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This page was generated on 2024-06-21 17:38 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 788/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDRcore 1.2.0  (landing page)
Arkadiusz Gladki
Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024)
git_url: https://git.bioconductor.org/packages/gDRcore
git_branch: RELEASE_3_19
git_last_commit: 8b5ff22
git_last_commit_date: 2024-04-30 11:50:21 -0400 (Tue, 30 Apr 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 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for gDRcore on nebbiolo1

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: 1.2.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:gDRcore.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings gDRcore_1.2.0.tar.gz
StartedAt: 2024-06-19 23:23:10 -0400 (Wed, 19 Jun 2024)
EndedAt: 2024-06-19 23:28:39 -0400 (Wed, 19 Jun 2024)
EllapsedTime: 329.7 seconds
RetCode: 0
Status:   OK  
CheckDir: gDRcore.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:gDRcore.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings gDRcore_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/gDRcore.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘gDRcore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDRcore’ version ‘1.2.0’
* 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: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 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 16.276  0.442  16.181
add_CellLine_annotation                5.097  0.220   5.317
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/gDRcore.Rcheck/00check.log’
for details.


Installation output

gDRcore.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL gDRcore
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘gDRcore’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c gDRcore.cpp -o gDRcore.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o gDRcore.so gDRcore.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-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 version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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("gDRcore")
> library("testthat")
> 
> test_check("gDRcore")
INFO [2024-06-19 23:24:46] Merge with Cell line info
INFO [2024-06-19 23:24:46] Merge with Cell line info
INFO [2024-06-19 23:27:44] 
INFO [2024-06-19 23:27:59] Manifest loaded successfully
INFO [2024-06-19 23:27:59] Reading Template_7daytreated.xlsx with load_templates_xlsx
INFO [2024-06-19 23:27:59] Loading Template_7daytreated.xlsx
INFO [2024-06-19 23:27:59] Loading Template_Untreated.xlsx
INFO [2024-06-19 23:27:59] Templates loaded successfully!
INFO [2024-06-19 23:27:59] Reading file /home/biocbuild/bbs-3.19-bioc/R/site-library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-06-19 23:27:59] Plate 201904190a read; 384 wells
INFO [2024-06-19 23:27:59] Plate 201904190b read; 384 wells
INFO [2024-06-19 23:27:59] Plate 201904190c read; 384 wells
INFO [2024-06-19 23:27:59] Plate 201904190d read; 384 wells
INFO [2024-06-19 23:27:59] Plate 201904190e read; 384 wells
INFO [2024-06-19 23:27:59] Plate 201904190f read; 384 wells
INFO [2024-06-19 23:27:59] File done
INFO [2024-06-19 23:27:59] Reading file /home/biocbuild/bbs-3.19-bioc/R/site-library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-06-19 23:28:00] Plate 201904197a read; 384 wells
INFO [2024-06-19 23:28:00] Plate 201904197b read; 384 wells
INFO [2024-06-19 23:28:00] Plate 201904197c read; 384 wells
INFO [2024-06-19 23:28:00] Plate 201904197d read; 384 wells
INFO [2024-06-19 23:28:00] Plate 201904197e read; 384 wells
INFO [2024-06-19 23:28:00] Plate 201904197f read; 384 wells
INFO [2024-06-19 23:28:00] File done
INFO [2024-06-19 23:28:00] Manifest loaded successfully
INFO [2024-06-19 23:28:00] Reading Template_7daytreated.xlsx with load_templates_xlsx
INFO [2024-06-19 23:28:00] Loading Template_7daytreated.xlsx
INFO [2024-06-19 23:28:00] Loading Template_Untreated.xlsx
INFO [2024-06-19 23:28:00] Templates loaded successfully!
INFO [2024-06-19 23:28:00] Reading file /home/biocbuild/bbs-3.19-bioc/R/site-library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-06-19 23:28:00] Plate 201904190a read; 384 wells
INFO [2024-06-19 23:28:00] Plate 201904190b read; 384 wells
INFO [2024-06-19 23:28:00] Plate 201904190c read; 384 wells
INFO [2024-06-19 23:28:00] Plate 201904190d read; 384 wells
INFO [2024-06-19 23:28:00] Plate 201904190e read; 384 wells
INFO [2024-06-19 23:28:00] Plate 201904190f read; 384 wells
INFO [2024-06-19 23:28:00] File done
INFO [2024-06-19 23:28:00] Reading file /home/biocbuild/bbs-3.19-bioc/R/site-library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-06-19 23:28:01] Plate 201904197a read; 384 wells
INFO [2024-06-19 23:28:01] Plate 201904197b read; 384 wells
INFO [2024-06-19 23:28:01] Plate 201904197c read; 384 wells
INFO [2024-06-19 23:28:01] Plate 201904197d read; 384 wells
INFO [2024-06-19 23:28:01] Plate 201904197e read; 384 wells
INFO [2024-06-19 23:28:01] Plate 201904197f read; 384 wells
INFO [2024-06-19 23:28:01] File done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 197 ]
> 
> proc.time()
   user  system elapsed 
211.873   3.109 207.365 

Example timings

gDRcore.Rcheck/gDRcore-Ex.timings

nameusersystemelapsed
add_CellLine_annotation5.0970.2205.317
add_Drug_annotation0.8960.0360.932
calculate_GR_value0.0020.0000.003
calculate_excess0.060.000.06
calculate_matrix_metric0.0170.0040.021
cleanup_metadata0.0220.0040.026
convert_mae_to_raw_data1.0430.0561.072
convert_se_to_raw_data0.8180.0680.867
data_model0.0010.0000.001
dot-standardize_conc0.0020.0000.001
fit_SE.combinations2.7360.0682.796
get_default_nested_identifiers0.0010.0000.001
grr_matches0.0120.0000.013
identify_data_type0.0410.0000.041
identify_keys0.0970.0000.097
map_conc_to_standardized_conc0.0040.0000.004
map_df0.0990.0120.111
map_ids_to_fits0.0020.0000.002
merge_data1.3570.1241.426
prepare_input1.2070.0201.161
remove_drug_batch0.0010.0000.000
replace_conc_with_standardized_conc0.0010.0000.001
round_concentration000
runDrugResponseProcessingPipelineFxns16.276 0.44216.181
split_raw_data0.2850.0040.259
test_synthetic_data0.7990.0200.790