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This page was generated on 2025-03-10 12:12 -0400 (Mon, 10 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4670
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4355
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4446
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4439
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4306
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: 2025-03-06 13:00 -0500 (Thu, 06 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 -0500 (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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: gDRutils
Version: 1.4.10
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gDRutils_1.4.10.tar.gz
StartedAt: 2025-03-07 07:16:28 -0000 (Fri, 07 Mar 2025)
EndedAt: 2025-03-07 07:21:08 -0000 (Fri, 07 Mar 2025)
EllapsedTime: 279.4 seconds
RetCode: 0
Status:   OK  
CheckDir: gDRutils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --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: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gDRutils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRutils’ version ‘1.4.10’
* 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 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:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL gDRutils
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.3/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: aarch64-unknown-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 
 73.094   2.349  75.427 

Example timings

gDRutils.Rcheck/gDRutils-Ex.timings

nameusersystemelapsed
MAEpply0.7440.0440.789
SE_metadata0.0500.0000.049
addClass0.0030.0000.002
aggregate_assay1.4410.0081.452
apply_bumpy_function2.3710.1082.485
assert_choices0.0010.0000.001
average_biological_replicates_dt0.0790.0080.087
calc_sd000
capVals0.3800.0080.390
cap_assay_infinities0.3750.0590.435
cap_xc500.0010.0010.001
convert_colData_to_json0.0730.0270.101
convert_combo_data_to_dt0.4160.1360.550
convert_combo_field_to_assay0.0020.0000.002
convert_mae_assay_to_dt0.0820.0080.090
convert_mae_to_json0.0150.0080.023
convert_metadata_to_json0.0130.0000.013
convert_rowData_to_json0.0040.0000.004
convert_se_assay_to_custom_dt1.1120.7871.900
convert_se_assay_to_dt0.0780.0000.077
convert_se_to_json0.0170.0000.016
define_matrix_grid_positions0.0660.0060.071
demote_fields0.4960.0050.497
df_to_bm_assay0.1860.0000.187
dot-set_invalid_fit_params000
extend_normalization_type_name000
fit_curves0.1740.0040.177
flatten0.010.000.01
gen_synthetic_data0.0070.0000.007
geometric_mean000
get_MAE_identifiers0.0090.0000.009
get_additional_variables0.010.000.01
get_assay_dt_duplicated_rows0.1270.0000.128
get_assay_names000
get_assay_req_uniq_cols0.090.000.09
get_combo_assay_names0.0010.0000.001
get_combo_base_assay_names0.0010.0000.001
get_combo_excess_field_names0.0020.0000.002
get_combo_score_assay_names0.0010.0000.001
get_combo_score_field_names0.0010.0000.001
get_default_identifiers0.0000.0000.001
get_duplicated_rows0.0030.0000.004
get_env_assay_names000
get_env_var000
get_expect_one_identifiers000
get_experiment_groups000
get_identifiers_dt0.0060.0000.008
get_idfs_synonyms0.0000.0000.001
get_isobologram_columns0.0430.0000.043
get_non_empty_assays0.0640.0000.063
get_required_identifiers000
get_settings_from_json0.0010.0000.001
get_supported_experiments000
get_synthetic_data0.0130.0000.013
get_testdata0.1010.0040.105
get_testdata_codilution0.0990.0000.101
get_testdata_combo0.2700.0070.292
has_assay_dt_duplicated_rows0.0890.0040.092
has_dt_duplicated_rows0.0010.0000.001
has_single_codrug_data0.0980.0000.098
has_valid_codrug_data0.0970.0000.097
headers0.0110.0040.014
identifiers000
identify_unique_se_metadata_fields0.0090.0000.009
is_any_exp_empty0.0590.0000.059
is_combo_data0.1950.0200.216
is_exp_empty0.0630.0000.062
is_mae_empty0.0640.0000.064
logisticFit0.0310.0000.031
loop000
mcolData0.0170.0000.017
merge_SE2.0630.0162.074
merge_assay0.4160.0000.416
merge_metadata0.0090.0000.009
modifyData0.1440.0040.148
mrowData0.0170.0000.018
predict_conc_from_efficacy000
predict_efficacy_from_conc000
prettify_flat_metrics0.0270.0000.026
promote_fields0.2330.0000.232
refine_coldata0.0120.0000.013
refine_rowdata0.0590.0040.063
remove_codrug_data0.0430.0000.044
remove_drug_batch0.0020.0000.002
rename_DFrame0.0120.0000.012
rename_bumpy0.0350.0040.039
round_concentration000
set_constant_fit_params000
set_unique_cl_names0.0630.0000.063
set_unique_cl_names_dt0.0250.0000.025
set_unique_drug_names0.0910.0000.091
set_unique_drug_names_dt0.050.000.05
set_unique_identifiers0.4260.0000.428
set_unique_names_dt0.0270.0000.026
shorten_normalization_type_name0.0010.0000.000
split_SE_components0.0770.0000.077
standardize_mae0.1480.0000.149
standardize_se0.0370.0040.040
throw_msg_if_duplicates0.0960.0000.096
update_env_idfs_from_mae0.0020.0000.002
update_idfs_synonyms0.0010.0000.001
validate_MAE0.0990.0040.104
validate_SE0.0370.0000.038
validate_identifiers0.0090.0000.010
validate_json000
validate_mae_with_schema0.7170.0521.472
validate_se_assay_name0.0090.0000.008