BioC 3.5: CHECK report for Mergeomics on malbec2

Package: Mergeomics

Version: 1.4.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Mergeomics_1.4.0.tar.gz

StartedAt: 2017-08-16 00:24:35 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:34:06 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 570.8 seconds

RetCode: 0

Status:  OK

CheckDir: Mergeomics.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Mergeomics_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/Mergeomics.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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  8.6Mb
  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 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            14.932  0.012  14.964
kda.analyze.exec     11.364  0.028  11.402
kda.analyze.simulate 10.988  0.004  11.004
kda.analyze.test      9.740  0.000   9.754
kda.prepare           8.940  0.004   8.946
ssea2kda              7.796  0.016   7.814
ssea2kda.analyze      7.436  0.028   7.471
ssea2kda.import       5.692  0.004   5.701
ssea.analyze          5.084  0.004   5.090
* 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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/Mergeomics.Rcheck/00check.log’
for details.

* installing *source* package ‘Mergeomics’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Mergeomics)

name	user	system	elapsed
MSEA.KDA.onestep	0.000	0.000	0.002
job.kda	0.012	0.000	0.013
kda.analyze	0.012	0.000	0.012
kda.analyze.exec	11.364	0.028	11.402
kda.analyze.simulate	10.988	0.004	11.004
kda.analyze.test	9.740	0.000	9.754
kda.configure	0.004	0.000	0.004
kda.finish	0.216	0.012	0.229
kda.finish.estimate	0.120	0.008	0.129
kda.finish.save	0.128	0.024	0.154
kda.finish.summarize	0.124	0.008	0.133
kda.finish.trim	0.128	0.012	0.138
kda.prepare	8.940	0.004	8.946
kda.prepare.overlap	0.000	0.000	0.001
kda.prepare.screen	0.000	0.000	0.001
kda.start	1.204	0.008	1.214
kda.start.edges	0.000	0.000	0.002
kda.start.identify	0.008	0.000	0.005
kda.start.modules	0.004	0.000	0.003
kda2cytoscape	0.464	0.028	0.492
kda2cytoscape.colorize	0	0	0
kda2cytoscape.colormap	0.032	0.000	0.029
kda2cytoscape.drivers	0.140	0.004	0.146
kda2cytoscape.edges	0.120	0.004	0.125
kda2cytoscape.exec	0.148	0.012	0.161
kda2cytoscape.identify	0.008	0.000	0.005
kda2himmeli	0.416	0.008	0.425
kda2himmeli.colorize	0	0	0
kda2himmeli.colormap	0.028	0.000	0.027
kda2himmeli.drivers	0.148	0.008	0.155
kda2himmeli.edges	0.152	0.004	0.156
kda2himmeli.exec	0.220	0.008	0.225
kda2himmeli.identify	0.004	0.000	0.004
ssea.analyze	5.084	0.004	5.090
ssea.analyze.observe	3.708	0.004	3.713
ssea.analyze.randgenes	3.816	0.008	3.826
ssea.analyze.randloci	3.876	0.000	3.884
ssea.analyze.simulate	4.936	0.004	4.947
ssea.analyze.statistic	0.004	0.000	0.000
ssea.control	3.660	0.004	3.668
ssea.finish	4.936	0.008	4.949
ssea.finish.details	4.836	0.008	4.848
ssea.finish.fdr	4.752	0.000	4.756
ssea.finish.genes	4.972	0.012	4.985
ssea.meta	14.932	0.012	14.964
ssea.prepare	4.040	0.000	4.042
ssea.prepare.counts	3.576	0.008	3.588
ssea.prepare.structure	3.836	0.000	3.837
ssea.start	3.728	0.000	3.730
ssea.start.configure	0.564	0.004	0.570
ssea.start.identify	0.000	0.004	0.004
ssea.start.relabel	3.676	0.008	3.684
ssea2kda	7.796	0.016	7.814
ssea2kda.analyze	7.436	0.028	7.471
ssea2kda.import	5.692	0.004	5.701
tool.aggregate	0.004	0.000	0.002
tool.cluster	0.012	0.000	0.014
tool.cluster.static	0.000	0.000	0.001
tool.coalesce	0.04	0.00	0.04
tool.coalesce.exec	0.120	0.000	0.118
tool.coalesce.find	0.112	0.000	0.113
tool.coalesce.merge	0.124	0.000	0.123
tool.fdr	0.000	0.000	0.001
tool.fdr.bh	0.000	0.000	0.001
tool.fdr.empirical	0.000	0.000	0.001
tool.graph	1.404	0.004	1.409
tool.graph.degree	1.360	0.000	1.361
tool.graph.list	1.156	0.004	1.162
tool.metap	0.000	0.000	0.003
tool.normalize	0.012	0.000	0.012
tool.normalize.quality	0.008	0.000	0.010
tool.overlap	0.008	0.000	0.007
tool.read	0.260	0.000	0.259
tool.save	0.004	0.000	0.003
tool.subgraph	0.088	0.004	0.091
tool.subgraph.find	0.140	0.008	0.149
tool.subgraph.search	0.076	0.020	0.095
tool.subgraph.stats	0.100	0.004	0.102
tool.translate	0.032	0.000	0.033
tool.unify	0.004	0.000	0.002