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CHECK report for Mergeomics on merida2

This page was generated on 2019-04-09 13:32:44 -0400 (Tue, 09 Apr 2019).

Package 934/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Mergeomics 1.11.0
Zeyneb Kurt
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/Mergeomics
Branch: master
Last Commit: a824958
Last Changed Date: 2018-10-30 11:54:35 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: Mergeomics
Version: 1.11.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Mergeomics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Mergeomics_1.11.0.tar.gz
StartedAt: 2019-04-09 02:02:49 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:16:15 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 805.9 seconds
RetCode: 0
Status:  OK 
CheckDir: Mergeomics.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Mergeomics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Mergeomics_1.11.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Mergeomics.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.11.0’
* 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  8.3Mb
  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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
ssea.meta             18.597  0.309  19.053
kda.analyze.exec      12.937  0.224  13.269
kda.analyze.test      13.005  0.149  13.282
kda.prepare           12.918  0.145  13.186
kda.analyze.simulate  12.613  0.166  12.904
ssea2kda               7.823  0.507   8.383
ssea2kda.analyze       7.617  0.476   8.169
ssea2kda.import        6.431  0.237   6.739
ssea.finish.genes      6.322  0.237   6.630
ssea.finish.details    6.337  0.219   6.639
ssea.finish            6.078  0.195   6.318
ssea.analyze           6.008  0.247   6.299
ssea.finish.fdr        5.572  0.223   5.849
ssea.analyze.simulate  5.212  0.194   5.462
ssea.prepare.counts    4.905  0.057   5.015
* 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-3.9-bioc/meat/Mergeomics.Rcheck/00check.log’
for details.



Installation output

Mergeomics.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Mergeomics
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘Mergeomics’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Mergeomics)

Tests output

Mergeomics.Rcheck/tests/runTests.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("Mergeomics")

KDA Version:12.7.2015

Parameters:
  Search depth: 1
  Search direction: 1
  Maximum overlap: 0.33
  Minimum module size: 20
  Minimum degree: automatic
  Maximum degree: automatic
  Edge factor: 0
  Random seed: 1

Importing edges...
     TAIL               HEAD               WEIGHT 
 Length:140663      Length:140663      Min.   :1  
 Class :character   Class :character   1st Qu.:1  
 Mode  :character   Mode  :character   Median :1  
                                       Mean   :1  
                                       3rd Qu.:1  
                                       Max.   :1  

Importing modules...
    MODULE              NODE          
 Length:1643        Length:1643       
 Class :character   Class :character  
 Mode  :character   Mode  :character  
Graph: 7.694687 Mb

Minimum degree set to 20 

Maximum degree set to 278 

Collecting hubs...
4876 hubs (25.21%)
Graph: 13.28496 Mb

Analyzing network...
6675: Dhcr7, n=114, p=1.09e-15
6648: Brap, n=20, p=5.50e-01
6643: Usp38, n=23, p=4.72e-07
5582: Yes1, n=319, p=3.53e-03
4746: Tcf7l2, n=73, p=1.57e-02
4708: Tpte, n=86, p=9.49e-02
4511: Plg, n=160, p=1.45e-01
4464: Tsc22d3, n=487, p=7.03e-13
4407: Dntt, n=93, p=9.53e-21
4360: Slc10a6, n=132, p=3.28e-08
4588,..: Lrg1, n=86, p=1.17e-09

MSEA Version:01.04.2016

Parameters:
  Permutation type: gene
  Permutations: 100
  Random seed: 1
  Minimum gene count: 10
  Maximum gene count: 500
  Maximum overlap between genes: 0.33

Importing modules...
    MODULE             DESCR          
 Length:20          Length:20         
 Class :character   Class :character  
 Mode  :character   Mode  :character  
    MODULE              GENE          
 Length:2906        Length:2906       
 Class :character   Class :character  
 Mode  :character   Mode  :character  

Importing marker values...
    MARKER              VALUE         
 Length:76866       Min.   :  0.8094  
 Class :character   1st Qu.:  0.9450  
 Mode  :character   Median :  1.1374  
                    Mean   :  1.3944  
                    3rd Qu.:  1.4688  
                    Max.   :323.0100  

Importing mapping data...
     GENE              MARKER         
 Length:132705      Length:132705     
 Class :character   Class :character  
 Mode  :character   Mode  :character  

Merging genes containing shared markers...
WARNING! Limited overlap analysis due to large number of groups.

