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BioC 3.3: CHECK report for Mergeomics on oaxaca

This page was generated on 2016-10-13 13:02:55 -0700 (Thu, 13 Oct 2016).

Package 681/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Mergeomics 1.0.0
Zeyneb Kurt
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/Mergeomics
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Mergeomics
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Mergeomics_1.0.0.tar.gz
StartedAt: 2016-10-13 03:27:10 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 03:38:50 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 700.4 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/Mergeomics.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.0.0’
* 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 10.1Mb
  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 ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
kda.analyze            93.474  3.107  99.766
kda.prepare            21.736  1.211  22.981
kda.analyze.test       21.477  1.405  22.914
kda.analyze.exec       20.635  1.166  21.826
kda.analyze.simulate   20.206  1.242  21.472
ssea.meta              11.250  0.133  11.403
tool.graph              8.251  1.222   9.519
tool.graph.degree       7.978  1.097   9.100
tool.graph.list         7.497  1.230   8.769
kda.start               7.427  1.148   8.582
ssea2kda                7.080  0.098   7.201
ssea2kda.analyze        6.298  0.066   6.376
ssea2kda.import         6.021  0.068   6.102
ssea.finish.details     6.009  0.064   6.091
ssea.finish.genes       5.870  0.067   6.647
ssea.finish.fdr         5.830  0.057   6.022
ssea.analyze.observe    5.735  0.046   5.801
ssea.analyze.simulate   5.713  0.064   5.881
ssea.prepare.counts     5.694  0.039   5.739
ssea.control            5.664  0.049   5.742
ssea.prepare            5.598  0.057   5.670
ssea.finish             5.564  0.062   5.777
ssea.analyze.randloci   5.434  0.040   5.484
ssea.prepare.structure  5.397  0.044   5.455
ssea.analyze.randgenes  5.380  0.048   5.545
ssea.start              5.235  0.037   5.297
ssea.analyze            5.080  0.075   5.244
ssea.start.relabel      5.082  0.030   5.117
* 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-3.3-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
job.kda0.0230.0040.026
kda.analyze93.474 3.10799.766
kda.analyze.exec20.635 1.16621.826
kda.analyze.simulate20.206 1.24221.472
kda.analyze.test21.477 1.40522.914
kda.configure0.0020.0000.004
kda.finish0.1970.0120.210
kda.finish.estimate0.1110.0060.118
kda.finish.save0.1030.0060.108
kda.finish.summarize0.1120.0050.118
kda.finish.trim0.1130.0050.118
kda.prepare21.736 1.21122.981
kda.prepare.overlap0.0020.0010.002
kda.prepare.screen0.0020.0000.003
kda.start7.4271.1488.582
kda.start.edges0.0030.0010.004
kda.start.identify0.0080.0010.008
kda.start.modules0.0040.0000.004
kda2cytoscape0.5130.0160.529
kda2cytoscape.colorize0.0010.0000.001
kda2cytoscape.colormap0.0000.0000.001
kda2cytoscape.drivers0.1750.0110.187
kda2cytoscape.edges0.1780.0110.190
kda2cytoscape.exec0.2090.0120.223
kda2cytoscape.identify0.0060.0010.006
kda2himmeli0.6250.0190.644
kda2himmeli.colorize0.0010.0000.001
kda2himmeli.colormap0.0010.0010.002
kda2himmeli.drivers0.2020.0120.214
kda2himmeli.edges0.2020.0130.215
kda2himmeli.exec0.3600.0130.390
kda2himmeli.identify0.0070.0000.007
ssea.analyze5.0800.0755.244
ssea.analyze.observe5.7350.0465.801
ssea.analyze.randgenes5.3800.0485.545
ssea.analyze.randloci5.4340.0405.484
ssea.analyze.simulate5.7130.0645.881
ssea.analyze.statistic0.0010.0010.001
ssea.control5.6640.0495.742
ssea.finish5.5640.0625.777
ssea.finish.details6.0090.0646.091
ssea.finish.fdr5.8300.0576.022
ssea.finish.genes5.8700.0676.647
ssea.meta11.250 0.13311.403
ssea.prepare5.5980.0575.670
ssea.prepare.counts5.6940.0395.739
ssea.prepare.structure5.3970.0445.455
ssea.start5.2350.0375.297
ssea.start.configure1.6670.0231.693
ssea.start.identify0.0060.0000.007
ssea.start.relabel5.0820.0305.117
ssea2kda7.0800.0987.201
ssea2kda.analyze6.2980.0666.376
ssea2kda.import6.0210.0686.102
tool.aggregate0.0020.0010.002
tool.cluster0.5120.0080.520
tool.cluster.static0.0020.0000.002
tool.coalesce0.650.010.66
tool.coalesce.exec0.1990.0010.202
tool.coalesce.find0.1890.0010.190
tool.coalesce.merge0.1840.0010.185
tool.fdr0.0020.0000.002
tool.fdr.bh0.0010.0000.002
tool.fdr.empirical0.0010.0000.002
tool.graph8.2511.2229.519
tool.graph.degree7.9781.0979.100
tool.graph.list7.4971.2308.769
tool.metap0.0060.0000.006
tool.normalize0.0110.0000.012
tool.normalize.quality0.0110.0010.011
tool.overlap0.4960.0140.510
tool.read0.8500.0220.877
tool.save0.0020.0010.002
tool.subgraph0.1030.0060.108
tool.subgraph.find0.0950.0040.101
tool.subgraph.search0.1250.0060.132
tool.subgraph.stats0.1140.0060.119
tool.translate0.6280.0120.641
tool.unify0.0020.0010.002