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This page was generated on 2025-03-20 12:05 -0400 (Thu, 20 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4756
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4487
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4514
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4441
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4406
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 781/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRutils 1.4.10  (landing page)
Arkadiusz Gladki
Snapshot Date: 2025-03-17 13:00 -0400 (Mon, 17 Mar 2025)
git_url: https://git.bioconductor.org/packages/gDRutils
git_branch: RELEASE_3_20
git_last_commit: 18d3e76
git_last_commit_date: 2025-02-11 06:44:03 -0400 (Tue, 11 Feb 2025)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows 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
taishanLinux (openEuler 24.03 LTS) / 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: 1.4.10
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_1.4.10.tar.gz
StartedAt: 2025-03-17 23:10:24 -0400 (Mon, 17 Mar 2025)
EndedAt: 2025-03-17 23:13:59 -0400 (Mon, 17 Mar 2025)
EllapsedTime: 215.3 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_1.4.10.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/gDRutils.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘gDRutils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRutils’ version ‘1.4.10’
* 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 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 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 727 ]
> 
> proc.time()
   user  system elapsed 
 48.775   1.038  48.803 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.5110.0480.560
SE_metadata0.0340.0010.034
addClass0.0020.0000.002
aggregate_assay1.2220.0101.228
apply_bumpy_function1.4030.1271.528
assert_choices0.0010.0000.000
average_biological_replicates_dt0.0450.0000.044
calc_sd0.0010.0000.000
capVals0.2420.0040.247
cap_assay_infinities0.2650.0030.230
cap_xc500.0000.0000.001
convert_colData_to_json0.0530.0000.047
convert_combo_data_to_dt0.3510.0080.287
convert_combo_field_to_assay0.0020.0000.001
convert_mae_assay_to_dt0.0590.0010.060
convert_mae_to_json0.0160.0000.015
convert_metadata_to_json0.0080.0000.008
convert_rowData_to_json0.0020.0000.002
convert_se_assay_to_custom_dt1.1460.0031.127
convert_se_assay_to_dt0.060.000.06
convert_se_to_json0.0150.0000.015
define_matrix_grid_positions0.0630.0000.053
demote_fields0.4370.0000.391
df_to_bm_assay0.1490.0000.150
dot-set_invalid_fit_params000
extend_normalization_type_name000
fit_curves0.1300.0030.133
flatten0.0070.0000.007
gen_synthetic_data0.0050.0000.004
geometric_mean000
get_MAE_identifiers0.0070.0000.007
get_additional_variables0.0070.0000.007
get_assay_dt_duplicated_rows0.0870.0000.087
get_assay_names000
get_assay_req_uniq_cols0.0730.0000.072
get_combo_assay_names000
get_combo_base_assay_names0.0000.0000.001
get_combo_excess_field_names0.0010.0000.001
get_combo_score_assay_names0.0010.0000.001
get_combo_score_field_names0.0000.0000.001
get_default_identifiers000
get_duplicated_rows0.0030.0000.002
get_env_assay_names000
get_env_var000
get_expect_one_identifiers000
get_experiment_groups000
get_identifiers_dt0.0050.0010.006
get_idfs_synonyms0.0010.0000.000
get_isobologram_columns0.0330.0000.034
get_non_empty_assays0.0550.0000.046
get_required_identifiers0.0010.0000.001
get_settings_from_json0.0020.0000.001
get_supported_experiments000
get_synthetic_data0.0110.0000.011
get_testdata0.0870.0010.082
get_testdata_codilution0.0810.0000.084
get_testdata_combo0.2730.0120.276
has_assay_dt_duplicated_rows0.0700.0030.073
has_dt_duplicated_rows0.0000.0000.001
has_single_codrug_data0.0680.0000.069
has_valid_codrug_data0.0690.0000.069
headers0.0100.0010.010
identifiers000
identify_unique_se_metadata_fields0.0080.0000.007
is_any_exp_empty0.0660.0000.048
is_combo_data0.1820.0060.178
is_exp_empty0.0570.0010.046
is_mae_empty0.0570.0000.045
logisticFit0.0260.0000.022
loop0.0010.0000.000
mcolData0.0140.0000.014
merge_SE1.6410.0011.515
merge_assay0.3530.0000.325
merge_metadata0.0090.0000.008
modifyData0.1120.0000.112
mrowData0.0140.0000.015
predict_conc_from_efficacy000
predict_efficacy_from_conc0.0010.0000.000
prettify_flat_metrics0.0190.0000.020
promote_fields0.1920.0000.180
refine_coldata0.0090.0000.010
refine_rowdata0.0450.0000.046
remove_codrug_data0.0280.0000.028
remove_drug_batch0.0010.0000.001
rename_DFrame0.0100.0000.009
rename_bumpy0.0290.0000.029
round_concentration000
set_constant_fit_params0.0010.0000.001
set_unique_cl_names0.0450.0000.045
set_unique_cl_names_dt0.0160.0010.017
set_unique_drug_names0.0690.0010.069
set_unique_drug_names_dt0.0330.0000.033
set_unique_identifiers0.2810.0000.281
set_unique_names_dt0.0170.0000.017
shorten_normalization_type_name000
split_SE_components0.050.000.05
standardize_mae0.1070.0000.108
standardize_se0.0310.0000.031
throw_msg_if_duplicates0.0700.0000.069
update_env_idfs_from_mae0.0010.0000.001
update_idfs_synonyms0.0000.0010.001
validate_MAE0.0750.0000.076
validate_SE0.0270.0000.028
validate_identifiers0.0070.0000.007
validate_json000
validate_mae_with_schema0.3990.0260.387
validate_se_assay_name0.0060.0000.006