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This page was generated on 2024-09-12 11:40 -0400 (Thu, 12 Sep 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4713
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4450
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4483
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4430
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4428
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 773/2258HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRutils 1.3.12  (landing page)
Arkadiusz Gladki
Snapshot Date: 2024-09-11 14:00 -0400 (Wed, 11 Sep 2024)
git_url: https://git.bioconductor.org/packages/gDRutils
git_branch: devel
git_last_commit: d40cd77
git_last_commit_date: 2024-09-10 05:30:47 -0400 (Tue, 10 Sep 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows 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
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  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: 1.3.12
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_1.3.12.tar.gz
StartedAt: 2024-09-11 22:54:10 -0400 (Wed, 11 Sep 2024)
EndedAt: 2024-09-11 22:57:45 -0400 (Wed, 11 Sep 2024)
EllapsedTime: 214.4 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_1.3.12.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 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘gDRutils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRutils’ version ‘1.3.12’
* 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 641 ]
> 
> proc.time()
   user  system elapsed 
 45.377   2.366  47.172 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.5010.0240.525
SE_metadata0.0370.0000.036
addClass0.0030.0000.002
aggregate_assay1.0640.0361.093
apply_bumpy_function1.3260.1001.427
assert_choices0.0010.0000.000
average_biological_replicates_dt0.0420.0000.042
calc_sd0.0000.0000.001
capVals0.2370.0070.246
cap_xc50000
convert_colData_to_json0.0490.0000.049
convert_combo_data_to_dt0.2530.0160.255
convert_combo_field_to_assay0.0010.0000.001
convert_mae_assay_to_dt0.0570.0000.057
convert_mae_to_json0.0160.0000.016
convert_metadata_to_json0.0090.0000.009
convert_rowData_to_json0.0020.0000.003
convert_se_assay_to_custom_dt0.4250.0280.436
convert_se_assay_to_dt0.0570.0040.061
convert_se_to_json0.0140.0000.014
define_matrix_grid_positions0.0490.0040.052
demote_fields1.0380.0801.076
df_to_bm_assay0.1170.0000.116
dot-set_invalid_fit_params0.0010.0000.000
extend_normalization_type_name000
fit_curves0.1160.0120.128
flatten0.0080.0000.007
gen_synthetic_data0.0050.0000.004
geometric_mean000
get_MAE_identifiers0.0070.0000.008
get_additional_variables0.0060.0000.006
get_assay_names0.0000.0000.001
get_combo_assay_names0.0000.0000.001
get_combo_base_assay_names0.0010.0000.001
get_combo_excess_field_names0.0010.0000.002
get_combo_score_assay_names0.0010.0000.001
get_combo_score_field_names0.0000.0000.001
get_default_identifiers0.0000.0000.001
get_duplicated_rows0.0020.0000.002
get_env_assay_names0.0000.0000.001
get_expect_one_identifiers0.0010.0000.000
get_experiment_groups000
get_identifiers_dt0.0050.0000.006
get_idfs_synonyms0.0000.0000.001
get_isobologram_columns0.0320.0000.032
get_non_empty_assays0.0460.0000.045
get_required_identifiers000
get_settings_from_json0.0050.0000.001
get_supported_experiments000
get_synthetic_data0.0180.0000.010
get_testdata0.0900.0080.083
get_testdata_codilution0.0870.0000.074
get_testdata_combo0.2110.0190.224
has_single_codrug_data0.0670.0010.067
has_valid_codrug_data0.0630.0000.063
headers0.010.000.01
identifiers000
identify_unique_se_metadata_fields0.0080.0000.007
is_any_exp_empty0.0460.0000.044
is_combo_data0.1640.0110.162
is_exp_empty0.0450.0000.042
is_mae_empty0.0540.0000.041
logisticFit0.0340.0010.020
loop000
mcolData0.0120.0000.013
merge_SE2.2070.0802.189
merge_assay0.2940.0200.308
merge_metadata0.0090.0000.008
modifyData0.0860.0000.086
mrowData0.0150.0000.015
predict_conc_from_efficacy000
predict_efficacy_from_conc0.0010.0000.000
prettify_flat_metrics0.0210.0000.021
promote_fields0.1930.0040.191
refine_coldata0.0090.0000.009
refine_rowdata0.0480.0000.048
remove_codrug_data0.0290.0000.029
rename_DFrame0.0090.0000.009
rename_bumpy0.0290.0000.029
round_concentration000
set_constant_fit_params000
set_unique_cl_names0.0450.0000.045
set_unique_drug_names0.0460.0000.046
set_unique_identifiers0.2750.0000.275
shorten_normalization_type_name000
split_SE_components0.0450.0080.053
standardize_mae0.1020.0040.107
standardize_se0.0310.0000.031
update_env_idfs_from_mae0.0010.0000.001
update_idfs_synonyms000
validate_MAE0.0720.0000.072
validate_SE0.0250.0000.025
validate_identifiers0.0060.0000.006
validate_json000
validate_mae_with_schema0.3570.0150.366
validate_se_assay_name0.0080.0000.008