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BioC 3.4: CHECK report for miRLAB on morelia

This page was generated on 2016-09-21 03:54:40 -0700 (Wed, 21 Sep 2016).

Package 756/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
miRLAB 1.3.2
Thuc Duy Le
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/miRLAB
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: miRLAB
Version: 1.3.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings miRLAB_1.3.2.tar.gz
StartedAt: 2016-09-20 09:24:31 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 09:26:53 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 142.1 seconds
RetCode: 0
Status:  OK 
CheckDir: miRLAB.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings miRLAB_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-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 ‘1.3.2’
* 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 ‘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 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-3.4-bioc/meat/miRLAB.Rcheck/00check.log’
for details.


miRLAB.Rcheck/00install.out:

* 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)

miRLAB.Rcheck/miRLAB-Ex.timings:

nameusersystemelapsed
Borda0.0980.0040.171
BordaTopk0.0780.0020.080
Dcov0.0380.0020.040
Elastic0.0600.0010.061
Extopk0.0080.0000.008
GOBPenrichment0.0010.0000.001
Hoeffding0.0320.0010.042
IDA0.0600.0000.061
ImputeNormData0.010.000.01
KEGGenrichment0.0010.0000.001
Kendall0.0150.0000.015
Lasso0.0510.0010.051
MI0.0770.0020.079
Pearson0.0080.0010.009
ProMISe0.0200.0010.021
RDC0.0570.0010.058
Read0.0030.0000.004
ReadExtResult0.0010.0000.001
Spearman0.0130.0000.014
Standardise0.0000.0010.001
ValidateAll0.0010.0000.001
Validation0.0190.0010.019
ValidationT0.0010.0000.001
Zscore0.0100.0000.009
bRank0.0090.0000.009
convert0.0180.0010.018
filterAndCompare000
getData0.0010.0000.000
readHeader0.0050.0000.005