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This page was generated on 2024-11-04 12:02 -0500 (Mon, 04 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4503
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4506
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4538
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: 2024-11-03 13:40 -0500 (Sun, 03 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: 2024-11-04 01:59:29 -0500 (Mon, 04 Nov 2024)
EndedAt: 2024-11-04 02:03:13 -0500 (Mon, 04 Nov 2024)
EllapsedTime: 223.8 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 4.4.1 (2024-06-14)
* 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 4.4.1 (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 687 ]
> 
> proc.time()
   user  system elapsed 
 38.263   1.204  45.211 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.9680.0481.849
SE_metadata0.0230.0030.051
addClass0.0020.0000.002
aggregate_assay0.3670.0600.442
apply_bumpy_function1.4450.1021.601
assert_choices0.0010.0000.000
average_biological_replicates_dt0.0290.0000.030
calc_sd000
capVals0.2210.0030.226
cap_xc500.0010.0000.000
convert_colData_to_json0.0350.0010.039
convert_combo_data_to_dt1.0310.0041.218
convert_combo_field_to_assay0.0020.0000.002
convert_mae_assay_to_dt0.0430.0000.044
convert_mae_to_json0.0110.0000.011
convert_metadata_to_json0.0060.0000.006
convert_rowData_to_json0.0020.0000.002
convert_se_assay_to_custom_dt0.2740.0110.319
convert_se_assay_to_dt0.0430.0000.040
convert_se_to_json0.0090.0000.009
define_matrix_grid_positions0.0390.0010.038
demote_fields0.3050.0000.277
df_to_bm_assay0.0870.0000.087
dot-set_invalid_fit_params000
extend_normalization_type_name0.0000.0000.001
fit_curves0.0960.0050.145
flatten0.0050.0000.005
gen_synthetic_data0.0030.0000.003
geometric_mean0.0010.0000.000
get_MAE_identifiers0.0050.0010.006
get_additional_variables0.0040.0000.004
get_assay_dt_duplicated_rows0.0610.0000.062
get_assay_names000
get_assay_req_uniq_cols0.0600.0010.061
get_combo_assay_names000
get_combo_base_assay_names0.0010.0000.000
get_combo_excess_field_names0.0010.0000.001
get_combo_score_assay_names0.0000.0000.001
get_combo_score_field_names0.0010.0000.000
get_default_identifiers000
get_duplicated_rows0.0020.0010.002
get_env_assay_names000
get_expect_one_identifiers000
get_experiment_groups0.0000.0000.001
get_identifiers_dt0.0020.0020.006
get_idfs_synonyms000
get_isobologram_columns0.0210.0010.024
get_non_empty_assays0.0330.0000.031
get_required_identifiers0.0000.0000.001
get_settings_from_json0.0010.0000.000
get_supported_experiments000
get_synthetic_data0.0090.0000.007
get_testdata0.0650.0030.057
get_testdata_codilution0.0580.0030.107
get_testdata_combo0.1570.0120.268
has_assay_dt_duplicated_rows0.0460.0020.048
has_dt_duplicated_rows0.0000.0000.001
has_single_codrug_data0.5410.0270.570
has_valid_codrug_data0.0470.0000.049
headers0.0080.0010.008
identifiers000
identify_unique_se_metadata_fields0.0060.0000.006
is_any_exp_empty0.0370.0000.034
is_combo_data0.1000.0210.225
is_exp_empty0.0720.0030.140
is_mae_empty0.0400.0000.063
logisticFit0.0200.0000.027
loop000
mcolData0.010.000.01
merge_SE1.1000.0011.054
merge_assay0.2490.0000.247
merge_metadata0.0060.0000.006
modifyData0.0630.0000.064
mrowData0.010.000.01
predict_conc_from_efficacy000
predict_efficacy_from_conc0.0010.0000.000
prettify_flat_metrics0.0130.0000.015
promote_fields0.1340.0000.227
refine_coldata0.0070.0020.019
refine_rowdata0.0360.0000.071
remove_codrug_data0.0240.0000.048
rename_DFrame0.0070.0000.014
rename_bumpy0.0220.0000.046
round_concentration000
set_constant_fit_params0.0000.0000.001
set_unique_cl_names0.0500.0000.097
set_unique_cl_names_dt0.0160.0000.031
set_unique_drug_names0.0510.0000.104
set_unique_drug_names_dt0.0210.0000.039
set_unique_identifiers0.2170.0020.417
shorten_normalization_type_name0.0010.0000.000
split_SE_components0.0430.0000.086
standardize_mae0.0820.0000.164
standardize_se0.0240.0000.050
throw_msg_if_duplicates0.0520.0010.108
update_env_idfs_from_mae0.0010.0000.001
update_idfs_synonyms0.0000.0000.001
validate_MAE0.3270.0000.652
validate_SE0.0180.0000.038
validate_identifiers0.0050.0000.008
validate_json000
validate_mae_with_schema0.3340.0500.902
validate_se_assay_name0.0050.0000.009