BioC 3.3: CHECK report for inSilicoMerging on morelia

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings inSilicoMerging_1.15.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/inSilicoMerging.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 ‘inSilicoMerging/DESCRIPTION’ ... OK
* this is package ‘inSilicoMerging’ version ‘1.15.1’
* 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 ‘inSilicoMerging’ can be installed ... [2s/3s] 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 ... NOTE
Package in Depends field not imported from: ‘Biobase’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
aprior: no visible global function definition for ‘var’
bprior: no visible global function definition for ‘var’
commonGenes : <anonymous>: no visible global function definition for
  ‘exprs’
geneBMCESet: no visible global function definition for ‘exprs<-’
geneBMCESet: no visible global function definition for ‘exprs’
geneNormESet: no visible global function definition for ‘exprs<-’
geneNormESet: no visible global function definition for ‘exprs’
geneNormESet : <anonymous>: no visible global function definition for
  ‘sd’
identify_common_genes: no visible global function definition for
  ‘exprs’
makeColorMap: no visible global function definition for ‘pData’
makeColorVec: no visible global function definition for ‘pData’
matchExprsPheno: no visible global function definition for ‘exprs’
matchExprsPheno: no visible global function definition for ‘pData<-’
matchExprsPheno: no visible global function definition for ‘pData’
mergeCOMBAT: no visible global function definition for ‘pData’
mergeCOMBAT: no visible global function definition for ‘exprs’
mergeCOMBAT: no visible binding for global variable ‘var’
mergeCOMBAT: no visible global function definition for ‘exprs<-’
mergeNONE: no visible global function definition for ‘annotation’
mergeNONE: no visible global function definition for ‘exprs’
mergeNONE: no visible global function definition for ‘new’
mergeNONE: no visible global function definition for ‘exprs<-’
mergeNONE: no visible global function definition for ‘pData<-’
mergeNONE: no visible global function definition for ‘fData<-’
mergeNONE: no visible global function definition for ‘annotation<-’
plotGeneWiseBoxPlot: no visible global function definition for ‘pdf’
plotGeneWiseBoxPlot: no visible global function definition for ‘exprs’
plotGeneWiseBoxPlot: no visible global function definition for ‘par’
plotGeneWiseBoxPlot: no visible global function definition for ‘pData’
plotGeneWiseBoxPlot: no visible global function definition for ‘plot’
plotGeneWiseBoxPlot: no visible global function definition for
  ‘boxplot’
plotGeneWiseBoxPlot: no visible global function definition for ‘rect’
plotGeneWiseBoxPlot: no visible global function definition for ‘axis’
plotGeneWiseBoxPlot: no visible global function definition for
  ‘dev.off’
plotMDS: no visible global function definition for ‘pdf’
plotMDS: no visible global function definition for ‘cmdscale’
plotMDS: no visible global function definition for ‘dist’
plotMDS: no visible global function definition for ‘exprs’
plotMDS: no visible global function definition for ‘par’
plotMDS: no visible global function definition for ‘plot’
plotMDS: no visible global function definition for ‘pData’
plotMDS: no visible global function definition for ‘rect’
plotMDS: no visible global function definition for ‘dev.off’
plotRLE: no visible global function definition for ‘pdf’
plotRLE: no visible global function definition for ‘exprs’
plotRLE: no visible global function definition for ‘rowMedians’
plotRLE: no visible global function definition for ‘par’
plotRLE: no visible global function definition for ‘plot’
plotRLE: no visible global function definition for ‘lines’
plotRLE: no visible global function definition for ‘rect’
plotRLE: no visible global function definition for ‘boxplot.matrix’
plotRLE: no visible global function definition for ‘dev.off’
xpn: no visible global function definition for ‘exprs’
xpn: no visible global function definition for ‘sd’
xpn: no visible global function definition for ‘exprs<-’
xpn: no visible global function definition for ‘median’
xpn: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  annotation annotation<- axis boxplot boxplot.matrix cmdscale dev.off
  dist exprs exprs<- fData<- kmeans lines median new pData pData<- par
  pdf plot rect rowMedians sd var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "axis", "boxplot", "boxplot.matrix", "lines",
             "par", "plot", "rect")
  importFrom("methods", "new")
  importFrom("stats", "cmdscale", "dist", "kmeans", "median", "sd",
             "var")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘inSilicoMerging-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: merge
> ### Title: General method to merge different ExpressionSets
> ### Aliases: merge
> 
> ### ** Examples
> 
> 
> # retrieve two datasets:
> library(inSilicoDb);
Loading required package: rjson
Loading required package: RCurl
Loading required package: bitops
> InSilicoLogin("rpackage_tester@insilicodb.com", "5c4d0b231e5cba4a0bc54783b385cc9a");
  INSILICODB: Welcome RPackage Tester
[1] 5296
> eset1 = getDataset("GSE18842", "GPL570", norm="FRMA", features="GENE");
  INSILICODB: The dataset you requested could not be computed. We are sorry for the inconvenience.
Error: Stopped because of previous errors
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘inSilicoMerging_unit_tests.R’ [1s/5s]
 ERROR
Running the tests in ‘tests/inSilicoMerging_unit_tests.R’ failed.
Last 13 lines of output:
  inSilicoMerging RUnit Tests - 1 test function, 1 error, 0 failures
  ERROR in test.compare_null_bmc_merge: Error : Stopped because of previous errors
  
  Test files with failing tests
  
     test_inSilicoMerging.R 
       test.compare_null_bmc_merge 
  
  
  Error in BiocGenerics:::testPackage("inSilicoMerging") : 
    unit tests failed for package inSilicoMerging
  Calls: <Anonymous> -> <Anonymous>
  Execution halted
* 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: 2 ERRORs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/inSilicoMerging.Rcheck/00check.log’
for details.


R version 3.3.0 beta (2016-04-06 r70435) -- "Supposedly Educational"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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.

> require("inSilicoMerging") || stop("unable to load inSilicoMerging package")
Loading required package: inSilicoMerging
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'inSilicoMerging'

The following object is masked from 'package:base':

    merge

[1] TRUE
> inSilicoMerging:::.test()
Loading required package: rjson
Loading required package: RCurl
Loading required package: bitops
  INSILICODB: Welcome RPackage Tester
  INSILICODB: The dataset you requested could not be computed. We are sorry for the inconvenience.
Timing stopped at: 0.165 0.01 3.837 
Error : Stopped because of previous errors


RUNIT TEST PROTOCOL -- Thu Apr 21 04:07:07 2016 
*********************************************** 
Number of test functions: 1 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
inSilicoMerging RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in test.compare_null_bmc_merge: Error : Stopped because of previous errors

Test files with failing tests

   test_inSilicoMerging.R 
     test.compare_null_bmc_merge 


Error in BiocGenerics:::testPackage("inSilicoMerging") : 
  unit tests failed for package inSilicoMerging
Calls: <Anonymous> -> <Anonymous>
Execution halted

BioC 3.3: CHECK report for inSilicoMerging on morelia

Summary

Command output