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This page was generated on 2024-03-28 11:32:21 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4376
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Package 777/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDR 1.0.0  (landing page)
Arkadiusz Gladki
Snapshot Date: 2024-03-26 09:00:03 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/gDR
git_branch: RELEASE_3_18
git_last_commit: 3b047b8
git_last_commit_date: 2023-10-24 11:49:57 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for gDR on kjohnson1


To the developers/maintainers of the gDR package:
- 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: gDR
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gDR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gDR_1.0.0.tar.gz
StartedAt: 2024-03-27 13:53:17 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 13:56:46 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 208.5 seconds
RetCode: 0
Status:   OK  
CheckDir: gDR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gDR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gDR_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/gDR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-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 Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gDR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDR’ version ‘1.0.0’
* 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 ‘gDR’ can be installed ... OK
* 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* 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 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: OK


Installation output

gDR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘gDR’ ...
** using staged installation
** R
** data
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gDR)

Tests output

gDR.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: aarch64-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(testthat)
> library(gDR)
Loading required package: gDRcore

Attaching package: 'gDRcore'

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

    matches

Loading required package: gDRimport
Loading required package: gDRutils
> 
> test_check("gDR")
INFO [2024-03-27 13:56:36] Manifest loaded successfully
INFO [2024-03-27 13:56:36] Reading Template_7daytreated.xlsx with load_templates_xlsx
INFO [2024-03-27 13:56:36] Loading Template_7daytreated.xlsx
INFO [2024-03-27 13:56:36] Loading Template_Untreated.xlsx
INFO [2024-03-27 13:56:36] Templates loaded successfully!
INFO [2024-03-27 13:56:36] Reading file /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-03-27 13:56:37] Plate 201904190a read; 384 wells
INFO [2024-03-27 13:56:37] Plate 201904190b read; 384 wells
INFO [2024-03-27 13:56:37] Plate 201904190c read; 384 wells
INFO [2024-03-27 13:56:37] Plate 201904190d read; 384 wells
INFO [2024-03-27 13:56:37] Plate 201904190e read; 384 wells
INFO [2024-03-27 13:56:37] Plate 201904190f read; 384 wells
INFO [2024-03-27 13:56:37] File done
INFO [2024-03-27 13:56:37] Reading file /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-03-27 13:56:37] Plate 201904197a read; 384 wells
INFO [2024-03-27 13:56:37] Plate 201904197b read; 384 wells
INFO [2024-03-27 13:56:37] Plate 201904197c read; 384 wells
INFO [2024-03-27 13:56:37] Plate 201904197d read; 384 wells
INFO [2024-03-27 13:56:37] Plate 201904197e read; 384 wells
INFO [2024-03-27 13:56:37] Plate 201904197f read; 384 wells
INFO [2024-03-27 13:56:37] File done
INFO [2024-03-27 13:56:37] Merging data
INFO [2024-03-27 13:56:37] Merging the metadata (manifest and treatment files)
WARN [2024-03-27 13:56:37] 4608 well loaded, 768 wells discarded for lack of annotation, 
    3840 data point selected

INFO [2024-03-27 13:56:37] Merge with Cell line info
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
> 
> proc.time()
   user  system elapsed 
 11.071   0.634  12.012 

Example timings

gDR.Rcheck/gDR-Ex.timings

nameusersystemelapsed
import_data1.3650.2451.654