Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:45 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 775/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
gDRutils 1.5.5 (landing page) Arkadiusz Gladki
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
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: 1.5.5 |
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_1.5.5.tar.gz |
StartedAt: 2024-12-22 19:25:34 -0500 (Sun, 22 Dec 2024) |
EndedAt: 2024-12-22 19:26:51 -0500 (Sun, 22 Dec 2024) |
EllapsedTime: 76.9 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_1.5.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/gDRutils.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘gDRutils/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘gDRutils’ version ‘1.5.5’ * 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 ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: SE_metadata.Rd: SummarizedExperiment-class convert_mae_assay_to_dt.Rd: SummarizedExperiment-class, MultiAssayExperiment-class convert_se_assay_to_dt.Rd: SummarizedExperiment-class is_exp_empty.Rd: SummarizedExperiment-class split_SE_components.Rd: SummarizedExperiment-class validate_se_assay_name.Rd: SummarizedExperiment-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 ‘/Users/biocbuild/bbs-3.21-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/4.5-arm64/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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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 690 ] > > proc.time() user system elapsed 15.297 0.595 15.849
gDRutils.Rcheck/gDRutils-Ex.timings
name | user | system | elapsed | |
MAEpply | 0.160 | 0.007 | 0.169 | |
SE_metadata | 0.014 | 0.002 | 0.017 | |
addClass | 0.001 | 0.000 | 0.001 | |
aggregate_assay | 0.392 | 0.007 | 0.400 | |
apply_bumpy_function | 0.381 | 0.016 | 0.397 | |
assert_choices | 0 | 0 | 0 | |
average_biological_replicates_dt | 0.015 | 0.001 | 0.016 | |
calc_sd | 0.001 | 0.000 | 0.001 | |
capVals | 0.088 | 0.005 | 0.093 | |
cap_xc50 | 0 | 0 | 0 | |
convert_colData_to_json | 0.016 | 0.000 | 0.016 | |
convert_combo_data_to_dt | 0.101 | 0.005 | 0.110 | |
convert_combo_field_to_assay | 0.000 | 0.000 | 0.001 | |
convert_mae_assay_to_dt | 0.019 | 0.000 | 0.021 | |
convert_mae_to_json | 0.007 | 0.000 | 0.007 | |
convert_metadata_to_json | 0.003 | 0.000 | 0.003 | |
convert_rowData_to_json | 0.001 | 0.000 | 0.001 | |
convert_se_assay_to_custom_dt | 0.387 | 0.017 | 0.407 | |
convert_se_assay_to_dt | 0.017 | 0.001 | 0.018 | |
convert_se_to_json | 0.004 | 0.000 | 0.004 | |
define_matrix_grid_positions | 0.016 | 0.001 | 0.018 | |
demote_fields | 0.113 | 0.003 | 0.116 | |
df_to_bm_assay | 0.042 | 0.003 | 0.045 | |
dot-set_invalid_fit_params | 0.000 | 0.000 | 0.001 | |
extend_normalization_type_name | 0 | 0 | 0 | |
fit_curves | 0.054 | 0.010 | 0.065 | |
flatten | 0.003 | 0.000 | 0.003 | |
gen_synthetic_data | 0.001 | 0.000 | 0.002 | |
geometric_mean | 0 | 0 | 0 | |
get_MAE_identifiers | 0.003 | 0.001 | 0.004 | |
get_additional_variables | 0.002 | 0.000 | 0.002 | |
get_assay_dt_duplicated_rows | 0.027 | 0.001 | 0.027 | |
get_assay_names | 0 | 0 | 0 | |
get_assay_req_uniq_cols | 0.021 | 0.001 | 0.021 | |
