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This page was generated on 2024-03-04 11:37:22 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 781/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRutils 1.0.0  (landing page)
Arkadiusz Gladki
Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024)
git_url: https://git.bioconductor.org/packages/gDRutils
git_branch: RELEASE_3_18
git_last_commit: b8a1d96
git_last_commit_date: 2023-10-24 11:49:34 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows 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
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

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: 1.0.0
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_1.0.0.tar.gz
StartedAt: 2024-03-03 20:44:12 -0500 (Sun, 03 Mar 2024)
EndedAt: 2024-03-03 20:48:14 -0500 (Sun, 03 Mar 2024)
EllapsedTime: 242.9 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/gDRutils.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    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 ‘1.0.0’
* 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 R 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 ... 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


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/4.3-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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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 461 ]
> 
> proc.time()
   user  system elapsed 
 51.263   1.937  53.548 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply1.3370.0701.420
SE_metadata0.0350.0050.040
aggregate_assay0.6940.0500.751
apply_bumpy_function1.9300.0992.047
assert_choices0.0000.0000.001
cap_xc50000
convert_combo_data_to_dt0.8780.0460.933
convert_mae_assay_to_dt0.0730.0030.076
convert_mae_to_json0.7660.0220.795
convert_se_assay_to_dt0.0720.0030.076
convert_se_to_json0.0200.0000.021
demote_fields0.3960.0060.407
df_to_bm_assay0.1070.0020.111
dot-convert_colData_to_json0.0030.0000.004
dot-convert_metadata_to_json0.0050.0000.006
dot-convert_rowData_to_json0.0030.0000.004
dot-set_constant_fit_params0.0000.0000.001
dot-set_invalid_fit_params0.0000.0000.001
extend_normalization_type_name0.0000.0000.001
fit_curves0.2390.0390.282
flatten0.0100.0010.011
gen_synthetic_data0.0080.0020.010
get_MAE_identifiers0.0270.0040.032
get_assay_names0.0000.0000.001
get_combo_assay_names0.0010.0000.001
get_combo_base_assay_names0.0010.0000.001
get_combo_col_settings0.0040.0010.005
get_combo_score_assay_names0.0000.0010.001
get_default_identifiers0.0000.0010.001
get_env_assay_names000
get_expect_one_identifiers0.0000.0010.000
get_experiment_groups000
get_identifiers_dt0.0070.0040.012
get_idfs_synonyms0.0000.0010.000
get_iso_colors0.0020.0010.002
get_non_empty_assays0.0660.0020.069
get_required_identifiers0.0000.0000.001
get_synthetic_data0.0130.0010.014
get_testdata0.0960.0200.117
headers0.0070.0060.014
identifiers0.0000.0010.001
identify_unique_se_metadata_fields0.0070.0010.008
is_any_exp_empty0.0490.0010.050
is_exp_empty0.0530.0010.056
is_mae_empty0.0500.0020.052
logisticFit0.0230.0010.024
loop000
mcolData0.0150.0010.016
merge_SE1.8680.0341.920
merge_assay0.3810.0100.393
merge_metadata0.0070.0010.007
mrowData0.0180.0020.020
predict_conc_from_efficacy0.0010.0000.001
predict_efficacy_from_conc0.0010.0000.000
prettify_flat_metrics0.0050.0010.006
promote_fields0.2540.0130.271
refine_coldata0.0120.0020.014
refine_rowdata0.0730.0030.078
rename_DFrame0.0100.0010.012
rename_bumpy0.0360.0010.038
shorten_normalization_type_name0.0000.0000.001
split_SE_components0.0360.0020.038
standardize_mae0.1780.0040.182
standardize_se0.0350.0020.037
update_env_idfs_from_mae0.0000.0000.001
update_idfs_synonyms0.0000.0000.001
validate_MAE0.0810.0010.082
validate_SE0.0260.0010.028
validate_identifiers0.0100.0010.012
validate_json0.0000.0010.000
validate_mae_with_schema0.4130.0760.523
validate_se_assay_name0.0060.0010.006