Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 781/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
gDRutils 1.4.0 (landing page) Arkadiusz Gladki
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
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: 1.4.0 |
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_1.4.0.tar.gz |
StartedAt: 2024-11-20 08:02:25 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 08:07:07 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 281.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: gDRutils.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/gDRutils.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) 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 ‘1.4.0’ * 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 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
gDRutils.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL gDRutils ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 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 687 ] > > proc.time() user system elapsed 67.633 2.118 69.563
gDRutils.Rcheck/gDRutils-Ex.timings
name | user | system | elapsed | |
MAEpply | 1.505 | 0.036 | 1.545 | |
SE_metadata | 0.046 | 0.000 | 0.046 | |
addClass | 0.002 | 0.000 | 0.003 | |
aggregate_assay | 0.704 | 0.044 | 0.749 | |
apply_bumpy_function | 2.182 | 0.103 | 2.291 | |
assert_choices | 0.000 | 0.000 | 0.001 | |
average_biological_replicates_dt | 0.062 | 0.000 | 0.063 | |
calc_sd | 0.001 | 0.000 | 0.000 | |
capVals | 0.429 | 0.001 | 0.431 | |
cap_xc50 | 0.000 | 0.000 | 0.001 | |
convert_colData_to_json | 0.076 | 0.000 | 0.076 | |
convert_combo_data_to_dt | 1.144 | 0.040 | 1.188 | |
convert_combo_field_to_assay | 0.002 | 0.000 | 0.002 | |
convert_mae_assay_to_dt | 0.099 | 0.000 | 0.099 | |
convert_mae_to_json | 0.023 | 0.000 | 0.024 | |
convert_metadata_to_json | 0.015 | 0.004 | 0.019 | |
convert_rowData_to_json | 0.004 | 0.000 | 0.004 | |
convert_se_assay_to_custom_dt | 0.581 | 0.012 | 0.593 | |
convert_se_assay_to_dt | 0.091 | 0.004 | 0.095 | |
convert_se_to_json | 0.019 | 0.000 | 0.019 | |
define_matrix_grid_positions | 0.071 | 0.004 | 0.074 | |
demote_fields | 0.569 | 0.004 | 0.566 | |
df_to_bm_assay | 0.198 | 0.000 | 0.198 | |
dot-set_invalid_fit_params | 0.001 | 0.000 | 0.000 | |
extend_normalization_type_name | 0 | 0 | 0 | |
fit_curves | 0.186 | 0.012 | 0.198 | |
flatten | 0.011 | 0.000 | 0.011 | |
gen_synthetic_data | 0.004 | 0.004 | 0.007 | |
geometric_mean | 0 | 0 | 0 | |
get_MAE_identifiers | 0.010 | 0.000 | 0.009 | |
get_additional_variables | 0.008 | 0.000 | 0.009 | |
get_assay_dt_duplicated_rows | 0.137 | 0.000 | 0.137 | |
get_assay_names | 0.001 | 0.000 | 0.000 | |
get_assay_req_uniq_cols | 0.132 | 0.000 | 0.132 | |
get_combo_assay_names | 0.001 | 0.000 | 0.001 | |
get_combo_base_assay_names | 0.002 | 0.000 | 0.002 | |
get_combo_excess_field_names | 0.003 | 0.000 | 0.002 | |
get_combo_score_assay_names | 0.002 | 0.000 | 0.001 | |
