Back to Multiple platform build/check report for BioC 3.18:   simplified   long
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-04-17 11:37:45 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 778/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRcore 1.0.1  (landing page)
Arkadiusz Gladki
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/gDRcore
git_branch: RELEASE_3_18
git_last_commit: 0405d87
git_last_commit_date: 2024-02-15 11:18:15 -0400 (Thu, 15 Feb 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for gDRcore on merida1


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.

raw results


Summary

Package: gDRcore
Version: 1.0.1
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_1.0.1.tar.gz
StartedAt: 2024-04-16 03:03:52 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 03:15:48 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 716.3 seconds
RetCode: 0
Status:   OK  
CheckDir: gDRcore.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/gDRcore.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gDRcore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRcore’ version ‘1.0.1’
* 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 R 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 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
Examples with CPU (user + system) or elapsed time > 5s
                                        user system elapsed
runDrugResponseProcessingPipelineFxns 40.073  1.051  43.650
add_CellLine_annotation               10.498  0.532  11.461
fit_SE.combinations                    6.522  0.243   7.325
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.18-bioc/meat/gDRcore.Rcheck/00check.log’
for details.



Installation output

gDRcore.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gDRcore
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘gDRcore’ ...
** 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 -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-gDRcore/00new/gDRcore/libs
** R
** 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)

Tests output

gDRcore.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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")

Attaching package: 'testthat'

The following object is masked from 'package:gDRcore':

    matches

> 
> test_check("gDRcore")
INFO [2024-04-16 03:07:19] Merge with Cell line info
INFO [2024-04-16 03:07:19] Merge with Cell line info
INFO [2024-04-16 03:14:39] 
INFO [2024-04-16 03:15:15] Manifest loaded successfully
INFO [2024-04-16 03:15:15] Reading Template_7daytreated.xlsx with load_templates_xlsx
INFO [2024-04-16 03:15:15] Loading Template_7daytreated.xlsx
INFO [2024-04-16 03:15:15] Loading Template_Untreated.xlsx
INFO [2024-04-16 03:15:15] Templates loaded successfully!
INFO [2024-04-16 03:15:16] Reading file /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-04-16 03:15:16] Plate 201904190a read; 384 wells
INFO [2024-04-16 03:15:16] Plate 201904190b read; 384 wells
INFO [2024-04-16 03:15:16] Plate 201904190c read; 384 wells
INFO [2024-04-16 03:15:16] Plate 201904190d read; 384 wells
INFO [2024-04-16 03:15:16] Plate 201904190e read; 384 wells
INFO [2024-04-16 03:15:16] Plate 201904190f read; 384 wells
INFO [2024-04-16 03:15:16] File done
INFO [2024-04-16 03:15:16] Reading file /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-04-16 03:15:17] Plate 201904197a read; 384 wells
INFO [2024-04-16 03:15:17] Plate 201904197b read; 384 wells
INFO [2024-04-16 03:15:17] Plate 201904197c read; 384 wells
INFO [2024-04-16 03:15:17] Plate 201904197d read; 384 wells
INFO [2024-04-16 03:15:17] Plate 201904197e read; 384 wells
INFO [2024-04-16 03:15:17] Plate 201904197f read; 384 wells
INFO [2024-04-16 03:15:17] File done
INFO [2024-04-16 03:15:18] Manifest loaded successfully
INFO [2024-04-16 03:15:18] Reading Template_7daytreated.xlsx with load_templates_xlsx
INFO [2024-04-16 03:15:18] Loading Template_7daytreated.xlsx
INFO [2024-04-16 03:15:18] Loading Template_Untreated.xlsx
INFO [2024-04-16 03:15:18] Templates loaded successfully!
INFO [2024-04-16 03:15:18] Reading file /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-04-16 03:15:19] Plate 201904190a read; 384 wells
INFO [2024-04-16 03:15:19] Plate 201904190b read; 384 wells
INFO [2024-04-16 03:15:19] Plate 201904190c read; 384 wells
INFO [2024-04-16 03:15:19] Plate 201904190d read; 384 wells
INFO [2024-04-16 03:15:19] Plate 201904190e read; 384 wells
INFO [2024-04-16 03:15:19] Plate 201904190f read; 384 wells
INFO [2024-04-16 03:15:19] File done
INFO [2024-04-16 03:15:19] Reading file /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-04-16 03:15:20] Plate 201904197a read; 384 wells
INFO [2024-04-16 03:15:20] Plate 201904197b read; 384 wells
INFO [2024-04-16 03:15:20] Plate 201904197c read; 384 wells
INFO [2024-04-16 03:15:20] Plate 201904197d read; 384 wells
INFO [2024-04-16 03:15:20] Plate 201904197e read; 384 wells
INFO [2024-04-16 03:15:20] Plate 201904197f read; 384 wells
INFO [2024-04-16 03:15:20] File done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 177 ]
> 
> proc.time()
   user  system elapsed 
474.655   5.854 510.141 

Example timings

gDRcore.Rcheck/gDRcore-Ex.timings

nameusersystemelapsed
add_CellLine_annotation10.498 0.53211.461
add_Drug_annotation1.1910.1251.372
calculate_GR_value0.0040.0030.007
calculate_excess0.1450.0180.172
calculate_matrix_metric0.0410.0230.066
cleanup_metadata0.0810.1120.200
convert_mae_to_raw_data3.2820.1613.536
convert_se_to_raw_data0.2010.0100.212
data_model0.0010.0010.002
dot-standardize_conc0.0010.0010.002
fit_SE.combinations6.5220.2437.325
get_default_nested_identifiers0.0020.0010.002
identify_data_type0.0950.0130.109
identify_keys0.1240.0200.146
map_conc_to_standardized_conc0.0070.0020.009
map_df0.1320.0200.153
map_ids_to_fits0.0030.0010.005
matches0.0290.0060.036
merge_data3.1460.2683.588
prepare_input2.8300.2403.202
remove_drug_batch0.0010.0000.001
replace_conc_with_standardized_conc0.0020.0010.002
round_concentration0.0010.0010.001
runDrugResponseProcessingPipelineFxns40.073 1.05143.650
split_raw_data0.6040.0220.657
test_synthetic_data2.0570.0362.226