BioC 3.3: CHECK report for miRLAB on oaxaca

Package: miRLAB

Version: 1.2.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings miRLAB_1.2.2.tar.gz

StartedAt: 2016-10-13 03:46:02 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 03:49:04 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 181.5 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_1.2.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/miRLAB.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.2.2’
* 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 ... 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 ... 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-3.3-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	0.138	0.003	0.254
BordaTopk	0.094	0.002	0.096
Dcov	0.050	0.008	0.059
Elastic	0.074	0.002	0.159
Extopk	0.018	0.000	0.018
GOBPenrichment	0.001	0.000	0.001
Hoeffding	0.029	0.000	0.030
IDA	0.060	0.000	0.061
ImputeNormData	0.013	0.001	0.013
KEGGenrichment	0	0	0
Kendall	0.012	0.001	0.013
Lasso	0.068	0.001	0.068
MI	0.104	0.002	0.106
Pearson	0.011	0.001	0.011
ProMISe	0.016	0.000	0.017
RDC	0.066	0.002	0.067
Read	0.004	0.000	0.004
ReadExtResult	0.001	0.000	0.001
Spearman	0.013	0.000	0.013
Standardise	0.001	0.000	0.001
ValidateAll	0.000	0.000	0.001
Validation	0.020	0.000	0.021
ValidationT	0.001	0.000	0.001
Zscore	0.015	0.001	0.016
bRank	0.015	0.001	0.015
convert	0.018	0.001	0.018
filterAndCompare	0.001	0.000	0.001
getData	0	0	0
readHeader	0.011	0.000	0.012