get_combo_score_field_names | 0.001 | 0.000 | 0.001 | |
get_default_identifiers | 0 | 0 | 0 | |
get_duplicated_rows | 0.004 | 0.000 | 0.004 | |
get_env_assay_names | 0.001 | 0.000 | 0.001 | |
get_expect_one_identifiers | 0.001 | 0.000 | 0.001 | |
get_experiment_groups | 0 | 0 | 0 | |
get_identifiers_dt | 0.007 | 0.000 | 0.007 | |
get_idfs_synonyms | 0 | 0 | 0 | |
get_isobologram_columns | 0.047 | 0.004 | 0.051 | |
get_non_empty_assays | 0.067 | 0.000 | 0.067 | |
get_required_identifiers | 0 | 0 | 0 | |
get_settings_from_json | 0.000 | 0.001 | 0.001 | |
get_supported_experiments | 0.000 | 0.001 | 0.001 | |
get_synthetic_data | 0.013 | 0.002 | 0.015 | |
get_testdata | 0.111 | 0.004 | 0.114 | |
get_testdata_codilution | 0.108 | 0.004 | 0.113 | |
get_testdata_combo | 0.287 | 0.003 | 0.308 | |
has_assay_dt_duplicated_rows | 0.1 | 0.0 | 0.1 | |
has_dt_duplicated_rows | 0.001 | 0.000 | 0.001 | |
has_single_codrug_data | 0.11 | 0.00 | 0.11 | |
has_valid_codrug_data | 0.106 | 0.000 | 0.106 | |
headers | 0.015 | 0.000 | 0.016 | |
identifiers | 0.000 | 0.000 | 0.001 | |
identify_unique_se_metadata_fields | 0.006 | 0.003 | 0.010 | |
is_any_exp_empty | 0.066 | 0.000 | 0.066 | |
is_combo_data | 0.182 | 0.020 | 0.202 | |
is_exp_empty | 0.110 | 0.004 | 0.114 | |
is_mae_empty | 0.076 | 0.004 | 0.080 | |
logisticFit | 0.030 | 0.008 | 0.038 | |
loop | 0 | 0 | 0 | |
mcolData | 0.021 | 0.000 | 0.022 | |
merge_SE | 2.325 | 0.036 | 2.365 | |
merge_assay | 0.498 | 0.000 | 0.501 | |
merge_metadata | 0.01 | 0.00 | 0.01 | |
modifyData | 0.139 | 0.004 | 0.144 | |
mrowData | 0.019 | 0.000 | 0.020 | |
predict_conc_from_efficacy | 0 | 0 | 0 | |
predict_efficacy_from_conc | 0.001 | 0.000 | 0.001 | |
prettify_flat_metrics | 0.03 | 0.00 | 0.03 | |
promote_fields | 0.293 | 0.000 | 0.293 | |
refine_coldata | 0.015 | 0.000 | 0.014 | |
refine_rowdata | 0.068 | 0.000 | 0.068 | |
remove_codrug_data | 0.048 | 0.000 | 0.048 | |
rename_DFrame | 0.013 | 0.000 | 0.013 | |
rename_bumpy | 0.039 | 0.004 | 0.043 | |
round_concentration | 0.001 | 0.000 | 0.001 | |
set_constant_fit_params | 0.001 | 0.000 | 0.001 | |
set_unique_cl_names | 0.097 | 0.000 | 0.097 | |
set_unique_cl_names_dt | 0.033 | 0.000 | 0.034 | |
set_unique_drug_names | 0.09 | 0.00 | 0.09 | |
set_unique_drug_names_dt | 0.045 | 0.000 | 0.044 | |
set_unique_identifiers | 0.411 | 0.000 | 0.411 | |
shorten_normalization_type_name | 0.001 | 0.000 | 0.000 | |
split_SE_components | 0.083 | 0.000 | 0.083 | |
standardize_mae | 0.164 | 0.000 | 0.165 | |
standardize_se | 0.045 | 0.000 | 0.045 | |
throw_msg_if_duplicates | 0.107 | 0.000 | 0.107 | |
update_env_idfs_from_mae | 0.001 | 0.000 | 0.002 | |
update_idfs_synonyms | 0.000 | 0.000 | 0.001 | |
validate_MAE | 0.111 | 0.000 | 0.112 | |
validate_SE | 0.028 | 0.008 | 0.037 | |
validate_identifiers | 0.009 | 0.000 | 0.010 | |
validate_json | 0 | 0 | 0 | |
validate_mae_with_schema | 0.668 | 0.040 | 0.931 | |
validate_se_assay_name | 0.008 | 0.000 | 0.008 | |