Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1.4.0  (landing page)
Arkadiusz Gladki
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/gDRutils
git_branch: RELEASE_3_20
git_last_commit: 1433886
git_last_commit_date: 2024-10-29 11:21:35 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for gDRutils on teran2

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: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2024-11-20 03:19:54 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 03:23:35 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 220.9 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/gDRutils.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘gDRutils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRutils’ version ‘1.4.0’
* 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 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 ‘/media/volume/teran2_disk/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
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 687 ]
> 
> proc.time()
   user  system elapsed 
 39.926   1.383  47.991 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.9610.0471.108
SE_metadata0.0220.0010.022
addClass0.0010.0000.001
aggregate_assay0.4060.0730.482
apply_bumpy_function0.9930.1201.175
assert_choices000
average_biological_replicates_dt0.0300.0000.051
calc_sd0.0000.0000.001
capVals0.2300.0070.437
cap_xc500.0000.0000.001
convert_colData_to_json0.0340.0010.035
convert_combo_data_to_dt1.0460.0061.054
convert_combo_field_to_assay0.0010.0000.001
convert_mae_assay_to_dt0.0430.0000.043
convert_mae_to_json0.0100.0010.011
convert_metadata_to_json0.0060.0000.006
convert_rowData_to_json0.0010.0000.002
convert_se_assay_to_custom_dt0.8140.0091.049
convert_se_assay_to_dt0.0400.0010.041
convert_se_to_json0.0090.0000.009
define_matrix_grid_positions0.1270.0010.128
demote_fields1.2540.0001.259
df_to_bm_assay0.0880.0000.089
dot-set_invalid_fit_params0.0010.0000.000
extend_normalization_type_name000
fit_curves0.090.010.10
flatten0.0060.0000.005
gen_synthetic_data0.0030.0010.003
geometric_mean000
get_MAE_identifiers0.0060.0010.006
get_additional_variables0.0040.0000.005
get_assay_dt_duplicated_rows0.0630.0000.064
get_assay_names000
get_assay_req_uniq_cols0.0620.0010.063
get_combo_assay_names000
get_combo_base_assay_names0.0000.0000.001
get_combo_excess_field_names0.0010.0000.002
get_combo_score_assay_names0.0000.0010.001
get_combo_score_field_names0.0010.0000.001
get_default_identifiers000
get_duplicated_rows0.0010.0000.002
get_env_assay_names000
get_expect_one_identifiers000
get_experiment_groups000
get_identifiers_dt0.0040.0010.007
get_idfs_synonyms000
get_isobologram_columns0.0230.0000.023
get_non_empty_assays0.1380.0000.138
get_required_identifiers000
get_settings_from_json0.0010.0000.001
get_supported_experiments000
get_synthetic_data0.0070.0000.008
get_testdata0.0910.0050.095
get_testdata_codilution0.0670.0020.117
get_testdata_combo0.1500.0180.224
has_assay_dt_duplicated_rows0.0490.0000.050
has_dt_duplicated_rows000
has_single_codrug_data0.050.000.05
has_valid_codrug_data0.0480.0000.048
headers0.0070.0010.009
identifiers0.0000.0010.000
identify_unique_se_metadata_fields0.0060.0000.005
is_any_exp_empty0.0340.0000.032
is_combo_data0.1020.0130.109
is_exp_empty0.0640.0020.065
is_mae_empty0.0370.0010.032
logisticFit0.0220.0000.016
loop000
mcolData0.0090.0010.010
merge_SE1.1610.0211.488
merge_assay0.2450.0030.240
merge_metadata0.0040.0010.006
modifyData0.0620.0010.063
mrowData0.0100.0000.011
predict_conc_from_efficacy000
predict_efficacy_from_conc0.0000.0000.001
prettify_flat_metrics0.0130.0000.013
promote_fields0.1330.0000.124
refine_coldata0.0070.0000.007
refine_rowdata0.0320.0010.033
remove_codrug_data0.0230.0000.022
rename_DFrame0.0070.0000.006
rename_bumpy0.020.000.02
round_concentration000
set_constant_fit_params000
set_unique_cl_names0.0460.0010.066
set_unique_cl_names_dt0.0160.0000.029
set_unique_drug_names0.0510.0010.104
set_unique_drug_names_dt0.0210.0000.041
set_unique_identifiers0.2010.0000.342
shorten_normalization_type_name000
split_SE_components0.0380.0000.039
standardize_mae0.0740.0010.074
standardize_se0.0210.0000.022
throw_msg_if_duplicates0.0480.0000.049
update_env_idfs_from_mae000
update_idfs_synonyms000
validate_MAE0.0510.0000.051
validate_SE0.0150.0010.020
validate_identifiers0.0050.0000.012
validate_json000
validate_mae_with_schema0.3310.0330.627
validate_se_assay_name0.0060.0000.009