Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-06-04 11:35:47 -0400 (Tue, 04 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4487
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4518
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: 2024-06-02 14:00:17 -0400 (Sun, 02 Jun 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
palomino3Windows 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


CHECK results for gDRutils on palomino3

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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gDRutils.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings gDRutils_1.2.0.tar.gz
StartedAt: 2024-06-03 01:42:32 -0400 (Mon, 03 Jun 2024)
EndedAt: 2024-06-03 01:46:38 -0400 (Mon, 03 Jun 2024)
EllapsedTime: 245.5 seconds
RetCode: 0
Status:   OK  
CheckDir: gDRutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gDRutils.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings gDRutils_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/gDRutils.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'gDRutils/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gDRutils' version '1.2.0'
* 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 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
  'F:/biocbuild/bbs-3.19-bioc/meat/gDRutils.Rcheck/00check.log'
for details.


Installation output

gDRutils.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL gDRutils
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
  48.31    1.70   62.32 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.530.070.59
SE_metadata0.150.010.17
addClass000
aggregate_assay1.140.051.19
apply_bumpy_function1.500.171.67
assert_choices000
average_biological_replicates_dt0.310.030.36
cap_xc50000
convert_colData_to_json0.060.000.06
convert_combo_data_to_dt0.370.000.38
convert_combo_field_to_assay000
convert_mae_assay_to_dt0.100.000.09
convert_mae_to_json0.010.000.02
convert_metadata_to_json0.010.000.02
convert_rowData_to_json000
convert_se_assay_to_dt0.100.000.09
convert_se_to_json0.030.000.03
demote_fields0.980.031.02
df_to_bm_assay0.130.000.12
dot-set_invalid_fit_params000
extend_normalization_type_name000
fit_curves0.170.100.27
flatten000
gen_synthetic_data0.010.000.02
geometric_mean000
get_MAE_identifiers0.020.000.01
get_assay_names000
get_combo_assay_names0.010.000.02
get_combo_base_assay_names000
get_combo_col_settings000
get_combo_excess_field_names000
get_combo_score_assay_names000
get_combo_score_field_names000
get_default_identifiers000
get_duplicated_rows000
get_env_assay_names000
get_expect_one_identifiers000
get_experiment_groups000
get_identifiers_dt0.010.000.01
get_idfs_synonyms0.020.000.02
get_iso_colors000
get_non_empty_assays0.060.000.06
get_required_identifiers000
get_synthetic_data0.020.000.02
get_testdata0.150.000.15
get_testdata_codilution0.130.000.14
get_testdata_combo0.200.010.25
headers0.000.020.02
identifiers000
identify_unique_se_metadata_fields0.020.000.01
is_any_exp_empty0.050.000.05
is_exp_empty0.040.000.05
is_mae_empty0.050.000.04
logisticFit0.030.000.04
loop000
mcolData0.020.000.01
merge_SE1.700.061.78
merge_assay0.440.000.44
merge_metadata0.000.020.02
modifyData0.230.000.23
mrowData0.010.000.01
predict_conc_from_efficacy000
predict_efficacy_from_conc000
prettify_flat_metrics0.050.000.05
promote_fields0.250.000.25
refine_coldata0.030.000.03
refine_rowdata0.060.000.06
rename_DFrame0.020.000.02
rename_bumpy0.050.010.06
set_constant_fit_params000
shorten_normalization_type_name000
split_SE_components0.100.000.11
standardize_mae0.150.000.14
standardize_se0.040.000.05
update_env_idfs_from_mae000
update_idfs_synonyms000
validate_MAE0.100.000.09
validate_SE0.030.020.05
validate_identifiers0.010.000.01
validate_json000
validate_mae_with_schema0.390.092.03
validate_se_assay_name0.020.000.02