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BioC 3.4: CHECK report for Mergeomics on morelia

This page was generated on 2017-04-15 16:27:26 -0400 (Sat, 15 Apr 2017).

Package 733/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Mergeomics 1.2.0
Zeyneb Kurt
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/Mergeomics
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / 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: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Mergeomics_1.2.0.tar.gz
StartedAt: 2017-04-15 04:39:40 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 04:53:27 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 827.4 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/Mergeomics.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.2.0’
* 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.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              21.862  0.225  22.251
kda.prepare            20.646  1.380  22.040
kda.analyze.simulate   20.273  1.191  21.488
kda.analyze.exec       19.925  1.068  21.007
kda.analyze.test       19.407  1.177  20.600
tool.graph.list         7.320  1.195   8.520
kda.start               7.463  1.017   8.487
tool.graph              7.056  1.226   8.287
tool.graph.degree       6.842  1.407   8.254
ssea.finish             7.694  0.100   7.803
ssea.analyze.simulate   7.591  0.074   7.673
ssea.analyze            7.404  0.074   7.489
ssea.finish.details     7.218  0.073   7.295
ssea.control            7.222  0.040   7.271
ssea.finish.fdr         7.157  0.090   7.258
ssea2kda                7.064  0.111   7.181
ssea.finish.genes       7.078  0.070   7.155
ssea.analyze.randloci   7.056  0.035   7.096
ssea2kda.analyze        6.881  0.133   7.079
ssea.analyze.randgenes  6.838  0.039   6.883
ssea2kda.import         6.614  0.088   6.794
ssea.analyze.observe    6.641  0.039   6.687
ssea.prepare.structure  6.176  0.038   6.219
ssea.prepare            5.860  0.049   5.918
ssea.start.relabel      5.613  0.026   5.672
ssea.prepare.counts     5.521  0.034   5.591
ssea.start              5.322  0.030   5.372
* 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.onestep0.0040.0000.003
job.kda0.0240.0030.027
kda.analyze0.0280.0020.029
kda.analyze.exec19.925 1.06821.007
kda.analyze.simulate20.273 1.19121.488
kda.analyze.test19.407 1.17720.600
kda.configure0.0030.0000.003
kda.finish0.1840.0130.197
kda.finish.estimate0.1010.0070.106
kda.finish.save0.1050.0060.111
kda.finish.summarize0.1060.0070.111
kda.finish.trim0.1010.0060.107
kda.prepare20.646 1.38022.040
kda.prepare.overlap0.0020.0010.003
kda.prepare.screen0.0020.0000.002
kda.start7.4631.0178.487
kda.start.edges0.0030.0000.004
kda.start.identify0.0080.0010.008
kda.start.modules0.0020.0000.003
kda2cytoscape0.5010.0140.515
kda2cytoscape.colorize000
kda2cytoscape.colormap0.0010.0000.001
kda2cytoscape.drivers0.1870.0080.196
kda2cytoscape.edges0.1850.0090.197
kda2cytoscape.exec0.2100.0100.221
kda2cytoscape.identify0.0040.0000.005
kda2himmeli0.5810.0140.612
kda2himmeli.colorize0.0010.0000.001
kda2himmeli.colormap0.0010.0000.001
kda2himmeli.drivers0.2030.0100.214
kda2himmeli.edges0.1780.0090.187
kda2himmeli.exec0.3220.0110.334
kda2himmeli.identify0.0070.0000.007
ssea.analyze7.4040.0747.489
ssea.analyze.observe6.6410.0396.687
ssea.analyze.randgenes6.8380.0396.883
ssea.analyze.randloci7.0560.0357.096
ssea.analyze.simulate7.5910.0747.673
ssea.analyze.statistic0.0010.0000.001
ssea.control7.2220.0407.271
ssea.finish7.6940.1007.803
ssea.finish.details7.2180.0737.295
ssea.finish.fdr7.1570.0907.258
ssea.finish.genes7.0780.0707.155
ssea.meta21.862 0.22522.251
ssea.prepare5.8600.0495.918
ssea.prepare.counts5.5210.0345.591
ssea.prepare.structure6.1760.0386.219
ssea.start5.3220.0305.372
ssea.start.configure1.1190.0161.169
ssea.start.identify0.0060.0000.006
ssea.start.relabel5.6130.0265.672
ssea2kda7.0640.1117.181
ssea2kda.analyze6.8810.1337.079
ssea2kda.import6.6140.0886.794
tool.aggregate0.0020.0000.002
tool.cluster0.0310.0000.031
tool.cluster.static0.0010.0000.001
tool.coalesce0.0780.0010.079
tool.coalesce.exec0.1540.0000.154
tool.coalesce.find0.1290.0010.130
tool.coalesce.merge0.1620.0000.162
tool.fdr0.0020.0000.001
tool.fdr.bh0.0010.0000.001
tool.fdr.empirical0.0010.0000.002
tool.graph7.0561.2268.287
tool.graph.degree6.8421.4078.254
tool.graph.list7.3201.1958.520
tool.metap0.0060.0010.006
tool.normalize0.0130.0000.013
tool.normalize.quality0.0100.0000.009
tool.overlap0.0130.0000.014
tool.read0.7900.0150.805
tool.save0.0030.0010.009
tool.subgraph0.1110.0090.120
tool.subgraph.find0.1000.0060.107
tool.subgraph.search0.0790.0060.087
tool.subgraph.stats0.0990.0070.107
tool.translate0.0750.0020.077
tool.unify0.0010.0000.002