BioC 3.3: CHECK report for Mergeomics on zin2

Package: Mergeomics

Version: 1.0.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Mergeomics_1.0.0.tar.gz

StartedAt: 2016-10-13 04:02:35 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 04:10:33 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 478.0 seconds

RetCode: 0

Status:  OK

CheckDir: Mergeomics.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Mergeomics_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-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 ‘1.0.0’
* 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 10.2Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
* 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          71.308  0.044  71.350
kda.analyze.exec     15.988  0.008  15.985
kda.prepare          15.683  0.004  15.679
kda.analyze.simulate 15.525  0.004  15.530
kda.analyze.test     15.383  0.012  15.390
ssea.meta             7.217  0.016   7.231
kda.start             5.925  0.004   5.927
tool.graph.degree     5.892  0.000   5.900
tool.graph            5.835  0.004   5.847
tool.graph.list       5.610  0.012   5.758
* 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-3.3-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
job.kda	0.013	0.004	0.017
kda.analyze	71.308	0.044	71.350
kda.analyze.exec	15.988	0.008	15.985
kda.analyze.simulate	15.525	0.004	15.530
kda.analyze.test	15.383	0.012	15.390
kda.configure	0.002	0.000	0.001
kda.finish	0.143	0.004	0.147
kda.finish.estimate	0.081	0.004	0.085
kda.finish.save	0.082	0.000	0.082
kda.finish.summarize	0.084	0.000	0.083
kda.finish.trim	0.082	0.000	0.083
kda.prepare	15.683	0.004	15.679
kda.prepare.overlap	0.002	0.000	0.001
kda.prepare.screen	0.000	0.000	0.002
kda.start	5.925	0.004	5.927
kda.start.edges	0.002	0.000	0.002
kda.start.identify	0.005	0.000	0.005
kda.start.modules	0.002	0.000	0.002
kda2cytoscape	0.367	0.000	0.367
kda2cytoscape.colorize	0.001	0.000	0.001
kda2cytoscape.colormap	0.000	0.000	0.001
kda2cytoscape.drivers	0.145	0.000	0.145
kda2cytoscape.edges	0.144	0.000	0.144
kda2cytoscape.exec	0.156	0.004	0.157
kda2cytoscape.identify	0.002	0.000	0.004
kda2himmeli	0.474	0.004	0.478
kda2himmeli.colorize	0.001	0.000	0.001
kda2himmeli.colormap	0	0	0
kda2himmeli.drivers	0.144	0.004	0.152
kda2himmeli.edges	0.146	0.004	0.150
kda2himmeli.exec	0.212	0.004	0.216
kda2himmeli.identify	0.001	0.000	0.004
ssea.analyze	3.683	0.008	3.701
ssea.analyze.observe	3.250	0.004	3.252
ssea.analyze.randgenes	3.453	0.000	3.449
ssea.analyze.randloci	3.451	0.004	3.452
ssea.analyze.simulate	3.663	0.004	3.672
ssea.analyze.statistic	0.001	0.000	0.001
ssea.control	3.269	0.016	3.297
ssea.finish	3.477	0.000	3.475
ssea.finish.details	3.546	0.020	3.566
ssea.finish.fdr	3.529	0.004	3.534
ssea.finish.genes	3.680	0.008	3.685
ssea.meta	7.217	0.016	7.231
ssea.prepare	3.450	0.004	3.451
ssea.prepare.counts	3.357	0.008	3.381
ssea.prepare.structure	3.354	0.004	3.378
ssea.start	3.286	0.000	3.284
ssea.start.configure	0.626	0.004	0.630
ssea.start.identify	0.004	0.000	0.004
ssea.start.relabel	3.265	0.004	3.266
ssea2kda	4.191	0.008	4.213
ssea2kda.analyze	3.874	0.004	3.876
ssea2kda.import	3.828	0.000	3.826
tool.aggregate	0.002	0.000	0.002
tool.cluster	0.197	0.000	0.197
tool.cluster.static	0.001	0.000	0.002
tool.coalesce	0.236	0.004	0.239
tool.coalesce.exec	0.129	0.000	0.129
tool.coalesce.find	0.122	0.000	0.124
tool.coalesce.merge	0.122	0.004	0.126
tool.fdr	0.001	0.000	0.000
tool.fdr.bh	0.001	0.000	0.001
tool.fdr.empirical	0.001	0.000	0.001
tool.graph	5.835	0.004	5.847
tool.graph.degree	5.892	0.000	5.900
tool.graph.list	5.610	0.012	5.758
tool.metap	0.004	0.000	0.004
tool.normalize	0.012	0.000	0.012
tool.normalize.quality	0.009	0.000	0.009
tool.overlap	0.221	0.000	0.221
tool.read	0.239	0.000	0.238
tool.save	0.001	0.000	0.002
tool.subgraph	0.090	0.000	0.089
tool.subgraph.find	0.091	0.000	0.096
tool.subgraph.search	0.099	0.000	0.099
tool.subgraph.stats	0.094	0.000	0.096
tool.translate	0.232	0.004	0.236
tool.unify	0.002	0.000	0.002