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This page was generated on 2024-07-16 17:41 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4742
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4484
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4513
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4462
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 787/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gDR 1.2.0  (landing page)
Arkadiusz Gladki
Snapshot Date: 2024-07-14 14:00 -0400 (Sun, 14 Jul 2024)
git_url: https://git.bioconductor.org/packages/gDR
git_branch: RELEASE_3_19
git_last_commit: b86b89e
git_last_commit_date: 2024-04-30 11:50:18 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
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 gDR on merida1

To the developers/maintainers of the gDR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gDR.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: gDR
Version: 1.2.0
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_1.2.0.tar.gz
StartedAt: 2024-07-15 04:47:21 -0400 (Mon, 15 Jul 2024)
EndedAt: 2024-07-15 04:54:14 -0400 (Mon, 15 Jul 2024)
EllapsedTime: 413.1 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/gDR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gDR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDR’ version ‘1.2.0’
* 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 ‘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 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 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 ... NOTE
checkRd: (-1) small_combo_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_combo_data.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_data.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_data.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_data.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_data.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_data.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_data.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) small_data.Rd:21: Lost braces in \itemize; meant \describe ?
* 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 ... 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/gDR.Rcheck/00check.log’
for details.


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/4.4-x86_64/Resources/library’
* installing *source* package ‘gDR’ ...
** using staged installation
** R
** data
** 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
** 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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(testthat)
> library(gDR)
Loading required package: gDRcore
Loading required package: gDRimport
Loading required package: gDRutils
> 
> test_check("gDR")
INFO [2024-07-15 04:53:54] Manifest loaded successfully
INFO [2024-07-15 04:53:54] Reading Template_7daytreated.xlsx with load_templates_xlsx
INFO [2024-07-15 04:53:54] Loading Template_7daytreated.xlsx
INFO [2024-07-15 04:53:55] Loading Template_Untreated.xlsx
INFO [2024-07-15 04:53:55] Templates loaded successfully!
INFO [2024-07-15 04:53:55] Reading file /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gDRimport/extdata/data1/RawData_day0.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-07-15 04:53:56] Plate 201904190a read; 384 wells
INFO [2024-07-15 04:53:56] Plate 201904190b read; 384 wells
INFO [2024-07-15 04:53:56] Plate 201904190c read; 384 wells
INFO [2024-07-15 04:53:56] Plate 201904190d read; 384 wells
INFO [2024-07-15 04:53:56] Plate 201904190e read; 384 wells
INFO [2024-07-15 04:53:56] Plate 201904190f read; 384 wells
INFO [2024-07-15 04:53:56] File done
INFO [2024-07-15 04:53:56] Reading file /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/gDRimport/extdata/data1/RawData_day7.xlsx, sheet Readout_0077vs0068_day7
INFO [2024-07-15 04:53:58] Plate 201904197a read; 384 wells
INFO [2024-07-15 04:53:58] Plate 201904197b read; 384 wells
INFO [2024-07-15 04:53:58] Plate 201904197c read; 384 wells
INFO [2024-07-15 04:53:58] Plate 201904197d read; 384 wells
INFO [2024-07-15 04:53:58] Plate 201904197e read; 384 wells
INFO [2024-07-15 04:53:58] Plate 201904197f read; 384 wells
INFO [2024-07-15 04:53:58] File done
INFO [2024-07-15 04:53:58] Merging data
INFO [2024-07-15 04:53:58] Merging the metadata (manifest and treatment files)
WARN [2024-07-15 04:53:58] 4608 well loaded, 768 wells discarded for lack of annotation, 
    3840 data point selected

INFO [2024-07-15 04:53:58] Merge with Cell line info
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
> 
> proc.time()
   user  system elapsed 
 19.773   1.413  24.240 

Example timings

gDR.Rcheck/gDR-Ex.timings

nameusersystemelapsed
import_data3.4880.4524.549