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This page was generated on 2024-07-16 11:39 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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 766/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRutils 1.3.5  (landing page)
Arkadiusz Gladki
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/gDRutils
git_branch: devel
git_last_commit: 0dd6524
git_last_commit_date: 2024-07-15 09:28:37 -0400 (Mon, 15 Jul 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  YES
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  YES
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


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: 1.3.5
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_1.3.5.tar.gz
StartedAt: 2024-07-15 23:01:49 -0400 (Mon, 15 Jul 2024)
EndedAt: 2024-07-15 23:05:22 -0400 (Mon, 15 Jul 2024)
EllapsedTime: 212.4 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_1.3.5.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 ‘1.3.5’
* 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 615 ]
> 
> proc.time()
   user  system elapsed 
 44.601   1.882  45.830 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.4950.0160.511
SE_metadata0.1360.0010.136
addClass0.0020.0000.002
aggregate_assay1.0660.0191.078
apply_bumpy_function1.3820.1201.502
assert_choices000
average_biological_replicates_dt0.2720.0060.278
capVals0.0600.0160.076
cap_xc500.0010.0000.000
convert_colData_to_json0.0500.0000.049
convert_combo_data_to_dt0.2510.0080.244
convert_combo_field_to_assay0.0010.0000.002
convert_mae_assay_to_dt0.0550.0040.059
convert_mae_to_json0.0220.0080.029
convert_metadata_to_json0.010.000.01
convert_rowData_to_json0.0000.0040.003
convert_se_assay_to_custom_dt0.4370.0240.447
convert_se_assay_to_dt0.0580.0040.063
convert_se_to_json0.0140.0000.015
define_matrix_grid_positions0.0600.0000.056
demote_fields1.1700.0881.232
df_to_bm_assay0.1170.0000.117
dot-set_invalid_fit_params000
extend_normalization_type_name0.0010.0000.001
fit_curves0.1330.0000.133
flatten0.0070.0000.007
gen_synthetic_data0.0050.0000.005
geometric_mean0.0010.0000.001
get_MAE_identifiers0.0070.0000.007
get_additional_variables0.1520.0000.152
get_assay_names000
get_combo_assay_names000
get_combo_base_assay_names0.0010.0000.000
get_combo_excess_field_names0.0010.0000.001
get_combo_score_assay_names0.0010.0000.001
get_combo_score_field_names000
get_default_identifiers000
get_duplicated_rows0.0020.0000.002
get_env_assay_names000
get_expect_one_identifiers000
get_experiment_groups000
get_identifiers_dt0.0020.0040.006
get_idfs_synonyms000
get_isobologram_columns0.0260.0040.030
get_non_empty_assays0.0450.0000.044
get_required_identifiers0.0000.0000.001
get_settings_from_json0.0010.0000.001
get_supported_experiments0.0010.0000.001
get_synthetic_data0.010.000.01
get_testdata0.0830.0040.081
get_testdata_codilution0.0770.0000.072
get_testdata_combo0.2060.0090.205
has_single_codrug_data0.0730.0000.073
has_valid_codrug_data0.0710.0000.071
headers0.0100.0000.011
identifiers0.0010.0000.000
identify_unique_se_metadata_fields0.0070.0000.007
is_any_exp_empty0.0430.0000.043
is_combo_data0.1050.0270.127
is_exp_empty0.0410.0040.041
is_mae_empty0.0780.0080.075
logisticFit0.0360.0000.023
loop000
mcolData0.0140.0000.014
merge_SE1.5630.0041.475
merge_assay0.3230.0210.328
merge_metadata0.0080.0000.007
modifyData0.080.000.08
mrowData0.0110.0040.015
predict_conc_from_efficacy000
predict_efficacy_from_conc0.0010.0000.000
prettify_flat_metrics0.0150.0040.020
promote_fields0.1820.0040.180
refine_coldata0.0120.0000.012
refine_rowdata0.0520.0000.052
remove_codrug_data0.0340.0000.034
rename_DFrame0.0110.0000.011
rename_bumpy0.0340.0000.034
round_concentration000
set_constant_fit_params000
shorten_normalization_type_name000
split_SE_components0.0550.0030.058
standardize_mae0.1400.0050.144
standardize_se0.0310.0000.031
update_env_idfs_from_mae0.0010.0000.001
update_idfs_synonyms000
validate_MAE0.0710.0000.071
validate_SE0.0280.0000.028
validate_identifiers0.0070.0000.007
validate_json000
validate_mae_with_schema0.3890.0040.383
validate_se_assay_name0.0080.0000.007