Package: sigsquared

Version: 1.14.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:sigsquared.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings sigsquared_1.14.0.tar.gz

StartedAt: 2019-04-16 03:06:07 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:07:20 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 73.4 seconds

RetCode: 0

Status:  OK

CheckDir: sigsquared.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:sigsquared.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings sigsquared_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/sigsquared.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sigsquared/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sigsquared’ version ‘1.14.0’
* 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 ‘sigsquared’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  GPL version 3
Standardizable: TRUE
Standardized license specification:
  GPL-3
* 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 ... NOTE
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
analysisPipeline,ExpressionSet-geneSignature: no visible binding for
  global variable ‘nCores’
analysisPipeline,ExpressionSet-geneSignature: no visible global
  function definition for ‘mcparallel’
analysisPipeline,ExpressionSet-geneSignature: no visible global
  function definition for ‘mccollect’
applySigSolnSpace,ExpressionSet-geneSignature-solnSpace: no visible
  binding for global variable ‘mc’
applySigSolnSpace,ExpressionSet-geneSignature-solnSpace: no visible
  binding for global variable ‘nCores’
applySigSolnSpace,ExpressionSet-geneSignature-solnSpace: no visible
  global function definition for ‘mcparallel’
applySigSolnSpace,ExpressionSet-geneSignature-solnSpace: no visible
  global function definition for ‘mccollect’
eJPDF,ExpressionSet-geneSignature-numeric: no visible global function
  definition for ‘new’
eJPDF,ExpressionSet-geneSignature-numeric: no visible binding for
  global variable ‘mc’
eJPDF,ExpressionSet-geneSignature-numeric: no visible binding for
  global variable ‘nCores’
eJPDF,ExpressionSet-geneSignature-numeric: no visible global function
  definition for ‘rnorm’
eJPDF,ExpressionSet-geneSignature-numeric: no visible global function
  definition for ‘mcparallel’
eJPDF,ExpressionSet-geneSignature-numeric: no visible global function
  definition for ‘mccollect’
genGeneDirect,matrix: no visible global function definition for ‘sd’
optCF,ExpressionSet-geneSignature: no visible global function
  definition for ‘new’
optCF,ExpressionSet-geneSignature: no visible global function
  definition for ‘rnorm’
optCF,ExpressionSet-geneSignature: no visible global function
  definition for ‘optim’
summarizeSolnSpace,solnSpace: no visible global function definition for
  ‘sd’
Undefined global functions or variables:
  mc mccollect mcparallel nCores new optim rnorm sd
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "optim", "rnorm", "sd")
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
Examples with CPU or elapsed time > 5s
                  user system elapsed
analysisPipeline 22.16  0.056   22.27
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/sigsquared.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL sigsquared
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘sigsquared’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘ensembleCostFcn’ with signature ‘dataSet="ExpressionSet",geneSig="geneSignature",jpdf="solnSpace"’: no definition for class “solnSpace”
in method for ‘getCVCuts’ with signature ‘cutoffResults="solnSpace"’: no definition for class “solnSpace”
in method for ‘summarizeCVCuts’ with signature ‘cutoffResults="solnSpace"’: no definition for class “solnSpace”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (sigsquared)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

> BiocGenerics:::testPackage("sigsquared")


RUNIT TEST PROTOCOL -- Tue Apr 16 03:07:17 2019 
*********************************************** 
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
sigsquared RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  2.344   0.120   2.491 

name	user	system	elapsed
analysisPipeline	22.160	0.056	22.270
ensembleAdjustable	0.12	0.00	0.12
geneSignature-class	0.004	0.000	0.001
setGeneSignature	0	0	0