BioC 3.5: CHECK report for Mergeomics on veracruz2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Mergeomics_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Mergeomics.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Mergeomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Mergeomics’ version ‘1.4.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘Mergeomics’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.5Mb
  sub-directories of 1Mb or more:
    extdata   7.5Mb
* 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
kda.analyze: no visible global function definition for ‘p.adjust’
kda.analyze.exec: no visible global function definition for ‘pnorm’
kda.analyze.simulate: no visible global function definition for ‘rnorm’
kda.prepare: no visible global function definition for ‘quantile’
kda.prepare: no visible global function definition for ‘object.size’
kda.prepare.screen: no visible global function definition for
  ‘quantile’
kda.prepare.screen: no visible global function definition for ‘median’
kda.start: no visible global function definition for ‘object.size’
kda2cytoscape: no visible global function definition for ‘write.table’
kda2cytoscape.colormap: no visible global function definition for
  ‘rainbow’
kda2cytoscape.colormap: no visible global function definition for
  ‘col2rgb’
kda2himmeli: no visible global function definition for ‘quantile’
kda2himmeli: no visible global function definition for ‘write.table’
kda2himmeli.colormap: no visible global function definition for
  ‘rainbow’
kda2himmeli.colormap: no visible global function definition for
  ‘col2rgb’
ssea.analyze: no visible global function definition for ‘qnorm’
ssea.analyze: no visible global function definition for ‘approx’
ssea.analyze: no visible global function definition for ‘pnorm’
ssea.analyze.simulate: no visible global function definition for
  ‘quantile’
ssea.control: no visible global function definition for ‘median’
ssea.control: no visible global function definition for ‘object.size’
ssea.meta: no visible global function definition for ‘qnorm’
ssea.meta: no visible global function definition for ‘quantile’
ssea.meta: no visible global function definition for ‘pnorm’
ssea.meta: no visible global function definition for ‘median’
ssea.meta: no visible global function definition for ‘na.omit’
ssea.prepare: no visible global function definition for ‘median’
ssea.prepare: no visible global function definition for ‘object.size’
ssea.start: no visible global function definition for ‘na.omit’
ssea.start: no visible global function definition for ‘object.size’
ssea.start.configure: no visible global function definition for
  ‘write.table’
ssea2kda: no visible global function definition for ‘na.omit’
ssea2kda.import: no visible global function definition for ‘na.omit’
tool.aggregate: no visible global function definition for ‘na.omit’
tool.cluster: no visible global function definition for ‘as.dist’
tool.cluster: no visible global function definition for ‘hclust’
tool.fdr.bh: no visible global function definition for ‘qnorm’
tool.fdr.bh: no visible global function definition for ‘p.adjust’
tool.fdr.bh: no visible global function definition for ‘approx’
tool.fdr.empirical: no visible global function definition for ‘qnorm’
tool.fdr.empirical: no visible global function definition for ‘approx’
tool.metap: no visible global function definition for ‘qnorm’
tool.metap: no visible global function definition for ‘pnorm’
tool.normalize: no visible global function definition for ‘sd’
tool.normalize: no visible global function definition for ‘median’
tool.normalize: no visible global function definition for ‘optim’
tool.normalize: no visible global function definition for ‘ks.test’
tool.normalize.quality: no visible global function definition for ‘sd’
tool.normalize.quality: no visible global function definition for
  ‘ks.test’
tool.overlap: no visible global function definition for ‘phyper’
tool.read: no visible global function definition for ‘read.delim’
tool.read: no visible global function definition for ‘na.omit’
tool.save: no visible global function definition for ‘write.table’
tool.unify: no visible global function definition for ‘sd’
tool.unify: no visible global function definition for ‘quantile’
tool.unify: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx as.dist col2rgb hclust ks.test median na.omit object.size
  optim p.adjust phyper pnorm qnorm quantile rainbow read.delim rnorm
  sd write.table
Consider adding
  importFrom("grDevices", "col2rgb", "rainbow")
  importFrom("stats", "approx", "as.dist", "hclust", "ks.test", "median",
             "na.omit", "optim", "p.adjust", "phyper", "pnorm", "qnorm",
             "quantile", "rnorm", "sd")
  importFrom("utils", "object.size", "read.delim", "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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
ssea.meta              19.658  0.252  20.822
kda.analyze.exec       13.029  0.161  13.673
kda.analyze.simulate   11.797  0.127  12.305
kda.analyze.test       11.682  0.139  12.210
kda.prepare            11.550  0.128  12.074
ssea2kda                8.102  0.186   8.528
ssea2kda.analyze        7.961  0.223   8.426
ssea.analyze            7.008  0.126   7.392
ssea2kda.import         6.717  0.127   7.087
ssea.finish.details     6.678  0.094   6.975
ssea.finish             6.345  0.108   6.630
ssea.finish.genes       6.314  0.124   6.948
ssea.analyze.simulate   6.135  0.095   6.378
ssea.finish.fdr         6.067  0.104   6.391
ssea.analyze.observe    5.317  0.047   5.499
ssea.prepare            5.271  0.056   5.657
ssea.analyze.randgenes  5.264  0.047   5.453
ssea.prepare.structure  5.111  0.053   5.423
ssea.analyze.randloci   4.911  0.043   5.098
ssea.start.relabel      4.854  0.050   5.167
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/Mergeomics.Rcheck/00check.log’
for details.

