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BioC 3.5: CHECK report for Mergeomics on veracruz2

This page was generated on 2017-08-16 13:34:14 -0400 (Wed, 16 Aug 2017).

Package 779/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Mergeomics 1.4.0
Zeyneb Kurt
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/Mergeomics
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Mergeomics
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Mergeomics_1.4.0.tar.gz
StartedAt: 2017-08-16 05:00:23 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 05:12:55 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 751.8 seconds
RetCode: 0
Status:  OK 
CheckDir: Mergeomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Mergeomics_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Mergeomics.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.4.0’
* 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  8.5Mb
  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              19.290  0.199  20.027
kda.analyze.exec       12.288  0.150  12.841
kda.analyze.simulate   11.388  0.136  11.854
kda.prepare            11.220  0.146  11.664
kda.analyze.test       11.166  0.133  11.629
ssea2kda.analyze        9.063  0.315   9.667
ssea2kda                8.317  0.313   8.898
ssea2kda.import         6.795  0.137   7.154
ssea.analyze            6.473  0.136   6.777
ssea.finish.genes       6.459  0.095   6.827
ssea.finish             6.382  0.138   6.780
ssea.finish.details     6.120  0.146   6.432
ssea.finish.fdr         6.112  0.086   6.422
ssea.analyze.simulate   5.954  0.140   6.308
ssea.prepare            5.395  0.049   5.556
ssea.prepare.counts     5.172  0.041   5.348
ssea.analyze.randloci   5.180  0.029   5.341
ssea.analyze.observe    5.159  0.035   5.360
ssea.start.relabel      5.080  0.033   5.264
ssea.start              5.047  0.030   5.235
ssea.control            4.916  0.031   5.077
ssea.analyze.randgenes  4.904  0.036   5.116
ssea.prepare.structure  4.877  0.046   5.017
* 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.

Mergeomics.Rcheck/00install.out:

* 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)

Mergeomics.Rcheck/Mergeomics-Ex.timings:

nameusersystemelapsed
MSEA.KDA.onestep0.0290.0010.029
job.kda0.0150.0030.018
kda.analyze0.0220.0020.024
kda.analyze.exec12.288 0.15012.841
kda.analyze.simulate11.388 0.13611.854
kda.analyze.test11.166 0.13311.629
kda.configure0.0030.0000.003
kda.finish0.1670.0090.180
kda.finish.estimate0.0920.0050.104
kda.finish.save0.0910.0040.099
kda.finish.summarize0.1040.0050.109
kda.finish.trim0.0950.0050.108
kda.prepare11.220 0.14611.664
kda.prepare.overlap0.0020.0000.002
kda.prepare.screen0.0020.0000.002
kda.start1.7080.0651.836
kda.start.edges0.0020.0000.003
kda.start.identify0.0060.0010.007
kda.start.modules0.0030.0010.003
kda2cytoscape0.6210.0080.651
kda2cytoscape.colorize0.0010.0010.001
kda2cytoscape.colormap0.0400.0000.045
kda2cytoscape.drivers0.1750.0050.197
kda2cytoscape.edges0.1450.0080.164
kda2cytoscape.exec0.1570.0060.176
kda2cytoscape.identify0.0040.0000.004
kda2himmeli0.5510.0120.597
kda2himmeli.colorize0.0010.0000.001
kda2himmeli.colormap0.0230.0000.023
kda2himmeli.drivers0.1840.0050.192
kda2himmeli.edges0.1540.0050.160
kda2himmeli.exec0.2650.0050.274
kda2himmeli.identify0.0030.0000.004
ssea.analyze6.4730.1366.777
ssea.analyze.observe5.1590.0355.360
ssea.analyze.randgenes4.9040.0365.116
ssea.analyze.randloci5.1800.0295.341
ssea.analyze.simulate5.9540.1406.308
ssea.analyze.statistic0.0050.0010.007
ssea.control4.9160.0315.077
ssea.finish6.3820.1386.780
ssea.finish.details6.1200.1466.432
ssea.finish.fdr6.1120.0866.422
ssea.finish.genes6.4590.0956.827
ssea.meta19.290 0.19920.027
ssea.prepare5.3950.0495.556
ssea.prepare.counts5.1720.0415.348
ssea.prepare.structure4.8770.0465.017
ssea.start5.0470.0305.235
ssea.start.configure0.7980.0180.825
ssea.start.identify0.0060.0000.007
ssea.start.relabel5.0800.0335.264
ssea2kda8.3170.3138.898
ssea2kda.analyze9.0630.3159.667
ssea2kda.import6.7950.1377.154
tool.aggregate0.0020.0000.003
tool.cluster0.0380.0020.040
tool.cluster.static0.0020.0000.002
tool.coalesce0.0460.0010.046
tool.coalesce.exec0.1580.0000.162
tool.coalesce.find0.1470.0000.156
tool.coalesce.merge0.1520.0010.153
tool.fdr0.0010.0000.002
tool.fdr.bh0.0020.0010.001
tool.fdr.empirical0.0010.0000.001
tool.graph1.8230.0581.924
tool.graph.degree1.7880.0681.919
tool.graph.list1.5630.0541.669
tool.metap0.0050.0000.006
tool.normalize0.0160.0010.016
tool.normalize.quality0.0130.0000.013
tool.overlap0.0100.0010.011
tool.read0.5770.0160.614
tool.save0.0030.0010.009
tool.subgraph0.0910.0050.097
tool.subgraph.find0.0940.0050.099
tool.subgraph.search0.0820.0040.094
tool.subgraph.stats0.1070.0050.117
tool.translate0.0730.0020.075
tool.unify0.0020.0010.002