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CHECK report for dcanr on merida1

This page was generated on 2021-05-06 12:34:44 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the dcanr package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 429/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dcanr 1.6.0  (landing page)
Dharmesh D. Bhuva
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/dcanr
Branch: RELEASE_3_12
Last Commit: 39a8446
Last Changed Date: 2020-10-27 11:45:37 -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: dcanr
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:dcanr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings dcanr_1.6.0.tar.gz
StartedAt: 2021-05-06 00:53:50 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 00:55:09 -0400 (Thu, 06 May 2021)
EllapsedTime: 78.7 seconds
RetCode: 0
Status:   OK  
CheckDir: dcanr.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:dcanr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings dcanr_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/dcanr.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 ‘dcanr/DESCRIPTION’ ... OK
* this is package ‘dcanr’ version ‘1.6.0’
* 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 ‘dcanr’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ...It is recommended to use ‘given’ instead of ‘middle’.
 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
ftgi.score: no visible binding for global variable ‘i’
ftgi.score: no visible binding for global variable ‘j’
Undefined global functions or variables:
  i j
* 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/dcanr.Rcheck/00check.log’
for details.



Installation output

dcanr.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘dcanr’ ...
** using staged installation
It is recommended to use ‘given’ instead of ‘middle’.
It is recommended to use ‘given’ instead of ‘middle’.
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘dcScore’ with signature ‘"Matrix","ANY","ANY"’: no definition for class “Matrix”
in method for ‘dcScore’ with signature ‘"ExpressionSet","ANY","ANY"’: no definition for class “ExpressionSet”
in method for ‘dcScore’ with signature ‘"SummarizedExperiment","ANY","ANY"’: no definition for class “SummarizedExperiment”
in method for ‘dcScore’ with signature ‘"DGEList","ANY","ANY"’: no definition for class “DGEList”
** 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 (dcanr)

Tests output

dcanr.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(dcanr)
> 
> test_check("dcanr")
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1 
Iteration: 2 
One-Stepper Time: 0.0119999999999987 
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287 

Estimating optimal shrinkage intensity lambda (correlation matrix): 1 

Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1 
Iteration: 2 
One-Stepper Time: 0.0120000000000005 
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287 

Estimating optimal shrinkage intensity lambda (correlation matrix): 1 

Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1 
Iteration: 2 
One-Stepper Time: 0.0129999999999981 
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287 

Estimating optimal shrinkage intensity lambda (correlation matrix): 1 

Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1 
Iteration: 2 
One-Stepper Time: 0.0130000000000017 
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287 

Estimating optimal shrinkage intensity lambda (correlation matrix): 1 

Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1 
Iteration: 2 
One-Stepper Time: 0.0139999999999993 
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1 
Iteration: 2 
One-Stepper Time: 0.00900000000000034 
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287 

Estimating optimal shrinkage intensity lambda (correlation matrix): 1 

Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6287 

Estimating optimal shrinkage intensity lambda (correlation matrix): 1 

Estimate (local) false discovery rates (partial correlations):
Estimate (local) false discovery rates (partial correlations):
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1 
Iteration: 2 
One-Stepper Time: 0.0120000000000005 
Begin Phase I (Initial E-Step) ...
Begin Phase II (M2-Step) ...
Begin Phase III ([E M1] Cycle) ...
Iteration: 1 
Iteration: 2 
One-Stepper Time: 0.0139999999999993 
[ FAIL 0 | WARN 299 | SKIP 0 | PASS 183 ]
> 
> proc.time()
   user  system elapsed 
 19.879   0.749  20.642 

Example timings

dcanr.Rcheck/dcanr-Ex.timings

nameusersystemelapsed
cor.pairs0.0030.0020.004
dcAdjust0.0060.0010.008
dcEvaluate2.0430.1322.178
dcMethods0.0000.0010.001
dcNetwork0.0900.0020.092
dcPipeline1.0620.0511.114
dcScore0.0030.0010.004
dcTest2.1200.0142.136
getSimData0.1150.0070.122
mi.ap0.2200.0010.221
perfMethods0.0010.0000.001
performanceMeasure0.0000.0010.001
plotSimNetwork0.2310.0120.244