Arkadiusz Gladki
| Snapshot Date: 2025-04-28 17:48 -0400 (Mon, 28 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/gDRcore |
| git_branch: RELEASE_3_21 |
| git_last_commit: 3a5ff78 |
| git_last_commit_date: 2025-04-15 13:17:49 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-05-01 11:41 -0400 (Thu, 01 May 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4832 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4574 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88129) -- "How About a Twenty-Six" | 4553 |
| 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 793/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gDRcore 1.6.0 (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 | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | 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: 1.6.0 |
| 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_1.6.0.tar.gz |
| StartedAt: 2025-04-29 07:09:20 -0400 (Tue, 29 Apr 2025) |
| EndedAt: 2025-04-29 07:21:26 -0400 (Tue, 29 Apr 2025) |
| EllapsedTime: 725.9 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/gDRcore.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gDRcore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRcore’ version ‘1.6.0’
* 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 ‘gDRcore’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
fit_SE.combinations.Rd: SummarizedExperiment-class
runDrugResponseProcessingPipelineFxns.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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘gDRcore/libs/gDRcore.so’:
Found non-API call to R: ‘STRING_PTR’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runDrugResponseProcessingPipelineFxns 38.329 0.997 39.921
annotate_dt_with_cell_line 10.504 0.530 11.484
fit_SE.combinations 6.390 0.236 6.846
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.21-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/4.5-x86_64/Resources/library’ * installing *source* package ‘gDRcore’ ... ** this is package ‘gDRcore’ version ‘1.6.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gDRcore.cpp -o gDRcore.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o gDRcore.so gDRcore.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/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 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 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("gDRcore")
> library("testthat")
>
> test_check("gDRcore")
INFO [2025-04-29 07:20:16]
INFO [2025-04-29 07:20:16]
INFO [2025-04-29 07:20:16]
INFO [2025-04-29 07:20:54] Manifest loaded successfully
INFO [2025-04-29 07:20:54] Reading Template_7daytreated.xlsx with load_templates_xlsx
INFO [2025-04-29 07:20:54] Loading Template_7daytreated.xlsx
INFO [2025-04-29 07:20:55] Loading Template_Untreated.xlsx
INFO [2025-04-29 07:20:55] Templates loaded successfully!
INFO [2025-04-29 07:20:55] Reading file /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7
INFO [2025-04-29 07:20:56] Plate 201904190a read; 384 wells
INFO [2025-04-29 07:20:56] Plate 201904190b read; 384 wells
INFO [2025-04-29 07:20:56] Plate 201904190c read; 384 wells
INFO [2025-04-29 07:20:56] Plate 201904190d read; 384 wells
INFO [2025-04-29 07:20:56] Plate 201904190e read; 384 wells
INFO [2025-04-29 07:20:56] Plate 201904190f read; 384 wells
INFO [2025-04-29 07:20:56] File done
INFO [2025-04-29 07:20:56] Reading file /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7
INFO [2025-04-29 07:20:57] Plate 201904197a read; 384 wells
INFO [2025-04-29 07:20:57] Plate 201904197b read; 384 wells
INFO [2025-04-29 07:20:57] Plate 201904197c read; 384 wells
INFO [2025-04-29 07:20:57] Plate 201904197d read; 384 wells
INFO [2025-04-29 07:20:57] Plate 201904197e read; 384 wells
INFO [2025-04-29 07:20:57] Plate 201904197f read; 384 wells
INFO [2025-04-29 07:20:57] File done
INFO [2025-04-29 07:20:57] Manifest loaded successfully
INFO [2025-04-29 07:20:57] Reading Template_7daytreated.xlsx with load_templates_xlsx
INFO [2025-04-29 07:20:57] Loading Template_7daytreated.xlsx
INFO [2025-04-29 07:20:57] Loading Template_Untreated.xlsx
INFO [2025-04-29 07:20:58] Templates loaded successfully!
INFO [2025-04-29 07:20:58] Reading file /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7
INFO [2025-04-29 07:20:58] Plate 201904190a read; 384 wells
INFO [2025-04-29 07:20:58] Plate 201904190b read; 384 wells
INFO [2025-04-29 07:20:58] Plate 201904190c read; 384 wells
INFO [2025-04-29 07:20:58] Plate 201904190d read; 384 wells
INFO [2025-04-29 07:20:58] Plate 201904190e read; 384 wells
INFO [2025-04-29 07:20:59] Plate 201904190f read; 384 wells
INFO [2025-04-29 07:20:59] File done
INFO [2025-04-29 07:20:59] Reading file /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7
INFO [2025-04-29 07:20:59] Plate 201904197a read; 384 wells
INFO [2025-04-29 07:20:59] Plate 201904197b read; 384 wells
INFO [2025-04-29 07:20:59] Plate 201904197c read; 384 wells
INFO [2025-04-29 07:20:59] Plate 201904197d read; 384 wells
INFO [2025-04-29 07:20:59] Plate 201904197e read; 384 wells
INFO [2025-04-29 07:20:59] Plate 201904197f read; 384 wells
INFO [2025-04-29 07:20:59] File done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 224 ]
>
> proc.time()
user system elapsed
504.000 5.337 519.391
gDRcore.Rcheck/gDRcore-Ex.timings
| name | user | system | elapsed | |
| annotate_dt_with_cell_line | 10.504 | 0.530 | 11.484 | |
| annotate_dt_with_drug | 0.047 | 0.055 | 0.128 | |
| calculate_GR_value | 0.004 | 0.003 | 0.009 | |
| calculate_excess | 0.137 | 0.007 | 0.149 | |
| calculate_matrix_metric | 0.056 | 0.020 | 0.085 | |
| calculate_score | 0.069 | 0.002 | 0.078 | |
| cleanup_metadata | 0.694 | 0.163 | 0.923 | |
| convert_mae_to_raw_data | 2.761 | 0.124 | 2.912 | |
| convert_se_to_raw_data | 0.207 | 0.007 | 0.218 | |
| data_model | 0.002 | 0.000 | 0.002 | |
| fit_SE.combinations | 6.390 | 0.236 | 6.846 | |
| get_cell_line_annotation | 0.031 | 0.057 | 0.093 | |
| get_cellline_annotation_from_dt | 0.017 | 0.001 | 0.018 | |
| get_default_nested_identifiers | 0.002 | 0.001 | 0.002 | |
| get_drug_annotation | 0.048 | 0.053 | 0.102 | |
| get_drug_annotation_from_dt | 0.01 | 0.00 | 0.01 | |
| grr_matches | 0.029 | 0.002 | 0.031 | |
| identify_data_type | 0.096 | 0.004 | 0.101 | |
| identify_keys | 0.251 | 0.004 | 0.260 | |
| map_df | 0.262 | 0.005 | 0.272 | |
| map_ids_to_fits | 0.003 | 0.001 | 0.004 | |
| merge_data | 3.594 | 0.329 | 4.007 | |
| prepare_input | 3.192 | 0.231 | 3.482 | |
| process_perturbations | 0.013 | 0.001 | 0.014 | |
| replace_conc_with_standardized_conc | 0.002 | 0.001 | 0.003 | |
| runDrugResponseProcessingPipelineFxns | 38.329 | 0.997 | 39.921 | |
| split_raw_data | 0.663 | 0.024 | 0.698 | |
| test_synthetic_data | 1.968 | 0.031 | 2.019 | |