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This page was generated on 2024-04-17 11:37:54 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 1188/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Mergeomics 1.30.0  (landing page)
Zeyneb Kurt
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/Mergeomics
git_branch: RELEASE_3_18
git_last_commit: e850a39
git_last_commit_date: 2023-10-24 10:47:32 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

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: 1.30.0
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_1.30.0.tar.gz
StartedAt: 2024-04-16 05:01:45 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 05:19:03 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 1038.9 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_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/Mergeomics.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Mergeomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Mergeomics’ version ‘1.30.0’
* 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 (user + system) or elapsed time > 5s
                         user system elapsed
kda.analyze.exec       16.748  0.356  17.652
kda.prepare            16.702  0.256  17.883
kda.analyze.test       16.637  0.267  17.716
kda.analyze.simulate   16.598  0.258  17.673
ssea2kda               11.369  0.228  12.253
ssea2kda.analyze       11.312  0.251  12.098
ssea.meta               9.611  0.180  10.372
ssea2kda.import         9.385  0.172  10.007
ssea.analyze            9.228  0.266  10.160
ssea.finish.details     9.036  0.226   9.846
ssea.finish.fdr         9.060  0.185   9.827
ssea.finish.genes       8.967  0.220   9.492
ssea.finish             8.954  0.169   9.456
ssea.analyze.simulate   8.480  0.177   9.197
ssea.analyze.randgenes  7.077  0.071   7.714
ssea.prepare            6.993  0.076   7.782
ssea.analyze.randloci   6.893  0.075   7.606
ssea.control            6.825  0.072   7.411
ssea.analyze.observe    6.812  0.070   7.405
ssea.prepare.structure  6.789  0.077   7.717
ssea.start              6.611  0.063   6.992
ssea.prepare.counts     6.558  0.079   7.341
ssea.start.relabel      6.473  0.075   6.967
* 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-3.18-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/4.3-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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...
4754 hubs (18598 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.

62789/1673535 
129401/1673535 
193344/1673535 
261083/1673535 
328477/1673535 
392320/1673535 
457906/1673535 
524499/1673535 
591749/1673535 
660160/1673535 
726081/1673535 
790182/1673535 
853278/1673535 
917194/1673535 
981270/1673535 
1046254/1673535 
1110017/1673535 
1177237/1673535 
1240390/1673535 
1304498/1673535 
1368144/1673535 
1433048/1673535 
1496997/1673535 
1560134/1673535 
1621201/1673535 
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 Apr 16 05:18:40 2024 
*********************************************** 
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 
655.997  14.959 710.502 

Example timings

Mergeomics.Rcheck/Mergeomics-Ex.timings

nameusersystemelapsed
MSEA.KDA.onestep0.0040.0030.007
job.kda0.0260.0080.035
kda.analyze0.0150.0060.022
kda.analyze.exec16.748 0.35617.652
kda.analyze.simulate16.598 0.25817.673
kda.analyze.test16.637 0.26717.716
kda.configure0.0010.0010.003
kda.finish0.2380.0210.300
kda.finish.estimate0.1400.0040.187
kda.finish.save0.1380.0040.158
kda.finish.summarize0.1400.0040.174
kda.finish.trim0.1410.0050.159
kda.prepare16.702 0.25617.883
kda.prepare.overlap0.0010.0030.003
kda.prepare.screen0.0000.0020.002
kda.start2.1100.0742.269
kda.start.edges0.0030.0030.006
kda.start.identify0.0080.0020.010
kda.start.modules0.0030.0020.006
kda2cytoscape0.6620.0190.723
kda2cytoscape.colorize0.0000.0010.001
kda2cytoscape.colormap0.0010.0000.001
kda2cytoscape.drivers0.2300.0110.253
kda2cytoscape.edges0.2210.0120.242
kda2cytoscape.exec0.2690.0170.312
kda2cytoscape.identify0.0060.0010.008
kda2himmeli0.6910.0210.818
kda2himmeli.colorize0.0010.0010.001
kda2himmeli.colormap0.0010.0010.001
kda2himmeli.drivers0.2230.0140.273
kda2himmeli.edges0.2320.0130.301
kda2himmeli.exec0.3860.0170.441
kda2himmeli.identify0.0060.0010.008
ssea.analyze 9.228 0.26610.160
ssea.analyze.observe6.8120.0707.405
ssea.analyze.randgenes7.0770.0717.714
ssea.analyze.randloci6.8930.0757.606
ssea.analyze.simulate8.4800.1779.197
ssea.analyze.statistic0.0000.0010.002
ssea.control6.8250.0727.411
ssea.finish8.9540.1699.456
ssea.finish.details9.0360.2269.846
ssea.finish.fdr9.0600.1859.827
ssea.finish.genes8.9670.2209.492
ssea.meta 9.611 0.18010.372
ssea.prepare6.9930.0767.782
ssea.prepare.counts6.5580.0797.341
ssea.prepare.structure6.7890.0777.717
ssea.start6.6110.0636.992
ssea.start.configure0.6040.0270.641
ssea.start.identify0.0060.0020.008
ssea.start.relabel6.4730.0756.967
ssea2kda11.369 0.22812.253
ssea2kda.analyze11.312 0.25112.098
ssea2kda.import 9.385 0.17210.007
tool.aggregate0.0020.0020.004
tool.cluster0.0310.0020.034
tool.cluster.static0.0010.0010.002
tool.coalesce0.0940.0040.098
tool.coalesce.exec0.2190.0020.222
tool.coalesce.find0.2230.0020.229
tool.coalesce.merge0.2370.0030.242
tool.fdr0.0010.0010.001
tool.fdr.bh0.0010.0000.001
tool.fdr.empirical0.0010.0010.002
tool.graph2.1470.0522.290
tool.graph.degree2.2640.0712.431
tool.graph.list1.9830.0552.125
tool.metap0.0070.0010.009
tool.normalize0.0260.0010.027
tool.normalize.quality0.0200.0010.021
tool.overlap0.0140.0020.016
tool.read0.3760.0080.406
tool.save0.0020.0020.003
tool.subgraph0.1440.0040.151
tool.subgraph.find0.1540.0110.166
tool.subgraph.search0.1450.0040.157
tool.subgraph.stats0.1710.0050.182
tool.translate0.0650.0030.070
tool.unify0.0020.0010.003