Arkadiusz Gladki
| Snapshot Date: 2024-05-21 14:00:15 -0400 (Tue, 21 May 2024) |
| git_url: https://git.bioconductor.org/packages/gDRutils |
| git_branch: RELEASE_3_19 |
| git_last_commit: d1f7215 |
| git_last_commit_date: 2024-04-30 11:49:57 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-22 11:35:41 -0400 (Wed, 22 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4751 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 3444 |
| 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 791/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gDRutils 1.2.0 (landing page) Arkadiusz Gladki
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: gDRutils |
| Version: 1.2.0 |
| Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gDRutils.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings gDRutils_1.2.0.tar.gz |
| StartedAt: 2024-05-22 02:07:39 -0400 (Wed, 22 May 2024) |
| EndedAt: 2024-05-22 02:11:45 -0400 (Wed, 22 May 2024) |
| EllapsedTime: 245.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gDRutils.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gDRutils.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings gDRutils_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/gDRutils.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'gDRutils/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gDRutils' version '1.2.0'
* 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 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 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 ... NOTE
checkRd: (-1) split_SE_components.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) split_SE_components.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) split_SE_components.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) split_SE_components.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) split_SE_components.Rd:35: Lost braces in \itemize; meant \describe ?
* 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: 1 NOTE
See
'F:/biocbuild/bbs-3.19-bioc/meat/gDRutils.Rcheck/00check.log'
for details.
gDRutils.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL gDRutils ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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 496 ]
>
> proc.time()
user system elapsed
49.96 1.93 64.53
gDRutils.Rcheck/gDRutils-Ex.timings
| name | user | system | elapsed | |
| MAEpply | 0.55 | 0.08 | 0.64 | |
| SE_metadata | 0.17 | 0.00 | 0.17 | |
| addClass | 0 | 0 | 0 | |
| aggregate_assay | 1.25 | 0.00 | 1.28 | |
| apply_bumpy_function | 1.86 | 0.15 | 2.01 | |
| assert_choices | 0 | 0 | 0 | |
| average_biological_replicates_dt | 0.25 | 0.08 | 0.33 | |
| cap_xc50 | 0 | 0 | 0 | |
| convert_colData_to_json | 0.06 | 0.00 | 0.06 | |
| convert_combo_data_to_dt | 0.29 | 0.02 | 0.32 | |
| convert_combo_field_to_assay | 0.02 | 0.00 | 0.01 | |
| convert_mae_assay_to_dt | 0.08 | 0.00 | 0.08 | |
| convert_mae_to_json | 0.01 | 0.00 | 0.01 | |
| convert_metadata_to_json | 0.02 | 0.00 | 0.02 | |
| convert_rowData_to_json | 0.02 | 0.00 | 0.02 | |
| convert_se_assay_to_dt | 0.07 | 0.01 | 0.09 | |
| convert_se_to_json | 0.02 | 0.00 | 0.02 | |
| demote_fields | 1.11 | 0.00 | 1.10 | |
| df_to_bm_assay | 0.17 | 0.02 | 0.19 | |
| dot-set_invalid_fit_params | 0 | 0 | 0 | |
| extend_normalization_type_name | 0 | 0 | 0 | |
| fit_curves | 0.23 | 0.06 | 0.37 | |
| flatten | 0.02 | 0.00 | 0.02 | |
| gen_synthetic_data | 0 | 0 | 0 | |
| geometric_mean | 0 | 0 | 0 | |
| get_MAE_identifiers | 0.01 | 0.00 | 0.01 | |
| get_assay_names | 0 | 0 | 0 | |
| get_combo_assay_names | 0 | 0 | 0 | |
| get_combo_base_assay_names | 0 | 0 | 0 | |
| get_combo_col_settings | 0.02 | 0.00 | 0.02 | |
| get_combo_excess_field_names | 0 | 0 | 0 | |
| get_combo_score_assay_names | 0 | 0 | 0 | |
| get_combo_score_field_names | 0 | 0 | 0 | |
| get_default_identifiers | 0 | 0 | 0 | |
| get_duplicated_rows | 0 | 0 | 0 | |
| get_env_assay_names | 0 | 0 | 0 | |
| get_expect_one_identifiers | 0 | 0 | 0 | |
| get_experiment_groups | 0.01 | 0.00 | 0.02 | |
| get_identifiers_dt | 0.00 | 0.00 | 0.03 | |
| get_idfs_synonyms | 0 | 0 | 0 | |
| get_iso_colors | 0 | 0 | 0 | |
| get_non_empty_assays | 0.07 | 0.00 | 0.06 | |
| get_required_identifiers | 0 | 0 | 0 | |
| get_synthetic_data | 0.01 | 0.00 | 0.01 | |
| get_testdata | 0.09 | 0.03 | 0.15 | |
| get_testdata_codilution | 0.1 | 0.0 | 0.1 | |
| get_testdata_combo | 0.22 | 0.03 | 0.27 | |
| headers | 0.03 | 0.00 | 0.03 | |
| identifiers | 0 | 0 | 0 | |
| identify_unique_se_metadata_fields | 0 | 0 | 0 | |
| is_any_exp_empty | 0.05 | 0.00 | 0.05 | |
| is_exp_empty | 0.05 | 0.00 | 0.05 | |
| is_mae_empty | 0.04 | 0.00 | 0.05 | |
| logisticFit | 0.02 | 0.00 | 0.01 | |
| loop | 0.02 | 0.00 | 0.02 | |
| mcolData | 0.01 | 0.00 | 0.01 | |
| merge_SE | 1.81 | 0.00 | 1.82 | |
| merge_assay | 0.43 | 0.00 | 0.42 | |
| merge_metadata | 0.01 | 0.00 | 0.01 | |
| modifyData | 0.25 | 0.00 | 0.25 | |
| mrowData | 0.02 | 0.00 | 0.02 | |
| predict_conc_from_efficacy | 0 | 0 | 0 | |
| predict_efficacy_from_conc | 0 | 0 | 0 | |
| prettify_flat_metrics | 0.03 | 0.00 | 0.03 | |
| promote_fields | 0.29 | 0.00 | 0.28 | |
| refine_coldata | 0.01 | 0.00 | 0.02 | |
| refine_rowdata | 0.08 | 0.00 | 0.08 | |
| rename_DFrame | 0.01 | 0.00 | 0.01 | |
| rename_bumpy | 0.05 | 0.00 | 0.05 | |
| set_constant_fit_params | 0 | 0 | 0 | |
| shorten_normalization_type_name | 0 | 0 | 0 | |
| split_SE_components | 0.11 | 0.00 | 0.11 | |
| standardize_mae | 0.24 | 0.01 | 0.28 | |
| standardize_se | 0.04 | 0.00 | 0.05 | |
| update_env_idfs_from_mae | 0 | 0 | 0 | |
| update_idfs_synonyms | 0 | 0 | 0 | |
| validate_MAE | 0.10 | 0.00 | 0.09 | |
| validate_SE | 0.03 | 0.00 | 0.03 | |
| validate_identifiers | 0.01 | 0.00 | 0.02 | |
| validate_json | 0 | 0 | 0 | |
| validate_mae_with_schema | 0.35 | 0.10 | 1.80 | |
| validate_se_assay_name | 0.01 | 0.00 | 0.01 | |