Multiple platform build/check report for BioC 3.13 - CHECK results for dcanr on machv2

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### Running command:
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###   /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_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/dcanr.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.8.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/dcanr.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL dcanr
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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


R version 4.1.1 (2021-08-10) -- "Kick Things"
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: 0.0109999999999992 
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: 0.011000000000001 
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: 0.0109999999999992 
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: 0.00799999999999912 
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: 0.00899999999999679 
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):
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: 0.00799999999999912 
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 
[ FAIL 0 | WARN 299 | SKIP 0 | PASS 183 ]
> 
> proc.time()
   user  system elapsed 
 20.152   0.803  21.000

name	user	system	elapsed
cor.pairs	0.002	0.001	0.002
dcAdjust	0.010	0.001	0.011
dcEvaluate	2.316	0.141	2.458
dcMethods	0.000	0.000	0.001
dcNetwork	0.089	0.002	0.092
dcPipeline	0.772	0.045	0.818
dcScore	0.002	0.001	0.002
dcTest	1.973	0.021	1.996
getSimData	0.127	0.004	0.133
mi.ap	0.237	0.003	0.242
perfMethods	0.000	0.001	0.001
performanceMeasure	0.001	0.000	0.001
plotSimNetwork	0.236	0.014	0.252

CHECK results for dcanr on machv2

Summary

Command output

Installation output

Tests output

Example timings