BioC 3.6: CHECK report for Mergeomics on veracruz1

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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_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/Mergeomics.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.5.0’
* 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              19.802  0.255  20.722
kda.analyze.exec       12.456  0.158  12.978
kda.analyze.test       10.788  0.098  11.157
kda.prepare            10.670  0.128  11.156
kda.analyze.simulate   10.115  0.112  10.506
ssea2kda.analyze        8.920  0.301   9.462
ssea2kda                8.517  0.224   8.959
ssea.analyze            7.076  0.146   7.449
ssea2kda.import         6.619  0.147   6.959
ssea.finish             6.218  0.151   6.551
ssea.finish.details     6.181  0.156   6.546
ssea.finish.genes       6.036  0.137   6.356
ssea.analyze.simulate   5.893  0.138   6.190
ssea.finish.fdr         5.854  0.151   6.206
ssea.analyze.observe    5.444  0.036   5.616
ssea.prepare            5.171  0.049   5.388
ssea.prepare.structure  5.146  0.036   5.360
ssea.start              5.091  0.032   5.211
ssea.start.relabel      5.036  0.031   5.168
ssea.prepare.counts     5.001  0.026   5.163
ssea.analyze.randloci   4.978  0.027   5.151
* 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-3.6-bioc/meat/Mergeomics.Rcheck/00check.log’
for details.

name	user	system	elapsed
MSEA.KDA.onestep	0.03	0.00	0.03
job.kda	0.019	0.002	0.022
kda.analyze	0.022	0.002	0.025
kda.analyze.exec	12.456	0.158	12.978
kda.analyze.simulate	10.115	0.112	10.506
kda.analyze.test	10.788	0.098	11.157
kda.configure	0.001	0.000	0.002
kda.finish	0.140	0.009	0.154
kda.finish.estimate	0.064	0.003	0.067
kda.finish.save	0.065	0.004	0.070
kda.finish.summarize	0.100	0.003	0.105
kda.finish.trim	0.086	0.005	0.092
kda.prepare	10.670	0.128	11.156
kda.prepare.overlap	0.001	0.000	0.002
kda.prepare.screen	0.001	0.000	0.002
kda.start	1.736	0.066	1.855
kda.start.edges	0.003	0.001	0.004
kda.start.identify	0.006	0.000	0.007
kda.start.modules	0.004	0.000	0.004
kda2cytoscape	0.586	0.010	0.627
kda2cytoscape.colorize	0.000	0.000	0.001
kda2cytoscape.colormap	0.035	0.000	0.039
kda2cytoscape.drivers	0.160	0.009	0.175
kda2cytoscape.edges	0.142	0.009	0.156
kda2cytoscape.exec	0.192	0.010	0.205
kda2cytoscape.identify	0.005	0.001	0.006
kda2himmeli	0.566	0.016	0.603
kda2himmeli.colorize	0.001	0.000	0.000
kda2himmeli.colormap	0.028	0.000	0.031
kda2himmeli.drivers	0.193	0.009	0.207
kda2himmeli.edges	0.150	0.007	0.164
kda2himmeli.exec	0.275	0.010	0.298
kda2himmeli.identify	0.003	0.000	0.003
ssea.analyze	7.076	0.146	7.449
ssea.analyze.observe	5.444	0.036	5.616
ssea.analyze.randgenes	4.698	0.032	4.885
ssea.analyze.randloci	4.978	0.027	5.151
ssea.analyze.simulate	5.893	0.138	6.190
ssea.analyze.statistic	0.005	0.001	0.006
ssea.control	4.588	0.040	4.752
ssea.finish	6.218	0.151	6.551
ssea.finish.details	6.181	0.156	6.546
ssea.finish.fdr	5.854	0.151	6.206
ssea.finish.genes	6.036	0.137	6.356
ssea.meta	19.802	0.255	20.722
ssea.prepare	5.171	0.049	5.388
ssea.prepare.counts	5.001	0.026	5.163
ssea.prepare.structure	5.146	0.036	5.360
ssea.start	5.091	0.032	5.211
ssea.start.configure	0.792	0.016	0.822
ssea.start.identify	0.005	0.000	0.005
ssea.start.relabel	5.036	0.031	5.168
ssea2kda	8.517	0.224	8.959
ssea2kda.analyze	8.920	0.301	9.462
ssea2kda.import	6.619	0.147	6.959
tool.aggregate	0.002	0.000	0.003
tool.cluster	0.031	0.001	0.033
tool.cluster.static	0.002	0.001	0.001
tool.coalesce	0.034	0.000	0.034
tool.coalesce.exec	0.153	0.001	0.160
tool.coalesce.find	0.126	0.001	0.131
tool.coalesce.merge	0.135	0.000	0.135
tool.fdr	0.001	0.001	0.001
tool.fdr.bh	0.001	0.000	0.001
tool.fdr.empirical	0.002	0.000	0.001
tool.graph	1.673	0.054	1.783
tool.graph.degree	1.637	0.063	1.771
tool.graph.list	1.623	0.049	1.714
tool.metap	0.003	0.001	0.004
tool.normalize	0.015	0.000	0.015
tool.normalize.quality	0.009	0.000	0.009
tool.overlap	0.011	0.001	0.012
tool.read	0.584	0.016	0.611
tool.save	0.002	0.001	0.002
tool.subgraph	0.100	0.005	0.105
tool.subgraph.find	0.088	0.005	0.097
tool.subgraph.search	0.102	0.004	0.106
tool.subgraph.stats	0.110	0.004	0.118
tool.translate	0.070	0.002	0.077
tool.unify	0.001	0.000	0.002

BioC 3.6: CHECK report for Mergeomics on veracruz1

Summary

Command output