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CHECK report for synlet on merida1

This page was generated on 2021-05-06 12:37:07 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the synlet package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1830/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
synlet 1.20.0  (landing page)
Chunxuan Shao
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/synlet
Branch: RELEASE_3_12
Last Commit: 83ffa0c
Last Changed Date: 2020-10-27 11:07:12 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: synlet
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:synlet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings synlet_1.20.0.tar.gz
StartedAt: 2021-05-06 06:45:18 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:46:54 -0400 (Thu, 06 May 2021)
EllapsedTime: 95.8 seconds
RetCode: 0
Status:   OK  
CheckDir: synlet.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:synlet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings synlet_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/synlet.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘synlet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘synlet’ version ‘1.20.0’
* 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 ‘synlet’ 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 ... NOTE
.ff_bscorePlate: no visible binding for global variable ‘PLATE’
.ff_bscorePlate: no visible binding for global variable
  ‘EXPERIMENT_TYPE’
.ff_bscorePlate: no visible global function definition for ‘medpolish’
.ff_bscorePlate: no visible global function definition for ‘mad’
.ff_contsiRNANorm: no visible binding for global variable
  ‘MASTER_PLATE’
.ff_contsiRNANorm: no visible binding for global variable
  ‘EXPERIMENT_TYPE’
.ff_contsiRNANorm: no visible binding for global variable
  ‘WELL_CONTENT_NAME’
.ff_contsiRNANorm: no visible binding for global variable ‘median’
.ff_masterPlateValue: no visible binding for global variable
  ‘EXPERIMENT_MODIFICATION’
.ff_plateNorm: no visible binding for global variable ‘MASTER_PLATE’
.ff_plateNorm: no visible binding for global variable ‘EXPERIMENT_TYPE’
.ff_plateNorm: no visible binding for global variable
  ‘WELL_CONTENT_NAME’
.ff_plateNorm: no visible binding for global variable ‘median’
.ff_ratio_madS: no visible global function definition for ‘median’
.ff_ratio_rsa: no visible global function definition for ‘median’
.ff_ttest: no visible global function definition for ‘t.test’
.ff_ttest: no visible global function definition for ‘is’
OPIScore: no visible global function definition for ‘phyper’
bScore: no visible binding for global variable
  ‘EXPERIMENT_MODIFICATION’
bScore: no visible binding for global variable ‘MASTER_PLATE’
bScore: no visible global function definition for ‘write.table’
madSelect: no visible global function definition for ‘write.table’
madSelect: no visible global function definition for ‘median’
madSelect: no visible global function definition for ‘mad’
plateHeatmap: no visible global function definition for
  ‘colorRampPalette’
plateHeatmap: no visible binding for global variable ‘COL_NAME’
plateHeatmap: no visible binding for global variable ‘ROW_NAME’
plateHeatmap: no visible binding for global variable ‘value’
rsaHits: no visible global function definition for ‘write.table’
scatterPlot: no visible binding for global variable ‘READOUT’
scatterPlot: no visible binding for global variable ‘condition’
siRNAPlot: no visible global function definition for ‘rainbow’
siRNAPlot: no visible binding for global variable ‘WELL_CONTENT_NAME’
siRNAPlot: no visible binding for global variable ‘READOUT’
siRNAPlot: no visible binding for global variable ‘PLATE’
siRNAPlot: no visible binding for global variable ‘MASTER_PLATE’
siRNAPlot: no visible binding for global variable ‘Var1’
siRNAPlot: no visible binding for global variable ‘value’
siRNAPlot: no visible binding for global variable ‘siRNA’
siRNAPlot: no visible binding for global variable ‘experiments’
siRNAPlot: no visible global function definition for ‘pdf’
siRNAPlot: no visible global function definition for ‘dev.off’
tTest: no visible global function definition for ‘p.adjust’
zFactor: no visible binding for global variable ‘condition’
zFactor: no visible binding for global variable ‘sd’
zFactor: no visible binding for global variable ‘median’
zFactor: no visible global function definition for ‘complete.cases’
Undefined global functions or variables:
  COL_NAME EXPERIMENT_MODIFICATION EXPERIMENT_TYPE MASTER_PLATE PLATE
  READOUT ROW_NAME Var1 WELL_CONTENT_NAME colorRampPalette
  complete.cases condition dev.off experiments is mad median medpolish
  p.adjust pdf phyper rainbow sd siRNA t.test value write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf",
             "rainbow")
  importFrom("methods", "is")
  importFrom("stats", "complete.cases", "mad", "median", "medpolish",
             "p.adjust", "phyper", "sd", "t.test")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/synlet.Rcheck/00check.log’
for details.



Installation output

synlet.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL synlet
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘synlet’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (synlet)

Tests output

synlet.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(synlet)
Loading required package: ggplot2
> data("exampleDat")
> 
> test_check("synlet")
1: 34257
Final: 33965.5
1: 35666
Final: 35464.75
1: 26858
Final: 26757
1: 33731
Final: 33589
1: 32981
2: 32617.25
Final: 32546.69
1: 37003
2: 36509
Final: 36360.38
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 6 ]
> 
> proc.time()
   user  system elapsed 
  4.421   0.298   4.709 

Example timings

synlet.Rcheck/synlet-Ex.timings

nameusersystemelapsed
bScore0.6090.0100.620
madSelect0.1880.0190.207
plateHeatmap1.4500.0421.495
rankProdHits0.6220.0270.650
rsaHits0.1960.0070.205
scatterPlot0.2530.0100.263
siRNAPlot2.4580.0142.475
tTest1.5410.0081.551
zFactor0.0330.0010.034