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CHECK report for Mergeomics on malbec1

This page was generated on 2020-04-15 12:10:57 -0400 (Wed, 15 Apr 2020).

Package 989/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Mergeomics 1.14.0
Zeyneb Kurt
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/Mergeomics
Branch: RELEASE_3_10
Last Commit: 70e92ab
Last Changed Date: 2019-10-29 13:09:33 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  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: 1.14.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:Mergeomics.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings Mergeomics_1.14.0.tar.gz
StartedAt: 2020-04-15 03:33:39 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 03:44:15 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 635.4 seconds
RetCode: 0
Status:  OK 
CheckDir: Mergeomics.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:Mergeomics.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings Mergeomics_1.14.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/Mergeomics.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.14.0’
* 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
kda.analyze.test      10.548  0.016  10.664
kda.prepare           10.420  0.008  10.442
kda.analyze.exec       9.804  0.048   9.883
kda.analyze.simulate   8.260  0.016   8.343
ssea2kda               7.852  0.012   7.908
ssea2kda.analyze       7.232  0.012   7.250
ssea.analyze           6.444  0.008   6.535
ssea.finish            5.960  0.004   5.968
ssea.finish.details    5.700  0.004   5.706
ssea.finish.genes      5.544  0.000   5.639
ssea.finish.fdr        5.488  0.004   5.499
ssea.meta              5.404  0.032   5.442
ssea.analyze.simulate  5.324  0.008   5.348
* 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-3.10-bioc/meat/Mergeomics.Rcheck/00check.log’
for details.



Installation output

Mergeomics.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL Mergeomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘Mergeomics’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Mergeomics)

Tests output

Mergeomics.Rcheck/tests/runTests.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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=2.24e-17
6648: Cit, n=20, p=7.89e-01
6643: Pbx4, n=23, p=2.32e-05
5582: Sypl, n=319, p=2.02e-02
4746: Tcf7l2, n=73, p=2.63e-02
4708: Tpte, n=86, p=5.05e-02
4511: Pzp, n=160, p=8.85e-03
4464: Tsc22d3, n=487, p=4.28e-13
4407: Dntt, n=93, p=2.40e-20
4360: Amica1, n=132, p=1.06e-06
4588,..: Lrg1, n=86, p=5.76e-12

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.

119569/1673535 
236914/1673535 
349198/1673535 
475038/1673535 
587278/1673535 
716794/1673535 
819628/1673535 
940122/1673535 
1055866/1673535 
1169851/1673535 
1295731/1673535 
1415757/1673535 
1526198/1673535 
1659867/1673535 
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 -- Wed Apr 15 03:44:08 2020 
*********************************************** 
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 
451.716   0.520 457.427 

Example timings

Mergeomics.Rcheck/Mergeomics-Ex.timings

nameusersystemelapsed
MSEA.KDA.onestep0.0040.0000.002
job.kda0.020.000.02
kda.analyze0.0200.0000.019
kda.analyze.exec9.8040.0489.883
kda.analyze.simulate8.2600.0168.343
kda.analyze.test10.548 0.01610.664
kda.configure000
kda.finish0.1880.0080.195
kda.finish.estimate0.1320.0000.134
kda.finish.save0.1400.0040.144
kda.finish.summarize0.1320.0000.133
kda.finish.trim0.1320.0000.132
kda.prepare10.420 0.00810.442
kda.prepare.overlap000
kda.prepare.screen000
kda.start1.0840.0081.092
kda.start.edges0.0040.0000.002
kda.start.identify0.0080.0000.007
kda.start.modules0.0000.0000.002
kda2cytoscape0.4560.0040.460
kda2cytoscape.colorize000
kda2cytoscape.colormap000
kda2cytoscape.drivers0.1440.0040.149
kda2cytoscape.edges0.1880.0000.192
kda2cytoscape.exec0.2040.0000.206
kda2cytoscape.identify0.0000.0040.003
kda2himmeli0.3480.0000.358
kda2himmeli.colorize000
kda2himmeli.colormap000
kda2himmeli.drivers0.1920.0000.191
kda2himmeli.edges0.1640.0040.166
kda2himmeli.exec0.2640.0040.268
kda2himmeli.identify0.0080.0000.005
ssea.analyze6.4440.0086.535
ssea.analyze.observe3.8440.0083.874
ssea.analyze.randgenes4.6760.0044.724
ssea.analyze.randloci4.5320.0084.584
ssea.analyze.simulate5.3240.0085.348
ssea.analyze.statistic000
ssea.control3.6320.0003.652
ssea.finish5.9600.0045.968
ssea.finish.details5.7000.0045.706
ssea.finish.fdr5.4880.0045.499
ssea.finish.genes5.5440.0005.639
ssea.meta5.4040.0325.442
ssea.prepare4.1920.0204.230
ssea.prepare.counts4.2480.0044.292
ssea.prepare.structure4.2440.0044.273
ssea.start3.6240.0043.655
ssea.start.configure0.5160.0040.518
ssea.start.identify0.0040.0000.005
ssea.start.relabel4.0720.0084.103
ssea2kda7.8520.0127.908
ssea2kda.analyze7.2320.0127.250
ssea2kda.import4.9040.0124.919
tool.aggregate0.0000.0000.001
tool.cluster0.0120.0040.014
tool.cluster.static000
tool.coalesce0.0400.0000.037
tool.coalesce.exec0.0880.0000.089
tool.coalesce.find0.0960.0000.096
tool.coalesce.merge0.0880.0000.090
tool.fdr0.0000.0000.001
tool.fdr.bh0.0040.0000.001
tool.fdr.empirical0.0000.0000.001
tool.graph1.0360.0081.044
tool.graph.degree1.1320.0041.136
tool.graph.list0.9840.0040.989
tool.metap0.0040.0000.004
tool.normalize0.0120.0000.011
tool.normalize.quality0.0040.0040.009
tool.overlap0.0080.0000.006
tool.read0.180.000.18
tool.save0.0040.0000.001
tool.subgraph0.0840.0040.091
tool.subgraph.find0.0760.0080.081
tool.subgraph.search0.0800.0000.082
tool.subgraph.stats0.0880.0040.092
tool.translate0.0320.0000.032
tool.unify0.0000.0000.001