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This page was generated on 2024-03-04 11:39:28 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 1175/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Mergeomics 1.31.0  (landing page)
Zeyneb Kurt
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/Mergeomics
git_branch: devel
git_last_commit: 23bb24b
git_last_commit_date: 2023-10-24 10:47:32 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 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 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / 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: 1.31.0
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_1.31.0.tar.gz
StartedAt: 2024-03-02 06:23:04 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 06:42:41 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 1177.1 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_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Mergeomics.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Mergeomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Mergeomics’ version ‘1.31.0’
* 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       17.483  0.346  20.724
kda.prepare            17.274  0.295  20.778
kda.analyze.test       17.250  0.301  20.153
kda.analyze.simulate   17.093  0.273  19.370
ssea2kda               11.657  0.299  14.243
ssea2kda.analyze       11.222  0.253  13.325
ssea.meta               9.702  0.205  11.406
ssea2kda.import         9.603  0.205  11.300
ssea.finish.details     9.447  0.191  11.184
ssea.analyze            9.237  0.262  10.997
ssea.finish.genes       9.265  0.180  11.129
ssea.finish             9.157  0.199  10.934
ssea.finish.fdr         9.068  0.203  10.808
ssea.analyze.simulate   8.713  0.183  10.241
ssea.analyze.randgenes  7.326  0.100   8.661
ssea.control            7.104  0.098   8.231
ssea.analyze.observe    7.066  0.101   8.327
ssea.analyze.randloci   7.060  0.085   8.091
ssea.prepare.counts     6.814  0.100   8.164
ssea.prepare.structure  6.775  0.087   7.958
ssea.prepare            6.720  0.092   8.106
ssea.start.relabel      6.697  0.106   7.903
ssea.start              6.606  0.087   7.869
* 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-3.19-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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
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...
4201 hubs (16446 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.

51269/1673535 
101616/1673535 
152371/1673535 
199349/1673535 
250418/1673535 
301997/1673535 
355578/1673535 
406264/1673535 
455958/1673535 
509518/1673535 
559209/1673535 
613983/1673535 
667468/1673535 
720930/1673535 
775257/1673535 
831392/1673535 
887153/1673535 
941436/1673535 
997437/1673535 
1054436/1673535 
1110216/1673535 
1166192/1673535 
1221721/1673535 
1277327/1673535 
1332379/1673535 
1387351/1673535 
1442486/1673535 
1498818/1673535 
1555023/1673535 
1609924/1673535 
1665231/1673535 
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 -- Sat Mar  2 06:42:15 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 
673.730  18.017 805.419 

Example timings

Mergeomics.Rcheck/Mergeomics-Ex.timings

nameusersystemelapsed
MSEA.KDA.onestep0.0040.0030.009
job.kda0.0290.0070.043
kda.analyze0.0180.0060.030
kda.analyze.exec17.483 0.34620.724
kda.analyze.simulate17.093 0.27319.370
kda.analyze.test17.250 0.30120.153
kda.configure0.0010.0010.003
kda.finish0.2250.0150.275
kda.finish.estimate0.1370.0050.158
kda.finish.save0.1360.0050.164
kda.finish.summarize0.1360.0050.153
kda.finish.trim0.2110.0110.257
kda.prepare17.274 0.29520.778
kda.prepare.overlap0.0000.0020.002
kda.prepare.screen0.0010.0010.004
kda.start2.3820.0762.857
kda.start.edges0.0030.0020.005
kda.start.identify0.0080.0010.013
kda.start.modules0.0040.0030.007
kda2cytoscape0.6730.0210.813
kda2cytoscape.colorize000
kda2cytoscape.colormap0.0010.0000.001
kda2cytoscape.drivers0.2330.0130.283
kda2cytoscape.edges0.2220.0120.278
kda2cytoscape.exec0.2750.0150.344
kda2cytoscape.identify0.0070.0010.009
kda2himmeli0.6970.0220.844
kda2himmeli.colorize0.0000.0010.001
kda2himmeli.colormap0.0010.0010.001
kda2himmeli.drivers0.2350.0130.292
kda2himmeli.edges0.2350.0130.312
kda2himmeli.exec0.4470.0220.542
kda2himmeli.identify0.0070.0020.010
ssea.analyze 9.237 0.26210.997
ssea.analyze.observe7.0660.1018.327
ssea.analyze.randgenes7.3260.1008.661
ssea.analyze.randloci7.0600.0858.091
ssea.analyze.simulate 8.713 0.18310.241
ssea.analyze.statistic0.0000.0000.001
ssea.control7.1040.0988.231
ssea.finish 9.157 0.19910.934
ssea.finish.details 9.447 0.19111.184
ssea.finish.fdr 9.068 0.20310.808
ssea.finish.genes 9.265 0.18011.129
ssea.meta 9.702 0.20511.406
ssea.prepare6.7200.0928.106
ssea.prepare.counts6.8140.1008.164
ssea.prepare.structure6.7750.0877.958
ssea.start6.6060.0877.869
ssea.start.configure0.5920.0330.734
ssea.start.identify0.0060.0020.010
ssea.start.relabel6.6970.1067.903
ssea2kda11.657 0.29914.243
ssea2kda.analyze11.222 0.25313.325
ssea2kda.import 9.603 0.20511.300
tool.aggregate0.0020.0020.005
tool.cluster0.0320.0020.038
tool.cluster.static0.0010.0010.002
tool.coalesce0.0910.0040.106
tool.coalesce.exec0.2380.0030.271
tool.coalesce.find0.2510.0060.308
tool.coalesce.merge0.2380.0050.288
tool.fdr0.0010.0000.005
tool.fdr.bh0.0010.0010.003
tool.fdr.empirical0.0010.0010.003
tool.graph2.1980.0642.641
tool.graph.degree2.2120.0642.671
tool.graph.list2.0930.0582.499
tool.metap0.0060.0020.008
tool.normalize0.0260.0010.032
tool.normalize.quality0.0200.0010.025
tool.overlap0.0130.0020.019
tool.read0.4160.0160.507
tool.save0.0020.0020.005
tool.subgraph0.1440.0050.171
tool.subgraph.find0.1380.0040.165
tool.subgraph.search0.1400.0050.165
tool.subgraph.stats0.1690.0070.220
tool.translate0.0760.0070.100
tool.unify0.0020.0000.002