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BioC 3.4: CHECK report for Mergeomics on morelia

This page was generated on 2016-09-21 03:55:35 -0700 (Wed, 21 Sep 2016).

Package 712/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Mergeomics 1.1.10
Zeyneb Kurt
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Mergeomics
Last Changed Rev: 120804 / Revision: 121152
Last Changed Date: 2016-09-08 07:55:28 -0700 (Thu, 08 Sep 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Mergeomics
Version: 1.1.10
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Mergeomics_1.1.10.tar.gz
StartedAt: 2016-09-20 08:55:42 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 09:06:39 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 657.5 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_1.1.10.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-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 ‘1.1.10’
* 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.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              17.331  0.180  17.791
kda.analyze.simulate   16.153  1.131  17.292
kda.analyze.exec       15.173  1.022  16.198
kda.analyze.test       14.980  1.092  16.077
kda.prepare            14.889  1.147  16.038
tool.graph              6.530  1.295   7.828
tool.graph.degree       6.184  1.286   7.471
kda.start               5.877  1.097   6.975
ssea2kda.analyze        6.392  0.120   6.515
tool.graph.list         5.240  1.182   6.422
ssea2kda                6.307  0.111   6.420
ssea.finish.genes       6.187  0.087   6.277
ssea.finish.details     6.187  0.081   6.270
ssea.finish.fdr         5.876  0.088   5.966
ssea2kda.import         5.609  0.089   5.700
ssea.analyze            5.611  0.087   5.700
ssea.finish             5.612  0.077   5.691
ssea.analyze.simulate   5.405  0.076   5.482
ssea.start              5.453  0.027   5.483
ssea.control            5.296  0.038   5.334
ssea.analyze.randloci   5.218  0.032   5.251
ssea.start.relabel      5.190  0.024   5.215
ssea.prepare.structure  5.178  0.030   5.211
ssea.analyze.observe    5.089  0.036   5.127
ssea.prepare            4.987  0.034   5.023
* 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-3.4-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.onestep0.0010.0000.003
job.kda0.0140.0020.029
kda.analyze0.0160.0010.017
kda.analyze.exec15.173 1.02216.198
kda.analyze.simulate16.153 1.13117.292
kda.analyze.test14.980 1.09216.077
kda.configure0.0020.0000.002
kda.finish0.1570.0130.170
kda.finish.estimate0.1090.0060.116
kda.finish.save0.0930.0070.099
kda.finish.summarize0.0900.0050.095
kda.finish.trim0.0710.0050.075
kda.prepare14.889 1.14716.038
kda.prepare.overlap0.0010.0000.001
kda.prepare.screen0.0010.0000.002
kda.start5.8771.0976.975
kda.start.edges0.0040.0000.004
kda.start.identify0.0070.0000.007
kda.start.modules0.0030.0000.004
kda2cytoscape0.3720.0110.383
kda2cytoscape.colorize0.0010.0000.001
kda2cytoscape.colormap0.0010.0000.001
kda2cytoscape.drivers0.1200.0050.126
kda2cytoscape.edges0.1200.0060.126
kda2cytoscape.exec0.1340.0050.139
kda2cytoscape.identify0.0040.0000.004
kda2himmeli0.4100.0090.419
kda2himmeli.colorize000
kda2himmeli.colormap0.0010.0000.001
kda2himmeli.drivers0.1360.0070.143
kda2himmeli.edges0.1690.0070.176
kda2himmeli.exec0.3670.0090.377
kda2himmeli.identify0.0060.0000.007
ssea.analyze5.6110.0875.700
ssea.analyze.observe5.0890.0365.127
ssea.analyze.randgenes4.9470.0344.982
ssea.analyze.randloci5.2180.0325.251
ssea.analyze.simulate5.4050.0765.482
ssea.analyze.statistic0.0010.0000.000
ssea.control5.2960.0385.334
ssea.finish5.6120.0775.691
ssea.finish.details6.1870.0816.270
ssea.finish.fdr5.8760.0885.966
ssea.finish.genes6.1870.0876.277
ssea.meta17.331 0.18017.791
ssea.prepare4.9870.0345.023
ssea.prepare.counts4.9060.0294.936
ssea.prepare.structure5.1780.0305.211
ssea.start5.4530.0275.483
ssea.start.configure0.8670.0130.881
ssea.start.identify0.0040.0010.004
ssea.start.relabel5.1900.0245.215
ssea2kda6.3070.1116.420
ssea2kda.analyze6.3920.1206.515
ssea2kda.import5.6090.0895.700
tool.aggregate0.0020.0000.001
tool.cluster0.0220.0010.022
tool.cluster.static0.0010.0000.001
tool.coalesce0.0490.0000.050
tool.coalesce.exec0.1200.0010.120
tool.coalesce.find0.1720.0000.173
tool.coalesce.merge0.1220.0010.122
tool.fdr0.0010.0000.001
tool.fdr.bh0.0010.0000.000
tool.fdr.empirical0.0010.0000.001
tool.graph6.5301.2957.828
tool.graph.degree6.1841.2867.471
tool.graph.list5.2401.1826.422
tool.metap0.0030.0000.003
tool.normalize0.0080.0000.009
tool.normalize.quality0.0070.0010.007
tool.overlap0.0100.0000.011
tool.read0.5730.0150.589
tool.save0.0020.0000.002
tool.subgraph0.0720.0040.076
tool.subgraph.find0.0710.0040.075
tool.subgraph.search0.0710.0030.074
tool.subgraph.stats0.0730.0040.077
tool.translate0.0660.0020.069
tool.unify0.0010.0000.001