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CHECK report for Mergeomics on malbec1

This page was generated on 2019-04-16 11:51:51 -0400 (Tue, 16 Apr 2019).

Package 909/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Mergeomics 1.10.0
Zeyneb Kurt
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/Mergeomics
Branch: RELEASE_3_8
Last Commit: d46f485
Last Changed Date: 2018-10-30 11:42:00 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Mergeomics
Version: 1.10.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:Mergeomics.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings Mergeomics_1.10.0.tar.gz
StartedAt: 2019-04-16 01:13:46 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:24:18 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 632.2 seconds
RetCode: 0
Status:  OK 
CheckDir: Mergeomics.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:Mergeomics.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings Mergeomics_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/Mergeomics.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 ‘1.10.0’
* 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  8.4Mb
  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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
ssea.meta            17.300  0.044  17.361
kda.analyze.exec     11.804  0.044  11.877
kda.analyze.test     10.852  0.008  10.873
kda.prepare           9.520  0.000   9.532
kda.analyze.simulate  9.384  0.016   9.410
ssea2kda              7.080  0.020   7.121
ssea2kda.analyze      6.708  0.008   6.723
ssea2kda.import       6.436  0.008   6.473
ssea.finish.details   6.088  0.000   6.102
ssea.analyze          5.664  0.000   5.702
ssea.finish           4.992  0.016   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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/Mergeomics.Rcheck/00check.log’
for details.



Installation output

Mergeomics.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL Mergeomics
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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 version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

131693/1673535 
247134/1673535 
367275/1673535 
502029/1673535 
621908/1673535 
745041/1673535 
853174/1673535 
989228/1673535 
1125619/1673535 
1275907/1673535 
1389717/1673535 
1496927/1673535 
1607136/1673535 
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 16 01:24:11 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 
452.420   0.456 454.917 

Example timings

Mergeomics.Rcheck/Mergeomics-Ex.timings

nameusersystemelapsed
MSEA.KDA.onestep0.0000.0000.002
job.kda0.0160.0000.018
kda.analyze0.0200.0000.045
kda.analyze.exec11.804 0.04411.877
kda.analyze.simulate9.3840.0169.410
kda.analyze.test10.852 0.00810.873
kda.configure0.0000.0000.001
kda.finish0.1200.0040.125
kda.finish.estimate0.0800.0000.082
kda.finish.save0.0760.0000.080
kda.finish.summarize0.0760.0080.087
kda.finish.trim0.0920.0000.091
kda.prepare9.5200.0009.532
kda.prepare.overlap000
kda.prepare.screen000
kda.start1.1200.0001.123
kda.start.edges0.0040.0000.001
kda.start.identify0.0040.0000.004
kda.start.modules0.0040.0000.001
kda2cytoscape0.3360.0000.338
kda2cytoscape.colorize000
kda2cytoscape.colormap0.0000.0000.001
kda2cytoscape.drivers0.1240.0000.125
kda2cytoscape.edges0.1200.0040.125
kda2cytoscape.exec0.1560.0000.154
kda2cytoscape.identify0.0040.0000.003
kda2himmeli0.4320.0000.442
kda2himmeli.colorize000
kda2himmeli.colormap0.0000.0000.001
kda2himmeli.drivers0.1440.0040.147
kda2himmeli.edges0.1360.0040.137
kda2himmeli.exec0.2560.0040.262
kda2himmeli.identify0.0040.0000.003
ssea.analyze5.6640.0005.702
ssea.analyze.observe3.0080.0043.015
ssea.analyze.randgenes2.9240.0042.929
ssea.analyze.randloci4.2520.0084.263
ssea.analyze.simulate4.6000.0084.613
ssea.analyze.statistic0.0000.0000.001
ssea.control3.2200.0003.219
ssea.finish4.9920.0165.015
ssea.finish.details6.0880.0006.102
ssea.finish.fdr4.6560.0164.683
ssea.finish.genes4.8760.0164.894
ssea.meta17.300 0.04417.361
ssea.prepare2.9520.0002.954
ssea.prepare.counts2.7280.0002.728
ssea.prepare.structure3.5000.0123.521
ssea.start3.8240.0043.830
ssea.start.configure0.3160.0000.316
ssea.start.identify0.0040.0000.003
ssea.start.relabel2.9600.0042.966
ssea2kda7.0800.0207.121
ssea2kda.analyze6.7080.0086.723
ssea2kda.import6.4360.0086.473
tool.aggregate0.0000.0000.002
tool.cluster0.0440.0000.044
tool.cluster.static0.0040.0000.001
tool.coalesce0.0440.0000.044
tool.coalesce.exec0.1040.0000.106
tool.coalesce.find0.1080.0000.109
tool.coalesce.merge0.1120.0000.112
tool.fdr0.0000.0000.001
tool.fdr.bh0.0000.0000.001
tool.fdr.empirical0.0000.0000.001
tool.graph1.1360.0081.146
tool.graph.degree1.4400.0201.461
tool.graph.list1.2720.0001.271
tool.metap0.0040.0000.004
tool.normalize0.0120.0000.014
tool.normalize.quality0.0120.0000.011
tool.overlap0.0080.0000.007
tool.read0.1960.0040.200
tool.save0.0040.0000.001
tool.subgraph0.0880.0000.089
tool.subgraph.find0.0880.0000.086
tool.subgraph.search0.0880.0040.094
tool.subgraph.stats0.0960.0000.097
tool.translate0.0440.0000.043
tool.unify0.0000.0000.002