Package: miRLAB

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:miRLAB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings miRLAB_1.10.0.tar.gz

StartedAt: 2018-10-16 22:41:47 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 22:44:47 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 179.4 seconds

RetCode: 0

Status:  OK

CheckDir: miRLAB.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:miRLAB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings miRLAB_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/miRLAB.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘miRLAB/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miRLAB’ version ‘1.10.0’
* 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 ‘miRLAB’ 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
CheckGeneSymbol: no visible global function definition for ‘data’
DiffExpAnalysis: no visible global function definition for ‘read.csv’
DiffExpAnalysis: no visible global function definition for ‘write.csv’
DownloadRNASeqData: no visible global function definition for
  ‘write.table’
DownloadmiRNASeqData: no visible global function definition for
  ‘write.table’
GOBPenrichment: no visible global function definition for ‘new’
GOBPenrichment: no visible global function definition for ‘p.adjust’
IDA: no visible global function definition for ‘cor’
IDA: no visible global function definition for ‘cov’
KEGGenrichment: no visible global function definition for ‘new’
KEGGenrichment: no visible global function definition for ‘p.adjust’
Kendall: no visible global function definition for ‘cor’
Pearson: no visible global function definition for ‘cor’
ProcessRNASeqData: no visible global function definition for
  ‘read.table’
ProcessRNASeqData: no visible global function definition for ‘png’
ProcessRNASeqData: no visible global function definition for ‘par’
ProcessRNASeqData: no visible global function definition for ‘boxplot’
ProcessRNASeqData: no visible global function definition for ‘dev.off’
ProcessRNASeqData: no visible global function definition for
  ‘write.table’
ProcessmiRNASeqData: no visible global function definition for
  ‘read.table’
ProcessmiRNASeqData: no visible global function definition for
  ‘write.table’
RDCParameter: no visible global function definition for ‘rnorm’
RDCParameter: no visible global function definition for ‘cancor’
Read: no visible global function definition for ‘read.csv’
ReadExtResult: no visible global function definition for ‘read.csv’
Spearman: no visible global function definition for ‘cor’
ValidateAll: no visible global function definition for ‘phyper’
Validation: no visible global function definition for ‘read.csv’
ValidationT: no visible global function definition for ‘read.csv’
Zscore: no visible global function definition for ‘read.csv’
Zscore: no visible global function definition for ‘median’
convert: no visible global function definition for ‘read.csv’
convert: no visible global function definition for ‘write.table’
readHeader: no visible global function definition for ‘read.csv’
urlReadTable: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  boxplot cancor cor cov data dev.off median new p.adjust par phyper
  png read.csv read.table rnorm write.csv write.table
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "boxplot", "par")
  importFrom("methods", "new")
  importFrom("stats", "cancor", "cor", "cov", "median", "p.adjust",
             "phyper", "rnorm")
  importFrom("utils", "data", "read.csv", "read.table", "write.csv",
             "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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/miRLAB.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL miRLAB
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘miRLAB’ ...
** R
** 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
* DONE (miRLAB)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> BiocGenerics:::testPackage("miRLAB")


RUNIT TEST PROTOCOL -- Tue Oct 16 22:44:41 2018 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
miRLAB RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  7.952   0.391   8.406 

name	user	system	elapsed
Borda	0.111	0.001	0.115
BordaTopk	0.080	0.004	0.084
Dcov	0.058	0.009	0.067
Elastic	0.076	0.001	0.077
Extopk	0.009	0.001	0.009
GOBPenrichment	0.001	0.000	0.001
Hoeffding	0.039	0.001	0.040
IDA	0.060	0.001	0.060
ImputeNormData	0.012	0.001	0.012
KEGGenrichment	0.001	0.000	0.001
Kendall	0.011	0.001	0.011
Lasso	0.050	0.001	0.053
MI	0.073	0.002	0.079
Pearson	0.006	0.000	0.007
ProMISe	0.017	0.001	0.017
RDC	0.049	0.003	0.052
Read	0.005	0.000	0.006
ReadExtResult	0.001	0.000	0.001
Spearman	0.010	0.000	0.011
Standardise	0.001	0.000	0.001
ValidateAll	0.001	0.000	0.002
Validation	0.019	0.002	0.022
ValidationT	0.001	0.000	0.002
Zscore	0.010	0.001	0.011
bRank	0.009	0.000	0.009
convert	0.013	0.001	0.013
filterAndCompare	0.001	0.001	0.001
getData	0.001	0.000	0.001
readHeader	0.005	0.001	0.005