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This page was generated on 2024-06-04 11:36:28 -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 lconway

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: /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_1.2.0.tar.gz
StartedAt: 2024-06-03 03:54:17 -0400 (Mon, 03 Jun 2024)
EndedAt: 2024-06-03 03:58:00 -0400 (Mon, 03 Jun 2024)
EllapsedTime: 222.7 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/gDRutils.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 12.7.1
* 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 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 ... 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/gDRutils.Rcheck/00check.log’
for details.


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 (2024-04-24) -- "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 496 ]
> 
> proc.time()
   user  system elapsed 
 45.549   1.543  47.150 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.6370.0500.694
SE_metadata0.0500.0060.056
addClass0.0020.0000.004
aggregate_assay1.1940.0321.229
apply_bumpy_function1.6540.0861.744
assert_choices000
average_biological_replicates_dt0.3370.0160.355
cap_xc500.0010.0010.001
convert_colData_to_json0.0710.0010.072
convert_combo_data_to_dt0.2520.0090.261
convert_combo_field_to_assay0.0020.0000.002
convert_mae_assay_to_dt0.0590.0030.062
convert_mae_to_json0.0170.0010.018
convert_metadata_to_json0.0080.0000.008
convert_rowData_to_json0.0030.0010.003
convert_se_assay_to_dt0.0670.0030.070
convert_se_to_json0.0210.0010.022
demote_fields0.4060.0080.415
df_to_bm_assay0.7480.0190.769
dot-set_invalid_fit_params0.0000.0000.001
extend_normalization_type_name0.0010.0000.000
fit_curves0.2000.0230.224
flatten0.0080.0000.008
gen_synthetic_data0.0040.0000.006
geometric_mean0.0000.0000.001
get_MAE_identifiers0.0070.0010.007
get_assay_names0.0000.0000.001
get_combo_assay_names0.0010.0000.001
get_combo_base_assay_names0.0010.0000.001
get_combo_col_settings0.0030.0000.003
get_combo_excess_field_names0.0010.0000.002
get_combo_score_assay_names0.0010.0000.001
get_combo_score_field_names0.0010.0000.001
get_default_identifiers0.0010.0010.001
get_duplicated_rows0.0030.0000.003
get_env_assay_names0.0010.0000.000
get_expect_one_identifiers0.0000.0010.001
get_experiment_groups000
get_identifiers_dt0.0060.0040.011
get_idfs_synonyms0.0000.0000.001
get_iso_colors0.0020.0000.001
get_non_empty_assays0.0660.0010.067
get_required_identifiers0.0000.0000.001
get_synthetic_data0.0120.0010.014
get_testdata0.0940.0230.117
get_testdata_codilution0.0770.0060.085
get_testdata_combo0.2040.0290.238
headers0.0140.0050.018
identifiers000
identify_unique_se_metadata_fields0.0080.0010.009
is_any_exp_empty0.0590.0030.063
is_exp_empty0.0520.0030.055
is_mae_empty0.0840.0050.090
logisticFit0.0300.0010.031
loop0.0010.0000.000
mcolData0.0130.0010.014
merge_SE1.5930.0231.619
merge_assay0.2800.0030.283
merge_metadata0.0080.0010.009
modifyData0.1050.0010.107
mrowData0.0190.0010.020
predict_conc_from_efficacy0.0010.0000.000
predict_efficacy_from_conc0.0010.0010.000
prettify_flat_metrics0.0250.0010.026
promote_fields0.2100.0020.212
refine_coldata0.0130.0020.015
refine_rowdata0.0610.0030.063
rename_DFrame0.0360.0020.039
rename_bumpy0.0290.0010.030
set_constant_fit_params0.0010.0000.001
shorten_normalization_type_name0.0010.0000.000
split_SE_components0.0470.0010.048
standardize_mae0.1380.0020.139
standardize_se0.0270.0010.028
update_env_idfs_from_mae0.0000.0000.001
update_idfs_synonyms0.0000.0000.001
validate_MAE0.0780.0010.080
validate_SE0.0350.0020.036
validate_identifiers0.0070.0010.007
validate_json000
validate_mae_with_schema0.4070.0590.489
validate_se_assay_name0.0090.0000.010