Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2025-03-06 12:08 -0500 (Thu, 06 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4769
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4504
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4527
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4480
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4416
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

Package 1191/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Mergeomics 1.34.0  (landing page)
Zeyneb Kurt
Snapshot Date: 2025-03-03 13:00 -0500 (Mon, 03 Mar 2025)
git_url: https://git.bioconductor.org/packages/Mergeomics
git_branch: RELEASE_3_20
git_last_commit: ec59426
git_last_commit_date: 2024-10-29 10:07:07 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for Mergeomics on merida1

To the developers/maintainers of the Mergeomics package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: Mergeomics
Version: 1.34.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Mergeomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Mergeomics_1.34.0.tar.gz
StartedAt: 2025-03-04 05:46:57 -0500 (Tue, 04 Mar 2025)
EndedAt: 2025-03-04 06:06:31 -0500 (Tue, 04 Mar 2025)
EllapsedTime: 1174.4 seconds
RetCode: 0
Status:   OK  
CheckDir: Mergeomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Mergeomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Mergeomics_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Mergeomics.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Mergeomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Mergeomics’ version ‘1.34.0’
* 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 code 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 (user + system) or elapsed time > 5s
                         user system elapsed
kda.analyze.exec       17.508  0.412  18.160
kda.prepare            16.968  0.277  17.730
kda.analyze.simulate   16.812  0.282  17.505
kda.analyze.test       16.694  0.297  17.272
ssea2kda               11.708  0.329  13.529
ssea2kda.analyze       11.689  0.281  12.635
ssea2kda.import         9.738  0.193  10.181
ssea.meta               9.566  0.180  10.350
ssea.analyze            9.355  0.308  10.212
ssea.finish.details     9.430  0.207  10.163
ssea.finish.genes       9.322  0.188   9.783
ssea.finish             9.303  0.189  10.109
ssea.finish.fdr         9.200  0.212   9.587
ssea.analyze.simulate   8.852  0.210   9.525
ssea.analyze.randgenes  7.407  0.079   8.121
ssea.analyze.randloci   7.277  0.079   7.885
ssea.analyze.observe    7.023  0.072   7.498
ssea.control            6.980  0.063   7.357
ssea.prepare.counts     6.962  0.079   7.236
ssea.prepare.structure  6.950  0.063   7.325
ssea.start.relabel      6.665  0.070   7.037
ssea.start              6.573  0.068   7.180
ssea.prepare            6.569  0.066   6.761
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.20-bioc/meat/Mergeomics.Rcheck/00check.log’
for details.


Installation output

Mergeomics.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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...
4347 hubs (16906 nodes)
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.

68877/1673535 
139551/1673535 
208355/1673535 
286546/1673535 
356305/1673535 
459198/1673535 
575129/1673535 
656582/1673535 
747807/1673535 
836986/1673535 
917915/1673535 
1004276/1673535 
1110097/1673535 
1227720/1673535 
1347399/1673535 
1467260/1673535 
1587029/1673535 
1673535 comparisons

21115 comparisons

13861 comparisons

12880 comparisons
Job: 11.66892 Mb

Preparing data structures...
Job: 17.11777 Mb

Adding positive controls...
Job: 17.42039 Mb

Estimating enrichment...
100/100 cycles

Normalizing scores...


RUNIT TEST PROTOCOL -- Tue Mar  4 06:02:04 2025 
*********************************************** 
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 
556.935  15.471 583.595 

Example timings

Mergeomics.Rcheck/Mergeomics-Ex.timings

nameusersystemelapsed
MSEA.KDA.onestep0.0050.0030.008
job.kda0.0280.0070.036
kda.analyze0.0180.0060.023
kda.analyze.exec17.508 0.41218.160
kda.analyze.simulate16.812 0.28217.505
kda.analyze.test16.694 0.29717.272
kda.configure0.0010.0010.003
kda.finish0.2200.0150.267
kda.finish.estimate0.1350.0040.140
kda.finish.save0.1340.0040.139
kda.finish.summarize0.1320.0050.140
kda.finish.trim0.1310.0040.136
kda.prepare16.968 0.27717.730
kda.prepare.overlap0.0000.0010.002
kda.prepare.screen0.0010.0010.001
kda.start2.3160.0862.504
kda.start.edges0.0030.0020.006
kda.start.identify0.0080.0010.009
kda.start.modules0.0030.0030.006
kda2cytoscape0.6700.0180.832
kda2cytoscape.colorize0.0010.0000.001
kda2cytoscape.colormap0.0010.0000.001
kda2cytoscape.drivers0.2360.0140.292
kda2cytoscape.edges0.2240.0110.324
kda2cytoscape.exec0.2780.0130.374
kda2cytoscape.identify0.0070.0010.009
kda2himmeli0.7050.0200.896
kda2himmeli.colorize0.0000.0000.001
kda2himmeli.colormap0.0010.0000.002
kda2himmeli.drivers0.2350.0130.290
kda2himmeli.edges0.2350.0130.316
kda2himmeli.exec0.3960.0260.462
kda2himmeli.identify0.0070.0010.008
ssea.analyze 9.355 0.30810.212
ssea.analyze.observe7.0230.0727.498
ssea.analyze.randgenes7.4070.0798.121
ssea.analyze.randloci7.2770.0797.885
ssea.analyze.simulate8.8520.2109.525
ssea.analyze.statistic0.0000.0010.001
ssea.control6.9800.0637.357
ssea.finish 9.303 0.18910.109
ssea.finish.details 9.430 0.20710.163
ssea.finish.fdr9.2000.2129.587
ssea.finish.genes9.3220.1889.783
ssea.meta 9.566 0.18010.350
ssea.prepare6.5690.0666.761
ssea.prepare.counts6.9620.0797.236
ssea.prepare.structure6.9500.0637.325
ssea.start6.5730.0687.180
ssea.start.configure0.4590.0230.672
ssea.start.identify0.0080.0020.011
ssea.start.relabel6.6650.0707.037
ssea2kda11.708 0.32913.529
ssea2kda.analyze11.689 0.28112.635
ssea2kda.import 9.738 0.19310.181
tool.aggregate0.0030.0030.005
tool.cluster0.0320.0020.036
tool.cluster.static0.0010.0010.002
tool.coalesce0.0870.0020.090
tool.coalesce.exec0.2430.0020.249
tool.coalesce.find0.2430.0020.248
tool.coalesce.merge0.2450.0030.252
tool.fdr0.0020.0010.002
tool.fdr.bh0.0010.0000.002
tool.fdr.empirical0.0010.0010.002
tool.graph2.1860.0532.293
tool.graph.degree2.2860.0682.392
tool.graph.list2.1400.0652.262
tool.metap0.0060.0020.008
tool.normalize0.0270.0010.029
tool.normalize.quality0.0210.0010.022
tool.overlap0.0250.0080.034
tool.read0.3820.0120.397
tool.save0.0020.0020.003
tool.subgraph0.1320.0030.140
tool.subgraph.find0.1350.0030.140
tool.subgraph.search0.1360.0040.141
tool.subgraph.stats0.1760.0150.194
tool.translate0.0590.0030.062
tool.unify0.0020.0000.002