BioC 3.4: CHECK report for Mergeomics on zin1

Package: Mergeomics

Version: 1.1.10

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Mergeomics_1.1.10.tar.gz

StartedAt: 2016-09-20 08:59:39 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 09:09:41 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 601.8 seconds

RetCode: 0

Status:  OK

CheckDir: Mergeomics.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Mergeomics_1.1.10.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/Mergeomics.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.1.10’
* 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.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
kda.analyze.exec     15.732  0.008  15.743
kda.analyze.simulate 15.528  0.012  15.539
kda.prepare          15.384  0.004  15.392
kda.analyze.test     14.940  0.000  14.941
ssea.meta            14.860  0.016  14.882
tool.graph            5.960  0.000   5.959
ssea2kda              5.728  0.004   5.735
kda.start             5.696  0.000   5.698
tool.graph.degree     5.524  0.004   5.527
ssea2kda.analyze      5.520  0.004   5.532
tool.graph.list       5.328  0.012   5.340
ssea.finish.genes     5.144  0.004   5.152
ssea.finish.fdr       5.100  0.012   5.116
ssea.finish.details   5.096  0.008   5.249
ssea.finish           5.088  0.008   5.111
* 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-3.4-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	0.016	0.000	0.017
kda.analyze	0.016	0.000	0.013
kda.analyze.exec	15.732	0.008	15.743
kda.analyze.simulate	15.528	0.012	15.539
kda.analyze.test	14.940	0.000	14.941
kda.configure	0.004	0.000	0.002
kda.finish	0.140	0.000	0.141
kda.finish.estimate	0.08	0.00	0.08
kda.finish.save	0.080	0.000	0.079
kda.finish.summarize	0.08	0.00	0.08
kda.finish.trim	0.076	0.004	0.079
kda.prepare	15.384	0.004	15.392
kda.prepare.overlap	0.000	0.000	0.001
kda.prepare.screen	0.004	0.000	0.001
kda.start	5.696	0.000	5.698
kda.start.edges	0.004	0.000	0.003
kda.start.identify	0.004	0.000	0.004
kda.start.modules	0.000	0.000	0.002
kda2cytoscape	0.356	0.000	0.354
kda2cytoscape.colorize	0	0	0
kda2cytoscape.colormap	0	0	0
kda2cytoscape.drivers	0.132	0.004	0.137
kda2cytoscape.edges	0.148	0.000	0.146
kda2cytoscape.exec	0.156	0.000	0.156
kda2cytoscape.identify	0.004	0.000	0.005
kda2himmeli	0.400	0.000	0.398
kda2himmeli.colorize	0.000	0.000	0.001
kda2himmeli.colormap	0	0	0
kda2himmeli.drivers	0.144	0.004	0.148
kda2himmeli.edges	0.144	0.012	0.161
kda2himmeli.exec	0.204	0.000	0.202
kda2himmeli.identify	0.004	0.000	0.004
ssea.analyze	4.776	0.004	4.780
ssea.analyze.observe	4.320	0.004	4.322
ssea.analyze.randgenes	4.504	0.004	4.511
ssea.analyze.randloci	4.600	0.004	4.606
ssea.analyze.simulate	4.924	0.004	4.929
ssea.analyze.statistic	0	0	0
ssea.control	4.552	0.008	4.558
ssea.finish	5.088	0.008	5.111
ssea.finish.details	5.096	0.008	5.249
ssea.finish.fdr	5.100	0.012	5.116
ssea.finish.genes	5.144	0.004	5.152
ssea.meta	14.860	0.016	14.882
ssea.prepare	4.724	0.004	4.727
ssea.prepare.counts	4.620	0.008	4.626
ssea.prepare.structure	4.516	0.004	4.521
ssea.start	4.568	0.000	4.569
ssea.start.configure	0.412	0.004	0.415
ssea.start.identify	0.004	0.000	0.004
ssea.start.relabel	4.456	0.008	4.467
ssea2kda	5.728	0.004	5.735
ssea2kda.analyze	5.520	0.004	5.532
ssea2kda.import	4.960	0.004	4.963
tool.aggregate	0.004	0.000	0.001
tool.cluster	0.020	0.000	0.022
tool.cluster.static	0.004	0.000	0.001
tool.coalesce	0.056	0.000	0.055
tool.coalesce.exec	0.128	0.000	0.130
tool.coalesce.find	0.132	0.000	0.132
tool.coalesce.merge	0.128	0.000	0.127
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	5.960	0.000	5.959
tool.graph.degree	5.524	0.004	5.527
tool.graph.list	5.328	0.012	5.340
tool.metap	0.004	0.000	0.004
tool.normalize	0.008	0.000	0.010
tool.normalize.quality	0.008	0.000	0.008
tool.overlap	0.008	0.000	0.008
tool.read	0.288	0.000	0.286
tool.save	0.000	0.000	0.002
tool.subgraph	0.080	0.004	0.081
tool.subgraph.find	0.080	0.004	0.082
tool.subgraph.search	0.084	0.000	0.084
tool.subgraph.stats	0.084	0.000	0.083
tool.translate	0.032	0.000	0.033
tool.unify	0.000	0.000	0.002