| Back to Multiple platform build/check report for BioC 3.18: simplified long | 
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This page was generated on 2023-11-02 11:40:43 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs | 
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 | 
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 | 
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 | 
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 | 
| 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 781/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gDRutils 1.0.0  (landing page) Arkadiusz Gladki 
 | nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK |  | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK |  | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
| 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. | 
| Package: gDRutils | 
| Version: 1.0.0 | 
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings gDRutils_1.0.0.tar.gz | 
| StartedAt: 2023-11-02 10:43:34 -0000 (Thu, 02 Nov 2023) | 
| EndedAt: 2023-11-02 10:48:00 -0000 (Thu, 02 Nov 2023) | 
| EllapsedTime: 265.4 seconds | 
| RetCode: 0 | 
| Status: OK | 
| CheckDir: gDRutils.Rcheck | 
| Warnings: 0 | 
##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings gDRutils_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/gDRutils.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gDRutils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRutils’ version ‘1.0.0’
* 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 R 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
gDRutils.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL gDRutils ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/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)
gDRutils.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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 461 ]
> 
> proc.time()
   user  system elapsed 
 59.664   1.695  61.192 
gDRutils.Rcheck/gDRutils-Ex.timings
| name | user | system | elapsed | |
| MAEpply | 1.336 | 0.040 | 1.396 | |
| SE_metadata | 0.046 | 0.000 | 0.046 | |
| aggregate_assay | 0.735 | 0.044 | 0.780 | |
| apply_bumpy_function | 2.185 | 0.095 | 2.285 | |
| assert_choices | 0 | 0 | 0 | |
| cap_xc50 | 0 | 0 | 0 | |
| convert_combo_data_to_dt | 1.623 | 0.076 | 1.704 | |
| convert_mae_assay_to_dt | 0.076 | 0.000 | 0.076 | |
| convert_mae_to_json | 0.103 | 0.011 | 0.115 | |
| convert_se_assay_to_dt | 0.074 | 0.003 | 0.077 | |
| convert_se_to_json | 0.024 | 0.000 | 0.024 | |
| demote_fields | 0.469 | 0.020 | 0.481 | |
| df_to_bm_assay | 0.144 | 0.004 | 0.148 | |
| dot-convert_colData_to_json | 0.003 | 0.000 | 0.003 | |
| dot-convert_metadata_to_json | 0.006 | 0.000 | 0.005 | |
| dot-convert_rowData_to_json | 0.004 | 0.000 | 0.003 | |
| dot-set_constant_fit_params | 0.001 | 0.000 | 0.001 | |
| dot-set_invalid_fit_params | 0 | 0 | 0 | |
| extend_normalization_type_name | 0.001 | 0.000 | 0.000 | |
| fit_curves | 0.241 | 0.016 | 0.264 | |
| flatten | 0.012 | 0.000 | 0.012 | |
| gen_synthetic_data | 0.003 | 0.000 | 0.003 | |
| get_MAE_identifiers | 0.006 | 0.004 | 0.009 | |
| get_assay_names | 0.001 | 0.000 | 0.000 | |
| get_combo_assay_names | 0.001 | 0.000 | 0.001 | |
| get_combo_base_assay_names | 0.001 | 0.000 | 0.001 | |
| get_combo_col_settings | 0.005 | 0.000 | 0.005 | |
| get_combo_score_assay_names | 0.001 | 0.000 | 0.001 | |
| get_default_identifiers | 0.001 | 0.000 | 0.000 | |
| get_env_assay_names | 0 | 0 | 0 | |
| get_expect_one_identifiers | 0 | 0 | 0 | |
| get_experiment_groups | 0.000 | 0.000 | 0.001 | |
| get_identifiers_dt | 0.007 | 0.000 | 0.007 | |
| get_idfs_synonyms | 0 | 0 | 0 | |
| get_iso_colors | 0.002 | 0.000 | 0.002 | |
| get_non_empty_assays | 0.071 | 0.000 | 0.071 | |
| get_required_identifiers | 0 | 0 | 0 | |
| get_synthetic_data | 0.013 | 0.000 | 0.013 | |
| get_testdata | 0.088 | 0.008 | 0.096 | |
| headers | 0.007 | 0.000 | 0.007 | |
| identifiers | 0 | 0 | 0 | |
| identify_unique_se_metadata_fields | 0.008 | 0.000 | 0.008 | |
| is_any_exp_empty | 0.064 | 0.000 | 0.062 | |
| is_exp_empty | 0.064 | 0.000 | 0.063 | |
| is_mae_empty | 0.064 | 0.000 | 0.062 | |
| logisticFit | 0.025 | 0.000 | 0.025 | |
| loop | 0 | 0 | 0 | |
| mcolData | 0.017 | 0.000 | 0.017 | |
| merge_SE | 2.262 | 0.012 | 2.266 | |
| merge_assay | 0.434 | 0.004 | 0.439 | |
| merge_metadata | 0.009 | 0.000 | 0.009 | |
| mrowData | 0.017 | 0.000 | 0.017 | |
| predict_conc_from_efficacy | 0 | 0 | 0 | |
| predict_efficacy_from_conc | 0 | 0 | 0 | |
| prettify_flat_metrics | 0.006 | 0.000 | 0.007 | |
| promote_fields | 0.299 | 0.008 | 0.306 | |
| refine_coldata | 0.011 | 0.000 | 0.012 | |
| refine_rowdata | 0.06 | 0.00 | 0.06 | |
| rename_DFrame | 0.011 | 0.000 | 0.012 | |
| rename_bumpy | 0.036 | 0.004 | 0.041 | |
| shorten_normalization_type_name | 0.000 | 0.000 | 0.001 | |
| split_SE_components | 0.039 | 0.000 | 0.040 | |
| standardize_mae | 0.199 | 0.000 | 0.204 | |
| standardize_se | 0.041 | 0.000 | 0.042 | |
| update_env_idfs_from_mae | 0.001 | 0.000 | 0.002 | |
| update_idfs_synonyms | 0.000 | 0.000 | 0.001 | |
| validate_MAE | 0.097 | 0.000 | 0.097 | |
| validate_SE | 0.034 | 0.004 | 0.038 | |
| validate_identifiers | 0.007 | 0.004 | 0.011 | |
| validate_json | 0 | 0 | 0 | |
| validate_mae_with_schema | 0.576 | 0.048 | 0.768 | |
| validate_se_assay_name | 0.006 | 0.003 | 0.008 | |