Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-10-28 11:48 -0400 (Mon, 28 Oct 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4501 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4761 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4504 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4535 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4483 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4491 |
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 778/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
gDRcore 1.3.13 (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 | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the gDRcore package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gDRcore.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: gDRcore |
Version: 1.3.13 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gDRcore.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gDRcore_1.3.13.tar.gz |
StartedAt: 2024-10-27 15:41:25 -0400 (Sun, 27 Oct 2024) |
EndedAt: 2024-10-27 15:46:38 -0400 (Sun, 27 Oct 2024) |
EllapsedTime: 313.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: gDRcore.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gDRcore.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gDRcore_1.3.13.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/gDRcore.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘gDRcore/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘gDRcore’ version ‘1.3.13’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘gDRcore’ can be installed ... OK * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 whether startup messages can be suppressed ... 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * 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-3.20-bioc/meat/gDRcore.Rcheck/00check.log’ for details.
gDRcore.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gDRcore ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘gDRcore’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gDRcore.cpp -o gDRcore.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o gDRcore.so gDRcore.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-gDRcore/00new/gDRcore/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (gDRcore)
gDRcore.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-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("gDRcore") > library("testthat") > > test_check("gDRcore") INFO [2024-10-27 15:45:41] Merge with Cell line info INFO [2024-10-27 15:45:41] Merge with Cell line info INFO [2024-10-27 15:46:29] INFO [2024-10-27 15:46:29] INFO [2024-10-27 15:46:29] INFO [2024-10-27 15:46:33] Manifest loaded successfully INFO [2024-10-27 15:46:33] Reading Template_7daytreated.xlsx with load_templates_xlsx INFO [2024-10-27 15:46:33] Loading Template_7daytreated.xlsx INFO [2024-10-27 15:46:33] Loading Template_Untreated.xlsx INFO [2024-10-27 15:46:33] Templates loaded successfully! INFO [2024-10-27 15:46:33] Reading file /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7 INFO [2024-10-27 15:46:33] Plate 201904190a read; 384 wells INFO [2024-10-27 15:46:33] Plate 201904190b read; 384 wells INFO [2024-10-27 15:46:33] Plate 201904190c read; 384 wells INFO [2024-10-27 15:46:33] Plate 201904190d read; 384 wells INFO [2024-10-27 15:46:33] Plate 201904190e read; 384 wells INFO [2024-10-27 15:46:33] Plate 201904190f read; 384 wells INFO [2024-10-27 15:46:33] File done INFO [2024-10-27 15:46:33] Reading file /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7 INFO [2024-10-27 15:46:33] Plate 201904197a read; 384 wells INFO [2024-10-27 15:46:33] Plate 201904197b read; 384 wells INFO [2024-10-27 15:46:33] Plate 201904197c read; 384 wells INFO [2024-10-27 15:46:33] Plate 201904197d read; 384 wells INFO [2024-10-27 15:46:33] Plate 201904197e read; 384 wells INFO [2024-10-27 15:46:33] Plate 201904197f read; 384 wells INFO [2024-10-27 15:46:33] File done INFO [2024-10-27 15:46:33] Manifest loaded successfully INFO [2024-10-27 15:46:33] Reading Template_7daytreated.xlsx with load_templates_xlsx INFO [2024-10-27 15:46:33] Loading Template_7daytreated.xlsx INFO [2024-10-27 15:46:33] Loading Template_Untreated.xlsx INFO [2024-10-27 15:46:33] Templates loaded successfully! INFO [2024-10-27 15:46:33] Reading file /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7 INFO [2024-10-27 15:46:33] Plate 201904190a read; 384 wells INFO [2024-10-27 15:46:33] Plate 201904190b read; 384 wells INFO [2024-10-27 15:46:33] Plate 201904190c read; 384 wells INFO [2024-10-27 15:46:33] Plate 201904190d read; 384 wells INFO [2024-10-27 15:46:33] Plate 201904190e read; 384 wells INFO [2024-10-27 15:46:33] Plate 201904190f read; 384 wells INFO [2024-10-27 15:46:33] File done INFO [2024-10-27 15:46:33] Reading file /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7 INFO [2024-10-27 15:46:33] Plate 201904197a read; 384 wells INFO [2024-10-27 15:46:33] Plate 201904197b read; 384 wells INFO [2024-10-27 15:46:33] Plate 201904197c read; 384 wells INFO [2024-10-27 15:46:33] Plate 201904197d read; 384 wells INFO [2024-10-27 15:46:33] Plate 201904197e read; 384 wells INFO [2024-10-27 15:46:33] Plate 201904197f read; 384 wells INFO [2024-10-27 15:46:33] File done [ FAIL 0 | WARN 0 | SKIP 0 | PASS 222 ] > > proc.time() user system elapsed 55.178 1.069 56.259
gDRcore.Rcheck/gDRcore-Ex.timings
name | user | system | elapsed | |
add_CellLine_annotation | 1.924 | 0.075 | 2.000 | |
add_Drug_annotation | 0.292 | 0.024 | 0.316 | |
calculate_GR_value | 0.001 | 0.000 | 0.001 | |
calculate_excess | 0.017 | 0.001 | 0.019 | |
calculate_matrix_metric | 0.004 | 0.001 | 0.006 | |
calculate_score | 0.01 | 0.00 | 0.01 | |
cleanup_metadata | 0.013 | 0.031 | 0.045 | |
convert_mae_to_raw_data | 0.340 | 0.015 | 0.357 | |
convert_se_to_raw_data | 0.258 | 0.002 | 0.259 | |
data_model | 0.001 | 0.000 | 0.000 | |
dot-standardize_conc | 0.000 | 0.000 | 0.001 | |
fit_SE.combinations | 0.857 | 0.018 | 0.876 | |
get_cellline_annotation_from_dt | 0.002 | 0.001 | 0.002 | |
get_default_nested_identifiers | 0.001 | 0.000 | 0.000 | |
get_drug_annotation_from_dt | 0.001 | 0.000 | 0.001 | |
grr_matches | 0.003 | 0.000 | 0.004 | |
identify_data_type | 0.010 | 0.001 | 0.010 | |
identify_keys | 0.025 | 0.000 | 0.025 | |
map_conc_to_standardized_conc | 0.001 | 0.000 | 0.001 | |
map_df | 0.026 | 0.000 | 0.027 | |
map_ids_to_fits | 0.001 | 0.000 | 0.001 | |
merge_data | 0.423 | 0.067 | 0.492 | |
prepare_input | 0.370 | 0.054 | 0.423 | |
process_perturbations | 0.001 | 0.000 | 0.001 | |
remove_drug_batch | 0 | 0 | 0 | |
replace_conc_with_standardized_conc | 0 | 0 | 0 | |
runDrugResponseProcessingPipelineFxns | 4.581 | 0.242 | 4.826 | |
split_raw_data | 0.074 | 0.003 | 0.077 | |
test_synthetic_data | 0.246 | 0.006 | 0.253 | |