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: 2017-10-18 00:36:13 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:45:13 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 540.2 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 3.4.2 (2017-09-28)
* 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            14.588  0.012  14.604
kda.analyze.exec     10.228  0.024  10.261
kda.analyze.simulate  9.468  0.004   9.479
kda.analyze.test      9.308  0.016   9.329
kda.prepare           9.228  0.012   9.251
ssea2kda              7.048  0.008   7.059
ssea2kda.analyze      6.480  0.012   6.494
ssea.analyze          5.188  0.008   5.198
ssea.finish.fdr       5.012  0.008   5.023
* 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	0.003
job.kda	0.016	0.000	0.015
kda.analyze	0.016	0.000	0.018
kda.analyze.exec	10.228	0.024	10.261
kda.analyze.simulate	9.468	0.004	9.479
kda.analyze.test	9.308	0.016	9.329
kda.configure	0.004	0.000	0.001
kda.finish	0.132	0.004	0.138
kda.finish.estimate	0.084	0.000	0.083
kda.finish.save	0.096	0.000	0.096
kda.finish.summarize	0.108	0.000	0.105
kda.finish.trim	0.092	0.000	0.094
kda.prepare	9.228	0.012	9.251
kda.prepare.overlap	0.000	0.000	0.002
kda.prepare.screen	0.004	0.000	0.001
kda.start	1.332	0.000	1.334
kda.start.edges	0.004	0.000	0.002
kda.start.identify	0.004	0.000	0.005
kda.start.modules	0.004	0.000	0.002
kda2cytoscape	0.488	0.000	0.488
kda2cytoscape.colorize	0	0	0
kda2cytoscape.colormap	0.032	0.000	0.032
kda2cytoscape.drivers	0.136	0.004	0.144
kda2cytoscape.edges	0.112	0.004	0.117
kda2cytoscape.exec	0.14	0.00	0.14
kda2cytoscape.identify	0.004	0.000	0.004
kda2himmeli	0.392	0.000	0.393
kda2himmeli.colorize	0	0	0
kda2himmeli.colormap	0.024	0.000	0.026
kda2himmeli.drivers	0.144	0.004	0.146
kda2himmeli.edges	0.140	0.004	0.144
kda2himmeli.exec	0.196	0.000	0.193
kda2himmeli.identify	0.004	0.000	0.004
ssea.analyze	5.188	0.008	5.198
ssea.analyze.observe	3.772	0.004	3.779
ssea.analyze.randgenes	3.996	0.000	3.999
ssea.analyze.randloci	4.192	0.008	4.204
ssea.analyze.simulate	4.596	0.000	4.599
ssea.analyze.statistic	0.000	0.000	0.001
ssea.control	3.636	0.008	3.643
ssea.finish	4.708	0.004	4.714
ssea.finish.details	4.832	0.004	4.841
ssea.finish.fdr	5.012	0.008	5.023
ssea.finish.genes	4.836	0.004	4.843
ssea.meta	14.588	0.012	14.604
ssea.prepare	3.704	0.004	3.709
ssea.prepare.counts	3.416	0.008	3.425
ssea.prepare.structure	3.568	0.004	3.573
ssea.start	3.720	0.004	3.729
ssea.start.configure	0.408	0.004	0.416
ssea.start.identify	0.004	0.000	0.004
ssea.start.relabel	3.344	0.000	3.347
ssea2kda	7.048	0.008	7.059
ssea2kda.analyze	6.480	0.012	6.494
ssea2kda.import	4.736	0.004	4.740
tool.aggregate	0.000	0.000	0.002
tool.cluster	0.012	0.004	0.015
tool.cluster.static	0.004	0.000	0.001
tool.coalesce	0.032	0.000	0.032
tool.coalesce.exec	0.112	0.000	0.114
tool.coalesce.find	0.112	0.000	0.115
tool.coalesce.merge	0.116	0.000	0.116
tool.fdr	0	0	0
tool.fdr.bh	0.000	0.000	0.001
tool.fdr.empirical	0.004	0.000	0.001
tool.graph	1.260	0.000	1.261
tool.graph.degree	1.216	0.004	1.219
tool.graph.list	1.112	0.004	1.115
tool.metap	0.004	0.000	0.003
tool.normalize	0.008	0.000	0.010
tool.normalize.quality	0.012	0.000	0.014
tool.overlap	0.004	0.000	0.007
tool.read	0.248	0.000	0.246
tool.save	0.000	0.000	0.001
tool.subgraph	0.080	0.000	0.081
tool.subgraph.find	0.080	0.004	0.083
tool.subgraph.search	0.076	0.004	0.079
tool.subgraph.stats	0.096	0.004	0.098
tool.translate	0.044	0.004	0.047
tool.unify	0.000	0.000	0.002