name	user	system	elapsed
MSEA.KDA.onestep	0.002	0.001	0.002
job.kda	0.010	0.001	0.012
kda.analyze	0.017	0.001	0.018
kda.analyze.exec	13.029	0.161	13.673
kda.analyze.simulate	11.797	0.127	12.305
kda.analyze.test	11.682	0.139	12.210
kda.configure	0.003	0.000	0.004
kda.finish	0.166	0.010	0.179
kda.finish.estimate	0.097	0.010	0.107
kda.finish.save	0.098	0.011	0.111
kda.finish.summarize	0.095	0.009	0.107
kda.finish.trim	0.091	0.008	0.102
kda.prepare	11.550	0.128	12.074
kda.prepare.overlap	0.002	0.001	0.003
kda.prepare.screen	0.002	0.000	0.003
kda.start	1.586	0.060	1.694
kda.start.edges	0.003	0.000	0.004
kda.start.identify	0.005	0.001	0.005
kda.start.modules	0.003	0.000	0.004
kda2cytoscape	0.568	0.010	0.592
kda2cytoscape.colorize	0.001	0.000	0.001
kda2cytoscape.colormap	0.034	0.000	0.035
kda2cytoscape.drivers	0.160	0.007	0.170
kda2cytoscape.edges	0.145	0.006	0.153
kda2cytoscape.exec	0.194	0.007	0.205
kda2cytoscape.identify	0.005	0.000	0.006
kda2himmeli	0.542	0.010	0.560
kda2himmeli.colorize	0.000	0.000	0.001
kda2himmeli.colormap	0.039	0.000	0.040
kda2himmeli.drivers	0.179	0.007	0.188
kda2himmeli.edges	0.137	0.006	0.144
kda2himmeli.exec	0.274	0.009	0.298
kda2himmeli.identify	0.005	0.000	0.006
ssea.analyze	7.008	0.126	7.392
ssea.analyze.observe	5.317	0.047	5.499
ssea.analyze.randgenes	5.264	0.047	5.453
ssea.analyze.randloci	4.911	0.043	5.098
ssea.analyze.simulate	6.135	0.095	6.378
ssea.analyze.statistic	0.001	0.000	0.001
ssea.control	4.734	0.041	4.947
ssea.finish	6.345	0.108	6.630
ssea.finish.details	6.678	0.094	6.975
ssea.finish.fdr	6.067	0.104	6.391
ssea.finish.genes	6.314	0.124	6.948
ssea.meta	19.658	0.252	20.822
ssea.prepare	5.271	0.056	5.657
ssea.prepare.counts	4.450	0.047	4.691
ssea.prepare.structure	5.111	0.053	5.423
ssea.start	4.655	0.045	4.907
ssea.start.configure	0.789	0.018	0.834
ssea.start.identify	0.005	0.001	0.006
ssea.start.relabel	4.854	0.050	5.167
ssea2kda	8.102	0.186	8.528
ssea2kda.analyze	7.961	0.223	8.426
ssea2kda.import	6.717	0.127	7.087
tool.aggregate	0.002	0.000	0.003
tool.cluster	0.022	0.001	0.024
tool.cluster.static	0.002	0.000	0.002
tool.coalesce	0.058	0.001	0.060
tool.coalesce.exec	0.156	0.002	0.161
tool.coalesce.find	0.210	0.008	0.229
tool.coalesce.merge	0.147	0.001	0.152
tool.fdr	0.000	0.001	0.001
tool.fdr.bh	0.002	0.000	0.002
tool.fdr.empirical	0.001	0.000	0.002
tool.graph	1.944	0.054	2.054
tool.graph.degree	1.761	0.065	1.877
tool.graph.list	1.683	0.059	1.797
tool.metap	0.004	0.000	0.005
tool.normalize	0.021	0.001	0.021
tool.normalize.quality	0.011	0.001	0.012
tool.overlap	0.013	0.000	0.013
tool.read	0.528	0.014	0.552
tool.save	0.002	0.002	0.004
tool.subgraph	0.147	0.008	0.158
tool.subgraph.find	0.098	0.004	0.105
tool.subgraph.search	0.092	0.004	0.101
tool.subgraph.stats	0.107	0.005	0.122
tool.translate	0.069	0.003	0.075
tool.unify	0.002	0.000	0.002

BioC 3.5: CHECK report for Mergeomics on veracruz2

Summary

Command output