get_combo_assay_names | 0.000 | 0.000 | 0.001 | |
get_combo_base_assay_names | 0.001 | 0.000 | 0.000 | |
get_combo_excess_field_names | 0.000 | 0.000 | 0.001 | |
get_combo_score_assay_names | 0.001 | 0.000 | 0.000 | |
get_combo_score_field_names | 0.000 | 0.000 | 0.001 | |
get_default_identifiers | 0 | 0 | 0 | |
get_duplicated_rows | 0.001 | 0.000 | 0.001 | |
get_env_assay_names | 0 | 0 | 0 | |
get_env_var | 0 | 0 | 0 | |
get_expect_one_identifiers | 0 | 0 | 0 | |
get_experiment_groups | 0.001 | 0.001 | 0.000 | |
get_identifiers_dt | 0.002 | 0.001 | 0.003 | |
get_idfs_synonyms | 0 | 0 | 0 | |
get_isobologram_columns | 0.010 | 0.001 | 0.010 | |
get_non_empty_assays | 0.014 | 0.000 | 0.016 | |
get_required_identifiers | 0.000 | 0.001 | 0.000 | |
get_settings_from_json | 0.000 | 0.000 | 0.001 | |
get_supported_experiments | 0 | 0 | 0 | |
get_synthetic_data | 0.005 | 0.000 | 0.005 | |
get_testdata | 0.027 | 0.008 | 0.036 | |
get_testdata_codilution | 0.023 | 0.002 | 0.025 | |
get_testdata_combo | 0.066 | 0.007 | 0.075 | |
has_assay_dt_duplicated_rows | 0.027 | 0.001 | 0.029 | |
has_dt_duplicated_rows | 0.001 | 0.000 | 0.000 | |
has_single_codrug_data | 0.020 | 0.001 | 0.023 | |
has_valid_codrug_data | 0.021 | 0.000 | 0.022 | |
headers | 0.003 | 0.003 | 0.006 | |
identifiers | 0 | 0 | 0 | |
identify_unique_se_metadata_fields | 0.004 | 0.000 | 0.004 | |
is_any_exp_empty | 0.013 | 0.000 | 0.013 | |
is_combo_data | 0.060 | 0.004 | 0.064 | |
is_exp_empty | 0.017 | 0.001 | 0.018 | |
is_mae_empty | 0.013 | 0.000 | 0.013 | |
logisticFit | 0.006 | 0.001 | 0.007 | |
loop | 0 | 0 | 0 | |
mcolData | 0.005 | 0.000 | 0.006 | |
merge_SE | 0.446 | 0.006 | 0.460 | |
merge_assay | 0.091 | 0.001 | 0.093 | |
merge_metadata | 0.004 | 0.000 | 0.004 | |
modifyData | 0.031 | 0.003 | 0.034 | |
mrowData | 0.006 | 0.001 | 0.007 | |
predict_conc_from_efficacy | 0.001 | 0.000 | 0.000 | |
predict_efficacy_from_conc | 0.000 | 0.000 | 0.001 | |
prettify_flat_metrics | 0.006 | 0.001 | 0.006 | |
promote_fields | 0.077 | 0.004 | 0.081 | |
refine_coldata | 0.004 | 0.001 | 0.006 | |
refine_rowdata | 0.018 | 0.000 | 0.019 | |
remove_codrug_data | 0.01 | 0.00 | 0.01 | |
rename_DFrame | 0.004 | 0.000 | 0.005 | |
rename_bumpy | 0.009 | 0.000 | 0.010 | |
round_concentration | 0 | 0 | 0 | |
set_constant_fit_params | 0 | 0 | 0 | |
set_unique_cl_names | 0.016 | 0.001 | 0.017 | |
set_unique_cl_names_dt | 0.005 | 0.000 | 0.005 | |
set_unique_drug_names | 0.017 | 0.000 | 0.017 | |
set_unique_drug_names_dt | 0.011 | 0.000 | 0.011 | |
set_unique_identifiers | 0.096 | 0.001 | 0.097 | |
set_unique_names_dt | 0.005 | 0.000 | 0.005 | |
shorten_normalization_type_name | 0 | 0 | 0 | |
split_SE_components | 0.015 | 0.001 | 0.016 | |
standardize_mae | 0.032 | 0.001 | 0.033 | |
standardize_se | 0.010 | 0.001 | 0.011 | |
throw_msg_if_duplicates | 0.022 | 0.002 | 0.024 | |
update_env_idfs_from_mae | 0.000 | 0.000 | 0.001 | |
update_idfs_synonyms | 0 | 0 | 0 | |
validate_MAE | 0.031 | 0.000 | 0.031 | |
validate_SE | 0.009 | 0.000 | 0.009 | |
validate_identifiers | 0.002 | 0.000 | 0.003 | |
validate_json | 0 | 0 | 0 | |
validate_mae_with_schema | 0.142 | 0.012 | 0.148 | |
validate_se_assay_name | 0.003 | 0.001 | 0.003 | |