt: 2024-07-23 23:40:42 -0400 (Tue, 23 Jul 2024)
EndedAt: 2024-07-23 23:44:20 -0400 (Tue, 23 Jul 2024)
EllapsedTime: 218.4 seconds
RetCode: 0
Status:   OK  
CheckDir: gDRutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings gDRutils_1.3.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/gDRutils.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘gDRutils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRutils’ version ‘1.3.6’
* 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

gDRutils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL gDRutils
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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: x86_64-pc-linux-gnu

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 621 ]
> 
> proc.time()
   user  system elapsed 
 43.708   1.416  44.546 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.4940.0240.518
SE_metadata0.1060.0010.107
addClass0.0020.0000.003
aggregate_assay0.9560.0240.975
apply_bumpy_function1.3110.0871.398
assert_choices0.0010.0010.000
average_biological_replicates_dt0.2530.0110.265
capVals0.0700.0010.071
cap_xc500.0000.0000.001
convert_colData_to_json0.0440.0030.048
convert_combo_data_to_dt0.2380.0090.231
convert_combo_field_to_assay0.0020.0000.002
convert_mae_assay_to_dt0.0580.0000.057
convert_mae_to_json0.0160.0000.016
convert_metadata_to_json0.0090.0000.008
convert_rowData_to_json0.0020.0000.002
convert_se_assay_to_custom_dt0.3930.0120.392
convert_se_assay_to_dt0.0550.0000.055
convert_se_to_json0.0100.0030.013
define_matrix_grid_positions0.0490.0000.048
demote_fields0.9870.0801.037
df_to_bm_assay0.1140.0000.115
dot-set_invalid_fit_params0.0000.0000.001
extend_normalization_type_name000
fit_curves0.1240.0120.135
flatten0.0070.0000.007
gen_synthetic_data0.0010.0040.005
geometric_mean0.0010.0000.000
get_MAE_identifiers0.0080.0000.007
get_additional_variables0.1570.0040.160
get_assay_names000
get_combo_assay_names0.0010.0000.000
get_combo_base_assay_names0.0010.0000.001
get_combo_excess_field_names0.0020.0000.001
get_combo_score_assay_names0.0010.0000.001
get_combo_score_field_names0.0010.0000.000
get_default_identifiers000
get_duplicated_rows0.0020.0000.003
get_env_assay_names000
get_expect_one_identifiers000
get_experiment_groups000
get_identifiers_dt0.0020.0040.006
get_idfs_synonyms000
get_isobologram_columns0.0340.0000.035
get_non_empty_assays0.0500.0000.048
get_required_identifiers0.0010.0000.000
get_settings_from_json0.0010.0000.001
get_supported_experiments0.0010.0000.000
get_synthetic_data0.0160.0000.010
get_testdata0.0990.0000.084
get_testdata_codilution0.0860.0040.076
get_testdata_combo0.2040.0200.206
has_single_codrug_data0.0610.0080.068
has_valid_codrug_data0.0680.0000.067
headers0.0110.0000.010
identifiers000
identify_unique_se_metadata_fields0.0070.0000.007
is_any_exp_empty0.0410.0040.041
is_combo_data0.1260.0040.125
is_exp_empty0.0360.0040.040
is_mae_empty0.0700.0040.069
logisticFit0.0250.0000.021
loop000
mcolData0.0130.0000.014
merge_SE1.5040.0121.441
merge_assay0.3190.0040.316
merge_metadata0.0080.0000.008
modifyData0.0770.0000.078
mrowData0.0130.0000.013
predict_conc_from_efficacy0.0010.0000.000
predict_efficacy_from_conc0.0000.0000.001
prettify_flat_metrics0.0180.0000.018
promote_fields0.1890.0000.174
refine_coldata0.010.000.01
refine_rowdata0.0440.0000.043
remove_codrug_data0.0290.0000.030
rename_DFrame0.0060.0040.010
rename_bumpy0.0300.0000.029
round_concentration000
set_constant_fit_params000
shorten_normalization_type_name000
split_SE_components0.0530.0000.053
standardize_mae0.1330.0120.145
standardize_se0.0310.0000.030
update_env_idfs_from_mae0.0010.0000.001
update_idfs_synonyms0.0000.0000.001
validate_MAE0.0620.0080.070
validate_SE0.0240.0000.024
validate_identifiers0.0060.0000.007
validate_json000
validate_mae_with_schema0.3560.0200.367
validate_se_assay_name0.0060.0000.006