Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:29 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for Mergeomics on nebbiolo1


To the developers/maintainers of the Mergeomics package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Mergeomics.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1112/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Mergeomics 1.24.0  (landing page)
Zeyneb Kurt
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/Mergeomics
git_branch: RELEASE_3_15
git_last_commit: a02cfdb
git_last_commit_date: 2022-04-26 11:29:18 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Mergeomics
Version: 1.24.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:Mergeomics.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings Mergeomics_1.24.0.tar.gz
StartedAt: 2022-10-18 20:27:50 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 20:34:14 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 384.1 seconds
RetCode: 0
Status:   OK  
CheckDir: Mergeomics.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:Mergeomics.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings Mergeomics_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/Mergeomics.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.24.0’
* 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 ... OK
* 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 (user + system) or elapsed time > 5s
                      user system elapsed
kda.analyze.exec     6.738  0.032   6.771
kda.prepare          6.586  0.001   6.587
kda.analyze.test     6.569  0.005   6.575
kda.analyze.simulate 6.517  0.024   6.542
ssea2kda.analyze     5.698  0.008   5.706
ssea2kda             5.209  0.048   5.258
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/Mergeomics.Rcheck/00check.log’
for details.



Installation output

Mergeomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL Mergeomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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: 13.28768 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.

216527/1673535 
431858/1673535 
656759/1673535 
872600/1673535 
1098246/1673535 
1320581/1673535 
1539633/1673535 
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 Oct 18 20:34:09 2022 
*********************************************** 
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 
259.275   0.570 259.838 

Example timings

Mergeomics.Rcheck/Mergeomics-Ex.timings

nameusersystemelapsed
MSEA.KDA.onestep0.0000.0020.002
job.kda0.0140.0000.015
kda.analyze0.0070.0040.012
kda.analyze.exec6.7380.0326.771
kda.analyze.simulate6.5170.0246.542
kda.analyze.test6.5690.0056.575
kda.configure0.0000.0010.001
kda.finish0.1080.0050.112
kda.finish.estimate0.0710.0040.075
kda.finish.save0.0760.0000.076
kda.finish.summarize0.0750.0000.075
kda.finish.trim0.0720.0030.077
kda.prepare6.5860.0016.587
kda.prepare.overlap0.0010.0000.001
kda.prepare.screen0.0010.0000.000
kda.start1.0710.0231.095
kda.start.edges0.0020.0000.002
kda.start.identify0.0050.0000.005
kda.start.modules0.0020.0000.002
kda2cytoscape0.2620.0040.267
kda2cytoscape.colorize0.0000.0000.001
kda2cytoscape.colormap0.0010.0000.001
kda2cytoscape.drivers0.1130.0000.113
kda2cytoscape.edges0.0940.0120.107
kda2cytoscape.exec0.1150.0120.128
kda2cytoscape.identify0.0020.0020.003
kda2himmeli0.2800.0130.295
kda2himmeli.colorize0.0010.0000.000
kda2himmeli.colormap0.0010.0000.000
kda2himmeli.drivers0.1050.0080.113
kda2himmeli.edges0.1140.0040.118
kda2himmeli.exec0.1980.0040.202
kda2himmeli.identify0.0030.0000.004
ssea.analyze3.9120.0093.925
ssea.analyze.observe2.5420.0122.553
ssea.analyze.randgenes2.5580.0122.570
ssea.analyze.randloci2.4930.0242.518
ssea.analyze.simulate3.4790.0123.490
ssea.analyze.statistic000
ssea.control2.5640.0122.575
ssea.finish3.7130.0163.730
ssea.finish.details3.7550.0083.763
ssea.finish.fdr3.7370.0123.749
ssea.finish.genes3.9000.0243.924
ssea.meta4.1130.0204.133
ssea.prepare2.4440.0202.464
ssea.prepare.counts2.3240.0082.332
ssea.prepare.structure2.2920.0082.300
ssea.start2.3840.1042.489
ssea.start.configure0.3580.0360.393
ssea.start.identify0.0040.0000.004
ssea.start.relabel2.4680.0322.500
ssea2kda5.2090.0485.258
ssea2kda.analyze5.6980.0085.706
ssea2kda.import4.1790.0084.186
tool.aggregate0.0010.0000.002
tool.cluster0.0150.0000.015
tool.cluster.static0.0000.0000.001
tool.coalesce0.0370.0030.039
tool.coalesce.exec0.0840.0000.084
tool.coalesce.find0.0880.0000.087
tool.coalesce.merge0.0940.0000.094
tool.fdr0.0000.0010.001
tool.fdr.bh000
tool.fdr.empirical0.0000.0000.001
tool.graph1.0280.0201.048
tool.graph.degree1.0790.0001.079
tool.graph.list0.9480.0030.951
tool.metap0.010.000.01
tool.normalize0.0150.0000.016
tool.normalize.quality0.0090.0000.009
tool.overlap0.0060.0000.007
tool.read0.1780.0000.179
tool.save0.0010.0000.002
tool.subgraph0.0770.0040.081
tool.subgraph.find0.0670.0120.078
tool.subgraph.search0.0850.0040.090
tool.subgraph.stats0.1400.0040.143
tool.translate0.0330.0000.034
tool.unify0.0000.0010.001