Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-03 11:38:22 -0400 (Fri, 03 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4660 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4391 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4422 |
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 762/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
gDRutils 1.3.0 (landing page) Arkadiusz Gladki
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 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: 1.3.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gDRutils_1.3.0.tar.gz |
StartedAt: 2024-05-02 04:38:10 -0400 (Thu, 02 May 2024) |
EndedAt: 2024-05-02 04:46:39 -0400 (Thu, 02 May 2024) |
EllapsedTime: 509.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: gDRutils.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gDRutils.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gDRutils_1.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/gDRutils.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘gDRutils/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘gDRutils’ version ‘1.3.0’ * 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 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed merge_SE 4.606 0.051 5.539 apply_bumpy_function 4.057 0.282 5.664 * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/gDRutils.Rcheck/00check.log’ for details.
gDRutils.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gDRutils ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 74.336 3.616 113.876
gDRutils.Rcheck/gDRutils-Ex.timings
name | user | system | elapsed | |
MAEpply | 1.295 | 0.096 | 1.804 | |
SE_metadata | 0.181 | 0.013 | 0.258 | |
addClass | 0.004 | 0.000 | 0.004 | |
aggregate_assay | 2.024 | 0.080 | 2.732 | |
apply_bumpy_function | 4.057 | 0.282 | 5.664 | |
assert_choices | 0.001 | 0.001 | 0.001 | |
average_biological_replicates_dt | 0.754 | 0.027 | 1.016 | |
cap_xc50 | 0.001 | 0.000 | 0.002 | |
convert_colData_to_json | 0.144 | 0.003 | 0.177 | |
convert_combo_data_to_dt | 0.571 | 0.032 | 0.713 | |
convert_combo_field_to_assay | 0.005 | 0.001 | 0.005 | |
convert_mae_assay_to_dt | 0.147 | 0.008 | 0.181 | |
convert_mae_to_json | 0.035 | 0.002 | 0.053 | |
convert_metadata_to_json | 0.023 | 0.000 | 0.035 | |
convert_rowData_to_json | 0.006 | 0.001 | 0.007 | |
convert_se_assay_to_dt | 0.140 | 0.007 | 0.208 | |
convert_se_to_json | 0.032 | 0.001 | 0.044 | |
demote_fields | 0.933 | 0.015 | 1.196 | |
df_to_bm_assay | 0.303 | 0.003 | 0.387 | |
dot-set_invalid_fit_params | 0.001 | 0.000 | 0.001 | |
extend_normalization_type_name | 0.001 | 0.001 | 0.001 | |
fit_curves | 0.483 | 0.038 | 0.655 | |
flatten | 0.021 | 0.002 | 0.029 | |
gen_synthetic_data | 0.015 | 0.003 | 0.023 | |
geometric_mean | 0.001 | 0.001 | 0.001 | |
get_MAE_identifiers | 0.014 | 0.004 | 0.023 | |
get_assay_names | 0.001 | 0.001 | 0.002 | |
get_combo_assay_names | 0.001 | 0.000 | 0.002 | |
get_combo_base_assay_names | 0.002 | 0.000 | 0.002 | |
get_combo_col_settings | 0.007 | 0.001 | 0.015 | |
get_combo_excess_field_names | 0.004 | 0.000 | 0.007 | |
get_combo_score_assay_names | 0.002 | 0.001 | 0.003 | |
get_combo_score_field_names | 0.002 | 0.001 | 0.007 | |
get_default_identifiers | 0.001 | 0.002 | 0.004 | |
get_duplicated_rows | 0.004 | 0.000 | 0.004 | |
get_env_assay_names | 0.001 | 0.001 | 0.002 | |
get_expect_one_identifiers | 0.000 | 0.001 | 0.005 | |
get_experiment_groups | 0.001 | 0.001 | 0.001 | |
get_identifiers_dt | 0.011 | 0.008 | 0.026 | |
get_idfs_synonyms | 0.000 | 0.001 | 0.001 | |
get_iso_colors | 0.003 | 0.001 | 0.004 | |
get_non_empty_assays | 0.121 | 0.002 | 0.160 | |
get_required_identifiers | 0.000 | 0.001 | 0.001 | |
get_synthetic_data | 0.023 | 0.002 | 0.032 | |
get_testdata | 0.202 | 0.057 | 0.327 | |
get_testdata_codilution | 0.196 | 0.015 | 0.269 | |
get_testdata_combo | 0.455 | 0.050 | 0.638 | |
headers | 0.030 | 0.017 | 0.069 | |
identifiers | 0.000 | 0.001 | 0.001 | |
identify_unique_se_metadata_fields | 0.016 | 0.003 | 0.025 | |
is_any_exp_empty | 0.199 | 0.019 | 0.274 | |
is_exp_empty | 0.115 | 0.002 | 0.155 | |
is_mae_empty | 0.117 | 0.003 | 0.151 | |
logisticFit | 0.064 | 0.002 | 0.079 | |
loop | 0.000 | 0.000 | 0.001 | |
mcolData | 0.032 | 0.002 | 0.041 | |
merge_SE | 4.606 | 0.051 | 5.539 | |
merge_assay | 0.805 | 0.040 | 0.974 | |
merge_metadata | 0.014 | 0.002 | 0.020 | |
modifyData | 0.227 | 0.009 | 0.266 | |
mrowData | 0.031 | 0.003 | 0.040 | |
predict_conc_from_efficacy | 0.000 | 0.000 | 0.001 | |
predict_efficacy_from_conc | 0.001 | 0.001 | 0.001 | |
prettify_flat_metrics | 0.050 | 0.004 | 0.062 | |
promote_fields | 0.472 | 0.007 | 0.535 | |
refine_coldata | 0.021 | 0.002 | 0.027 | |
refine_rowdata | 0.103 | 0.003 | 0.113 | |
rename_DFrame | 0.021 | 0.003 | 0.024 | |
rename_bumpy | 0.074 | 0.002 | 0.084 | |
set_constant_fit_params | 0.001 | 0.001 | 0.002 | |
shorten_normalization_type_name | 0.001 | 0.000 | 0.002 | |
split_SE_components | 0.141 | 0.004 | 0.166 | |
standardize_mae | 0.360 | 0.005 | 0.413 | |
standardize_se | 0.079 | 0.003 | 0.089 | |
update_env_idfs_from_mae | 0.003 | 0.000 | 0.007 | |
update_idfs_synonyms | 0.000 | 0.000 | 0.001 | |
validate_MAE | 0.182 | 0.002 | 0.201 | |
validate_SE | 0.060 | 0.001 | 0.069 | |
validate_identifiers | 0.015 | 0.003 | 0.019 | |
validate_json | 0.000 | 0.001 | 0.000 | |
validate_mae_with_schema | 0.650 | 0.062 | 2.564 | |
validate_se_assay_name | 0.010 | 0.001 | 0.030 | |