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This page was generated on 2024-03-04 11:39:14 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 776/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRcore 1.1.13  (landing page)
Arkadiusz Gladki
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/gDRcore
git_branch: devel
git_last_commit: 91bc8b0
git_last_commit_date: 2024-02-28 09:43:42 -0500 (Wed, 28 Feb 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

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: 1.1.13
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_1.1.13.tar.gz
StartedAt: 2024-03-02 04:16:53 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 04:30:52 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 838.6 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_1.1.13.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/gDRcore.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-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 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 ‘1.1.13’
* 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 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
Examples with CPU (user + system) or elapsed time > 5s
                                        user system elapsed
runDrugResponseProcessingPipelineFxns 37.742  1.194  46.456
add_CellLine_annotation               10.216  0.544  12.903
fit_SE.combinations                    5.974  0.237   7.479
* 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-3.19-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/4.4-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/4.4-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)

Tests output

gDRcore.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 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 [2024-03-02 04:20:45] Merge with Cell line info
INFO [2024-03-02 04:20:45] Merge with Cell line info
INFO [2024-03-02 04:29:26] 
INFO [2024-03-02 04:30:13] Manifest loaded successfully
INFO [2024-03-02 04:30:13] Reading Template_7daytreated.xlsx with load_templates_xlsx
INFO [2024-03-02 04:30:13] Loading Template_7daytreated.xlsx
INFO [2024-03-02 04:30:13] Loading Template_Untreated.xlsx
INFO [2024-03-02 04:30:13] Templates loaded successfully!
INFO [2024-03-02 04:30:13] Reading file /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-03-02 04:30:14] Plate 201904190a read; 384 wells
INFO [2024-03-02 04:30:14] Plate 201904190b read; 384 wells
INFO [2024-03-02 04:30:14] Plate 201904190c read; 384 wells
INFO [2024-03-02 04:30:14] Plate 201904190d read; 384 wells
INFO [2024-03-02 04:30:14] Plate 201904190e read; 384 wells
INFO [2024-03-02 04:30:14] Plate 201904190f read; 384 wells
INFO [2024-03-02 04:30:15] File done
INFO [2024-03-02 04:30:15] Reading file /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-03-02 04:30:16] Plate 201904197a read; 384 wells
INFO [2024-03-02 04:30:16] Plate 201904197b read; 384 wells
INFO [2024-03-02 04:30:16] Plate 201904197c read; 384 wells
INFO [2024-03-02 04:30:16] Plate 201904197d read; 384 wells
INFO [2024-03-02 04:30:16] Plate 201904197e read; 384 wells
INFO [2024-03-02 04:30:16] Plate 201904197f read; 384 wells
INFO [2024-03-02 04:30:16] File done
INFO [2024-03-02 04:30:16] Manifest loaded successfully
INFO [2024-03-02 04:30:16] Reading Template_7daytreated.xlsx with load_templates_xlsx
INFO [2024-03-02 04:30:16] Loading Template_7daytreated.xlsx
INFO [2024-03-02 04:30:17] Loading Template_Untreated.xlsx
INFO [2024-03-02 04:30:17] Templates loaded successfully!
INFO [2024-03-02 04:30:17] Reading file /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-03-02 04:30:18] Plate 201904190a read; 384 wells
INFO [2024-03-02 04:30:18] Plate 201904190b read; 384 wells
INFO [2024-03-02 04:30:18] Plate 201904190c read; 384 wells
INFO [2024-03-02 04:30:18] Plate 201904190d read; 384 wells
INFO [2024-03-02 04:30:18] Plate 201904190e read; 384 wells
INFO [2024-03-02 04:30:18] Plate 201904190f read; 384 wells
INFO [2024-03-02 04:30:18] File done
INFO [2024-03-02 04:30:18] Reading file /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-03-02 04:30:19] Plate 201904197a read; 384 wells
INFO [2024-03-02 04:30:19] Plate 201904197b read; 384 wells
INFO [2024-03-02 04:30:19] Plate 201904197c read; 384 wells
INFO [2024-03-02 04:30:19] Plate 201904197d read; 384 wells
INFO [2024-03-02 04:30:19] Plate 201904197e read; 384 wells
INFO [2024-03-02 04:30:19] Plate 201904197f read; 384 wells
INFO [2024-03-02 04:30:19] File done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 182 ]
> 
> proc.time()
   user  system elapsed 
502.342   8.034 608.119 

Example timings

gDRcore.Rcheck/gDRcore-Ex.timings

nameusersystemelapsed
add_CellLine_annotation10.216 0.54412.903
add_Drug_annotation1.2320.1371.674
calculate_GR_value0.0040.0020.006
calculate_excess0.1370.0030.178
calculate_matrix_metric0.0400.0180.071
cleanup_metadata0.0870.1120.238
convert_mae_to_raw_data3.2260.1604.677
convert_se_to_raw_data0.1990.0090.253
data_model0.0010.0010.002
dot-standardize_conc0.0020.0010.002
fit_SE.combinations5.9740.2377.479
get_default_nested_identifiers0.0020.0010.004
grr_matches0.0300.0050.046
identify_data_type0.1010.0140.138
identify_keys0.2720.0370.355
map_conc_to_standardized_conc0.0080.0020.014
map_df0.2860.0390.377
map_ids_to_fits0.0030.0010.004
merge_data3.4470.3274.362
prepare_input3.0800.2543.908
remove_drug_batch0.0000.0000.001
replace_conc_with_standardized_conc0.0020.0010.003
round_concentration0.0000.0010.001
runDrugResponseProcessingPipelineFxns37.742 1.19446.456
split_raw_data0.6450.0270.763
test_synthetic_data2.1080.0492.540