BioC 3.3: CHECK report for Mergeomics on morelia

Package: Mergeomics

Version: 0.99.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Mergeomics_0.99.1.tar.gz

StartedAt: 2016-04-21 04:43:16 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 04:53:37 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 621.6 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_0.99.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/Mergeomics.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘0.99.1’
* 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 ... [2s/2s] OK
* checking installed package size ... NOTE
  installed size is 10.1Mb
  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 ... [321s/322s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
kda.analyze           90.079  2.728  93.080
kda.prepare           19.569  1.493  21.099
kda.analyze.simulate  19.638  1.253  20.918
kda.analyze.exec      19.242  1.229  20.505
kda.analyze.test      18.756  1.280  20.053
ssea.meta             10.808  0.139  10.967
tool.graph             7.632  1.091   8.733
kda.start              7.312  1.181   8.504
tool.graph.list        7.285  1.142   8.434
tool.graph.degree      7.186  1.209   8.403
ssea2kda               6.231  0.083   6.343
ssea2kda.analyze       5.669  0.075   5.749
ssea2kda.import        5.381  0.077   5.463
ssea.analyze.simulate  5.393  0.046   5.446
ssea.finish            5.272  0.062   5.344
ssea.finish.fdr        5.219  0.059   5.287
ssea.control           5.160  0.041   5.209
ssea.finish.genes      5.124  0.051   5.193
ssea.analyze.observe   5.058  0.048   5.115
ssea.analyze           4.934  0.084   5.026
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [267s/267s]
 [267s/268s] 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-3.3-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	0.022	0.003	0.024
kda.analyze	90.079	2.728	93.080
kda.analyze.exec	19.242	1.229	20.505
kda.analyze.simulate	19.638	1.253	20.918
kda.analyze.test	18.756	1.280	20.053
kda.configure	0.001	0.000	0.002
kda.finish	0.172	0.012	0.184
kda.finish.estimate	0.114	0.007	0.121
kda.finish.save	0.107	0.008	0.115
kda.finish.summarize	0.106	0.007	0.113
kda.finish.trim	0.110	0.007	0.118
kda.prepare	19.569	1.493	21.099
kda.prepare.overlap	0.003	0.001	0.002
kda.prepare.screen	0.002	0.000	0.002
kda.start	7.312	1.181	8.504
kda.start.edges	0.003	0.000	0.004
kda.start.identify	0.005	0.001	0.005
kda.start.modules	0.002	0.000	0.003
kda2cytoscape	0.462	0.013	0.475
kda2cytoscape.colorize	0.001	0.000	0.001
kda2cytoscape.colormap	0.000	0.000	0.001
kda2cytoscape.drivers	0.151	0.007	0.159
kda2cytoscape.edges	0.179	0.007	0.187
kda2cytoscape.exec	0.232	0.012	0.245
kda2cytoscape.identify	0.008	0.000	0.007
kda2himmeli	0.583	0.012	0.596
kda2himmeli.colorize	0.000	0.000	0.001
kda2himmeli.colormap	0.001	0.000	0.001
kda2himmeli.drivers	0.156	0.006	0.162
kda2himmeli.edges	0.166	0.007	0.172
kda2himmeli.exec	0.324	0.009	0.335
kda2himmeli.identify	0.004	0.000	0.004
ssea.analyze	4.934	0.084	5.026
ssea.analyze.observe	5.058	0.048	5.115
ssea.analyze.randgenes	4.908	0.041	4.955
ssea.analyze.randloci	4.442	0.033	4.477
ssea.analyze.simulate	5.393	0.046	5.446
ssea.analyze.statistic	0.001	0.000	0.000
ssea.control	5.160	0.041	5.209
ssea.finish	5.272	0.062	5.344
ssea.finish.details	4.655	0.055	4.712
ssea.finish.fdr	5.219	0.059	5.287
ssea.finish.genes	5.124	0.051	5.193
ssea.meta	10.808	0.139	10.967
ssea.prepare	4.759	0.045	4.808
ssea.prepare.counts	4.816	0.043	4.861
ssea.prepare.structure	4.769	0.037	4.814
ssea.start	4.640	0.039	4.682
ssea.start.configure	1.549	0.016	1.567
ssea.start.identify	0.006	0.000	0.007
ssea.start.relabel	4.933	0.036	4.977
ssea2kda	6.231	0.083	6.343
ssea2kda.analyze	5.669	0.075	5.749
ssea2kda.import	5.381	0.077	5.463
tool.aggregate	0.003	0.000	0.004
tool.cluster	0.595	0.012	0.619
tool.cluster.static	0.002	0.000	0.002
tool.coalesce	0.566	0.006	0.573
tool.coalesce.exec	0.129	0.001	0.130
tool.coalesce.find	0.188	0.000	0.189
tool.coalesce.merge	0.129	0.001	0.130
tool.fdr	0.001	0.000	0.001
tool.fdr.bh	0.001	0.000	0.000
tool.fdr.empirical	0.001	0.000	0.001
tool.graph	7.632	1.091	8.733
tool.graph.degree	7.186	1.209	8.403
tool.graph.list	7.285	1.142	8.434
tool.metap	0.005	0.000	0.005
tool.normalize	0.014	0.001	0.015
tool.normalize.quality	0.009	0.000	0.009
tool.overlap	0.480	0.014	0.493
tool.read	0.631	0.020	0.652
tool.save	0.002	0.000	0.003
tool.subgraph	0.102	0.007	0.110
tool.subgraph.find	0.092	0.005	0.096
tool.subgraph.search	0.113	0.006	0.120
tool.subgraph.stats	0.092	0.005	0.097
tool.translate	0.548	0.013	0.561
tool.unify	0.002	0.000	0.002