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BioC 3.5: CHECK report for Mergeomics on toluca2

This page was generated on 2017-04-23 14:41:13 -0400 (Sun, 23 Apr 2017).

Package 777/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Mergeomics 1.3.1
Zeyneb Kurt
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Mergeomics
Last Changed Rev: 123729 / Revision: 129046
Last Changed Date: 2016-11-06 02:13:10 -0500 (Sun, 06 Nov 2016)
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
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
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: 1.3.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Mergeomics_1.3.1.tar.gz
StartedAt: 2017-04-23 06:19:49 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 06:35:04 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 915.2 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_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Mergeomics.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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              24.830  0.279  25.489
kda.analyze.exec       15.994  0.191  16.414
kda.analyze.simulate   14.780  0.200  15.119
kda.analyze.test       14.607  0.209  14.952
kda.prepare            14.301  0.171  14.577
ssea2kda.analyze       10.952  0.440  11.533
ssea2kda               10.607  0.463  11.210
ssea.analyze            8.908  0.215   9.221
ssea2kda.import         8.313  0.192   8.591
ssea.finish             8.125  0.208   8.480
ssea.finish.details     7.937  0.193   8.274
ssea.finish.genes       7.809  0.204   8.069
ssea.finish.fdr         7.781  0.197   8.053
ssea.analyze.simulate   7.253  0.165   7.509
ssea.analyze.observe    7.277  0.041   7.417
ssea.prepare.structure  6.818  0.045   6.955
ssea.prepare            6.676  0.042   6.772
ssea.prepare.counts     6.656  0.037   6.764
ssea.start              6.635  0.036   6.734
ssea.analyze.randgenes  6.586  0.046   6.726
ssea.analyze.randloci   6.567  0.039   6.687
ssea.control            6.540  0.042   6.687
ssea.start.relabel      6.350  0.041   6.433
* 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.onestep0.0300.0010.031
job.kda0.0190.0020.022
kda.analyze0.0290.0030.032
kda.analyze.exec15.994 0.19116.414
kda.analyze.simulate14.780 0.20015.119
kda.analyze.test14.607 0.20914.952
kda.configure0.0020.0000.003
kda.finish0.1890.0110.201
kda.finish.estimate0.1050.0060.113
kda.finish.save0.1050.0060.112
kda.finish.summarize0.1090.0070.116
kda.finish.trim0.1060.0060.112
kda.prepare14.301 0.17114.577
kda.prepare.overlap0.0010.0000.001
kda.prepare.screen0.0020.0000.002
kda.start2.2980.0732.379
kda.start.edges0.0030.0010.004
kda.start.identify0.0070.0000.007
kda.start.modules0.0030.0010.003
kda2cytoscape0.7560.0110.781
kda2cytoscape.colorize0.0010.0000.001
kda2cytoscape.colormap0.0500.0010.050
kda2cytoscape.drivers0.2020.0060.212
kda2cytoscape.edges0.1680.0060.180
kda2cytoscape.exec0.2120.0070.220
kda2cytoscape.identify0.0060.0010.007
kda2himmeli0.7150.0140.736
kda2himmeli.colorize0.0010.0010.001
kda2himmeli.colormap0.0410.0000.041
kda2himmeli.drivers0.2150.0060.223
kda2himmeli.edges0.1750.0060.188
kda2himmeli.exec0.3510.0090.365
kda2himmeli.identify0.0050.0000.006
ssea.analyze8.9080.2159.221
ssea.analyze.observe7.2770.0417.417
ssea.analyze.randgenes6.5860.0466.726
ssea.analyze.randloci6.5670.0396.687
ssea.analyze.simulate7.2530.1657.509
ssea.analyze.statistic0.0010.0010.001
ssea.control6.5400.0426.687
ssea.finish8.1250.2088.480
ssea.finish.details7.9370.1938.274
ssea.finish.fdr7.7810.1978.053
ssea.finish.genes7.8090.2048.069
ssea.meta24.830 0.27925.489
ssea.prepare6.6760.0426.772
ssea.prepare.counts6.6560.0376.764
ssea.prepare.structure6.8180.0456.955
ssea.start6.6350.0366.734
ssea.start.configure1.1390.0171.166
ssea.start.identify0.0060.0010.006
ssea.start.relabel6.3500.0416.433
ssea2kda10.607 0.46311.210
ssea2kda.analyze10.952 0.44011.533
ssea2kda.import8.3130.1928.591
tool.aggregate0.0020.0000.003
tool.cluster0.0410.0000.042
tool.cluster.static0.0020.0000.001
tool.coalesce0.0610.0010.062
tool.coalesce.exec0.2040.0010.207
tool.coalesce.find0.1760.0010.177
tool.coalesce.merge0.2030.0000.207
tool.fdr0.0010.0000.002
tool.fdr.bh0.0010.0000.001
tool.fdr.empirical0.0010.0000.002
tool.graph2.3740.0702.450
tool.graph.degree2.3310.0742.419
tool.graph.list2.2500.0792.374
tool.metap0.0060.0010.006
tool.normalize0.0180.0000.018
tool.normalize.quality0.0140.0000.015
tool.overlap0.0160.0000.016
tool.read0.8140.0200.868
tool.save0.0020.0000.002
tool.subgraph0.1040.0150.125
tool.subgraph.find0.1030.0130.118
tool.subgraph.search0.1040.0140.120
tool.subgraph.stats0.1340.0140.147
tool.translate0.0950.0020.101
tool.unify0.0020.0000.002