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CHECK report for miRLAB on tokay1

This page was generated on 2018-04-12 13:26:35 -0400 (Thu, 12 Apr 2018).

Package 867/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
miRLAB 1.8.0
Thuc Duy Le
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/miRLAB
Branch: RELEASE_3_6
Last Commit: 0e06437
Last Changed Date: 2017-10-30 12:40:53 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: miRLAB
Version: 1.8.0
Command: rm -rf miRLAB.buildbin-libdir miRLAB.Rcheck && mkdir miRLAB.buildbin-libdir miRLAB.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=miRLAB.buildbin-libdir miRLAB_1.8.0.tar.gz >miRLAB.Rcheck\00install.out 2>&1 && cp miRLAB.Rcheck\00install.out miRLAB-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=miRLAB.buildbin-libdir --install="check:miRLAB-install.out" --force-multiarch --no-vignettes --timings miRLAB_1.8.0.tar.gz
StartedAt: 2018-04-12 01:31:30 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 01:35:16 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 226.7 seconds
RetCode: 0
Status:  OK  
CheckDir: miRLAB.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf miRLAB.buildbin-libdir miRLAB.Rcheck && mkdir miRLAB.buildbin-libdir miRLAB.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=miRLAB.buildbin-libdir miRLAB_1.8.0.tar.gz >miRLAB.Rcheck\00install.out 2>&1 && cp miRLAB.Rcheck\00install.out miRLAB-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=miRLAB.buildbin-libdir --install="check:miRLAB-install.out" --force-multiarch --no-vignettes --timings miRLAB_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/miRLAB.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'miRLAB/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'miRLAB' version '1.8.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/miRLAB.Rcheck/00check.log'
for details.



Installation output

miRLAB.Rcheck/00install.out


install for i386

* installing *source* package 'miRLAB' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'miRLAB'
    finding HTML links ... done
    Borda                                   html  
    BordaTopk                               html  
    Dcov                                    html  
    DiffExpAnalysis                         html  
    Elastic                                 html  
    Extopk                                  html  
    GOBPenrichment                          html  
    Hoeffding                               html  
    IDA                                     html  
    ImputeNormData                          html  
    KEGGenrichment                          html  
    Kendall                                 html  
    Lasso                                   html  
    MI                                      html  
    Pearson                                 html  
    ProMISe                                 html  
    RDC                                     html  
    Read                                    html  
    ReadExtResult                           html  
    Spearman                                html  
    Standardise                             html  
    ValidateAll                             html  
    Validation                              html  
    ValidationT                             html  
    Zscore                                  html  
    bRank                                   html  
    convert                                 html  
    experiment                              html  
    filterAndCompare                        html  
    getData                                 html  
    miRLAB-package                          html  
    readHeader                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'miRLAB' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'miRLAB' as miRLAB_1.8.0.zip
* DONE (miRLAB)
In R CMD INSTALL
In R CMD INSTALL

Tests output

miRLAB.Rcheck/tests_i386/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 -- Thu Apr 12 01:35:05 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 
   5.34    0.20    5.54 

miRLAB.Rcheck/tests_x64/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 -- Thu Apr 12 01:35:12 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 
   6.96    0.17    7.14 

Example timings

miRLAB.Rcheck/examples_i386/miRLAB-Ex.timings

nameusersystemelapsed
Borda0.540.000.55
BordaTopk0.080.000.08
Dcov0.040.010.06
Elastic0.180.000.18
Extopk000
GOBPenrichment000
Hoeffding0.040.010.06
IDA0.050.000.05
ImputeNormData000
KEGGenrichment000
Kendall000
Lasso0.030.000.03
MI0.090.000.09
Pearson0.020.000.02
ProMISe000
RDC0.060.000.06
Read0.010.000.02
ReadExtResult000
Spearman000
Standardise000
ValidateAll000
Validation0.020.000.01
ValidationT000
Zscore0.020.000.02
bRank0.040.000.04
convert0.000.000.02
filterAndCompare000
getData000
readHeader000

miRLAB.Rcheck/examples_x64/miRLAB-Ex.timings

nameusersystemelapsed
Borda0.270.000.26
BordaTopk0.420.000.42
Dcov0.070.000.31
Elastic0.230.000.24
Extopk000
GOBPenrichment000
Hoeffding0.090.000.09
IDA0.040.000.03
ImputeNormData0.010.000.02
KEGGenrichment000
Kendall0.020.000.01
Lasso0.030.000.03
MI0.110.000.11
Pearson0.010.000.02
ProMISe000
RDC0.080.000.08
Read000
ReadExtResult000
Spearman000
Standardise000
ValidateAll000
Validation000
ValidationT000
Zscore0.010.000.02
bRank0.070.000.06
convert0.000.020.03
filterAndCompare000
getData000
readHeader000