BioC 3.3: CHECK report for miRLAB on morelia

Package: miRLAB

Version: 1.1.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings miRLAB_1.1.2.tar.gz

StartedAt: 2016-04-21 05:05:36 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 05:08:16 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 160.1 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 --no-vignettes --timings miRLAB_1.1.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/miRLAB.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.1.2’
* 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 ... [15s/16s] 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 loading without being on the library search path ... 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 ‘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 ‘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 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("stats", "cancor", "cor", "cov", "median", "p.adjust",
             "phyper", "rnorm")
  importFrom("utils", "data", "read.csv", "read.table", "write.csv",
             "write.table")
to your NAMESPACE file.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [7s/7s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [6s/6s]
 [7s/7s] 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-3.3-bioc/meat/miRLAB.Rcheck/00check.log’
for details.

* installing *source* package ‘miRLAB’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (miRLAB)

name	user	system	elapsed
Borda	0.079	0.004	0.084
BordaTopk	0.086	0.003	0.089
Dcov	0.043	0.006	0.064
Elastic	0.072	0.001	0.072
Extopk	0.013	0.000	0.013
GOBPenrichment	0.000	0.000	0.001
Hoeffding	0.038	0.001	0.055
IDA	0.052	0.000	0.053
ImputeNormData	0.009	0.001	0.009
KEGGenrichment	0.000	0.000	0.001
Kendall	0.009	0.000	0.009
Lasso	0.041	0.001	0.042
MI	0.068	0.001	0.069
Pearson	0.007	0.001	0.007
ProMISe	0.015	0.000	0.016
RDC	0.054	0.003	0.058
Read	0.005	0.000	0.006
ReadExtResult	0.001	0.000	0.001
Spearman	0.014	0.001	0.015
Standardise	0.000	0.001	0.000
ValidateAll	0.000	0.000	0.001
Validation	0.063	0.000	0.063
ValidationT	0.001	0.000	0.000
Zscore	0.01	0.00	0.01
bRank	0.012	0.001	0.013
convert	0.013	0.001	0.014
filterAndCompare	0.000	0.000	0.001
getData	0.001	0.000	0.001
readHeader	0.007	0.001	0.008