BioC 3.5: CHECK report for Mergeomics on oaxaca

Package: Mergeomics

Version: 1.3.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Mergeomics_1.3.1.tar.gz

StartedAt: 2017-03-04 05:27:15 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 05:38:57 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 701.7 seconds

RetCode: 0

Status:  OK

CheckDir: Mergeomics.Rcheck

Warnings: 0

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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_1.3.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Mergeomics.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.3.1’
* 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              20.766  0.258  21.032
kda.prepare            10.343  0.184  10.530
kda.analyze.exec       10.140  0.135  10.276
kda.analyze.simulate    9.242  0.142   9.382
kda.analyze.test        9.141  0.163   9.304
ssea2kda                7.240  0.392   7.642
ssea2kda.analyze        7.203  0.365   7.571
ssea.analyze            7.053  0.201   7.259
ssea.finish.genes       6.226  0.176   6.419
ssea.prepare.structure  6.045  0.036   6.084
ssea.finish.fdr         5.805  0.177   5.982
ssea.start              5.860  0.034   5.898
ssea2kda.import         5.437  0.160   5.597
ssea.prepare            5.541  0.053   5.596
ssea.finish.details     5.196  0.164   5.402
ssea.finish             5.207  0.138   5.345
ssea.start.relabel      5.115  0.027   5.153
ssea.analyze.simulate   4.936  0.153   5.104
* 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-3.5-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	0.024	0.001	0.024
job.kda	0.014	0.002	0.033
kda.analyze	0.022	0.002	0.024
kda.analyze.exec	10.140	0.135	10.276
kda.analyze.simulate	9.242	0.142	9.382
kda.analyze.test	9.141	0.163	9.304
kda.configure	0.001	0.000	0.002
kda.finish	0.120	0.009	0.128
kda.finish.estimate	0.070	0.003	0.074
kda.finish.save	0.071	0.004	0.075
kda.finish.summarize	0.075	0.005	0.080
kda.finish.trim	0.073	0.004	0.077
kda.prepare	10.343	0.184	10.530
kda.prepare.overlap	0.001	0.000	0.001
kda.prepare.screen	0.001	0.000	0.001
kda.start	1.937	0.066	2.003
kda.start.edges	0.003	0.000	0.004
kda.start.identify	0.008	0.001	0.009
kda.start.modules	0.003	0.000	0.004
kda2cytoscape	0.656	0.011	0.667
kda2cytoscape.colorize	0	0	0
kda2cytoscape.colormap	0.032	0.000	0.032
kda2cytoscape.drivers	0.142	0.005	0.146
kda2cytoscape.edges	0.113	0.004	0.117
kda2cytoscape.exec	0.209	0.008	0.217
kda2cytoscape.identify	0.004	0.000	0.004
kda2himmeli	0.664	0.018	0.684
kda2himmeli.colorize	0.000	0.000	0.001
kda2himmeli.colormap	0.039	0.000	0.039
kda2himmeli.drivers	0.221	0.008	0.229
kda2himmeli.edges	0.148	0.006	0.154
kda2himmeli.exec	0.305	0.008	0.313
kda2himmeli.identify	0.004	0.000	0.004
ssea.analyze	7.053	0.201	7.259
ssea.analyze.observe	4.796	0.033	4.830
ssea.analyze.randgenes	4.662	0.040	4.703
ssea.analyze.randloci	4.150	0.027	4.177
ssea.analyze.simulate	4.936	0.153	5.104
ssea.analyze.statistic	0.001	0.000	0.001
ssea.control	4.154	0.035	4.191
ssea.finish	5.207	0.138	5.345
ssea.finish.details	5.196	0.164	5.402
ssea.finish.fdr	5.805	0.177	5.982
ssea.finish.genes	6.226	0.176	6.419
ssea.meta	20.766	0.258	21.032
ssea.prepare	5.541	0.053	5.596
ssea.prepare.counts	4.910	0.033	4.943
ssea.prepare.structure	6.045	0.036	6.084
ssea.start	5.860	0.034	5.898
ssea.start.configure	0.833	0.013	0.847
ssea.start.identify	0.005	0.000	0.005
ssea.start.relabel	5.115	0.027	5.153
ssea2kda	7.240	0.392	7.642
ssea2kda.analyze	7.203	0.365	7.571
ssea2kda.import	5.437	0.160	5.597
tool.aggregate	0.002	0.000	0.001
tool.cluster	0.031	0.002	0.032
tool.cluster.static	0.001	0.000	0.001
tool.coalesce	0.039	0.001	0.040
tool.coalesce.exec	0.130	0.001	0.132
tool.coalesce.find	0.126	0.000	0.125
tool.coalesce.merge	0.137	0.001	0.138
tool.fdr	0.001	0.000	0.001
tool.fdr.bh	0.001	0.000	0.001
tool.fdr.empirical	0.001	0.000	0.001
tool.graph	1.610	0.071	1.680
tool.graph.degree	1.541	0.064	1.606
tool.graph.list	1.452	0.054	1.507
tool.metap	0.004	0.000	0.004
tool.normalize	0.011	0.000	0.012
tool.normalize.quality	0.009	0.000	0.009
tool.overlap	0.010	0.000	0.011
tool.read	0.545	0.016	0.561
tool.save	0.001	0.000	0.038
tool.subgraph	0.071	0.003	0.074
tool.subgraph.find	0.070	0.003	0.074
tool.subgraph.search	0.071	0.003	0.074
tool.subgraph.stats	0.087	0.002	0.090
tool.translate	0.059	0.001	0.061
tool.unify	0.001	0.000	0.001