105489/1673535 
195466/1673535 
280759/1673535 
372349/1673535 
478492/1673535 
563676/1673535 
646241/1673535 
727679/1673535 
808918/1673535 
889732/1673535 
971489/1673535 
1053141/1673535 
1134013/1673535 
1214034/1673535 
1295368/1673535 
1377728/1673535 
1460263/1673535 
1539251/1673535 
1620963/1673535 
1673535 comparisons

21115 comparisons

13861 comparisons

12880 comparisons
Job: 11.66891 Mb

Preparing data structures...
Job: 17.11776 Mb

Adding positive controls...
Job: 17.42039 Mb

Estimating enrichment...
100/100 cycles

Normalizing scores...


RUNIT TEST PROTOCOL -- Tue Apr  9 02:16:04 2019 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Mergeomics RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
562.979   9.354 580.414 

Example timings

Mergeomics.Rcheck/Mergeomics-Ex.timings

nameusersystemelapsed
MSEA.KDA.onestep0.0030.0010.004
job.kda0.0220.0030.025
kda.analyze0.0150.0020.023
kda.analyze.exec12.937 0.22413.269
kda.analyze.simulate12.613 0.16612.904
kda.analyze.test13.005 0.14913.282
kda.configure0.0020.0010.002
kda.finish0.1780.0100.190
kda.finish.estimate0.1200.0060.126
kda.finish.save0.1220.0060.130
kda.finish.summarize0.1260.0070.133
kda.finish.trim0.1030.0060.113
kda.prepare12.918 0.14513.186
kda.prepare.overlap0.0000.0000.001
kda.prepare.screen0.0000.0010.001
kda.start1.5710.1031.690
kda.start.edges0.0010.0010.002
kda.start.identify0.0050.0000.005
kda.start.modules0.0010.0010.002
kda2cytoscape0.4780.0110.495
kda2cytoscape.colorize0.0000.0000.001
kda2cytoscape.colormap0.0010.0000.001
kda2cytoscape.drivers0.1840.0090.194
kda2cytoscape.edges0.2040.0080.229
kda2cytoscape.exec0.1980.0100.214
kda2cytoscape.identify0.0060.0000.006
kda2himmeli0.4540.0120.467
kda2himmeli.colorize000
kda2himmeli.colormap0.0000.0010.001
kda2himmeli.drivers0.1870.0070.196
kda2himmeli.edges0.2080.0100.218
kda2himmeli.exec0.2450.0080.254
kda2himmeli.identify0.0060.0010.007
ssea.analyze6.0080.2476.299
ssea.analyze.observe4.5020.0494.576
ssea.analyze.randgenes4.2430.0564.327
ssea.analyze.randloci4.6280.0514.713
ssea.analyze.simulate5.2120.1945.462
ssea.analyze.statistic0.0010.0010.001
ssea.control4.1930.0504.284
ssea.finish6.0780.1956.318
ssea.finish.details6.3370.2196.639
ssea.finish.fdr5.5720.2235.849
ssea.finish.genes6.3220.2376.630
ssea.meta18.597 0.30919.053
ssea.prepare4.8570.0624.973
ssea.prepare.counts4.9050.0575.015
ssea.prepare.structure4.6040.0464.681
ssea.start4.0370.0404.103
ssea.start.configure0.3910.0260.422
ssea.start.identify0.0040.0000.004
ssea.start.relabel3.6860.0383.749
ssea2kda7.8230.5078.383
ssea2kda.analyze7.6170.4768.169
ssea2kda.import6.4310.2376.739
tool.aggregate0.0020.0010.001
tool.cluster0.0220.0000.022
tool.cluster.static0.0010.0000.002
tool.coalesce0.0650.0010.066
tool.coalesce.exec0.1610.0000.161
tool.coalesce.find0.1380.0000.140
tool.coalesce.merge0.1750.0010.178
tool.fdr0.0010.0000.002
tool.fdr.bh0.0010.0000.001
tool.fdr.empirical0.0010.0000.002
tool.graph1.5460.0921.645
tool.graph.degree1.6890.0941.803
tool.graph.list1.6750.0691.764
tool.metap0.0030.0000.004
tool.normalize0.020.000.02
tool.normalize.quality0.0340.0020.036
tool.overlap0.0100.0000.011
tool.read0.2580.0150.274
tool.save0.0020.0010.003
tool.subgraph0.1360.0070.145
tool.subgraph.find0.1050.0090.115
tool.subgraph.search0.1130.0080.122
tool.subgraph.stats0.1650.0130.177
tool.translate0.0560.0020.059
tool.unify0.0030.0010.003