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This page was generated on 2024-10-18 20:38 -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 nebbiolo1

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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings gDRutils_1.2.0.tar.gz
StartedAt: 2024-10-17 00:39:10 -0400 (Thu, 17 Oct 2024)
EndedAt: 2024-10-17 00:42:36 -0400 (Thu, 17 Oct 2024)
EllapsedTime: 206.5 seconds
RetCode: 0
Status:   OK  
CheckDir: gDRutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings gDRutils_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-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 22.04.5 LTS
* using session charset: UTF-8
* 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 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 ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/gDRutils.Rcheck/00check.log’
for details.


Installation output

gDRutils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL gDRutils
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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 496 ]
> 
> proc.time()
   user  system elapsed 
 39.683   1.955  41.120 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.4920.0190.511
SE_metadata0.0380.0010.040
addClass0.0020.0000.002
aggregate_assay0.9950.0441.034
apply_bumpy_function1.3190.0961.415
assert_choices0.0010.0000.001
average_biological_replicates_dt0.2540.0040.258
cap_xc50000
convert_colData_to_json0.0460.0000.046
convert_combo_data_to_dt0.2210.0120.217
convert_combo_field_to_assay0.0000.0020.002
convert_mae_assay_to_dt0.0560.0010.057
convert_mae_to_json0.0160.0000.016
convert_metadata_to_json0.0080.0000.009
convert_rowData_to_json0.0030.0000.003
convert_se_assay_to_dt0.0500.0040.054
convert_se_to_json0.0120.0000.012
demote_fields0.4040.0000.377
df_to_bm_assay0.710.000.71
dot-set_invalid_fit_params000
extend_normalization_type_name0.0000.0010.000
fit_curves0.1770.0100.187
flatten0.0090.0000.009
gen_synthetic_data0.0050.0000.006
geometric_mean0.0000.0000.001
get_MAE_identifiers0.0080.0000.009
get_assay_names0.0000.0000.001
get_combo_assay_names0.0010.0000.001
get_combo_base_assay_names0.0010.0000.001
get_combo_col_settings0.0020.0000.002
get_combo_excess_field_names0.0010.0000.002
get_combo_score_assay_names0.0000.0010.001
get_combo_score_field_names0.0000.0010.000
get_default_identifiers0.0000.0010.001
get_duplicated_rows0.0020.0000.002
get_env_assay_names000
get_expect_one_identifiers000
get_experiment_groups000
get_identifiers_dt0.0010.0060.007
get_idfs_synonyms000
get_iso_colors0.0020.0000.001
get_non_empty_assays0.0440.0040.047
get_required_identifiers0.0010.0000.000
get_synthetic_data0.0130.0000.011
get_testdata0.0670.0280.089
get_testdata_codilution0.0740.0040.073
get_testdata_combo0.1720.0240.185
headers0.0090.0080.017
identifiers0.0010.0000.000
identify_unique_se_metadata_fields0.0040.0030.007
is_any_exp_empty0.0420.0000.042
is_exp_empty0.0590.0000.042
is_mae_empty0.0780.0000.061
logisticFit0.0310.0000.020
loop0.0000.0000.001
mcolData0.0130.0000.013
merge_SE1.5130.0001.433
merge_assay0.3070.0000.292
merge_metadata0.0080.0000.008
modifyData0.0780.0000.079
mrowData0.0160.0000.015
predict_conc_from_efficacy0.0010.0000.000
predict_efficacy_from_conc0.0010.0000.000
prettify_flat_metrics0.0190.0000.019
promote_fields0.1950.0000.181
refine_coldata0.0070.0030.010
refine_rowdata0.0430.0040.047
rename_DFrame0.0110.0000.011
rename_bumpy0.0450.0000.044
set_constant_fit_params0.0010.0000.000
shorten_normalization_type_name000
split_SE_components0.0510.0000.052
standardize_mae0.1420.0000.142
standardize_se0.0320.0000.033
update_env_idfs_from_mae0.0010.0000.001
update_idfs_synonyms0.0000.0000.001
validate_MAE0.0730.0000.073
validate_SE0.0290.0000.028
validate_identifiers0.0030.0040.007
validate_json000
validate_mae_with_schema0.4460.0080.418
validate_se_assay_name0.0080.0000.008