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This page was generated on 2024-03-28 11:38:00 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 1184/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Mergeomics 1.31.0  (landing page)
Zeyneb Kurt
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 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 -0400 (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
lconwaymacOS 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 palomino3


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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Mergeomics.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings Mergeomics_1.31.0.tar.gz
StartedAt: 2024-03-28 03:44:23 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 03:53:58 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 574.4 seconds
RetCode: 0
Status:   OK  
CheckDir: Mergeomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Mergeomics.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings Mergeomics_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/Mergeomics.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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.prepare           8.81   0.67    9.48
kda.analyze.test      8.50   0.58    9.10
kda.analyze.exec      8.29   0.56   11.44
kda.analyze.simulate  7.90   0.56    8.46
ssea2kda.analyze      6.83   1.56    8.42
ssea2kda              7.03   1.25    8.67
ssea.meta             6.21   0.50    6.81
ssea.analyze          5.47   0.66    9.34
ssea.finish.genes     5.35   0.65    6.05
ssea.finish.details   5.23   0.76    6.06
ssea2kda.import       5.06   0.75    5.83
ssea.finish.fdr       4.81   0.96    5.80
ssea.analyze.simulate 4.52   0.79    5.36
ssea.finish           4.52   0.77    5.30
* 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
  'F:/biocbuild/bbs-3.19-bioc/meat/Mergeomics.Rcheck/00check.log'
for details.


Installation output

Mergeomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL Mergeomics
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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 Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

162629/1673535 
306484/1673535 
465705/1673535 
608312/1673535 
755820/1673535 
916336/1673535 
1087135/1673535 
1236223/1673535 
1402652/1673535 
1551262/1673535 
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 -- Thu Mar 28 03:53:42 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 
 345.35   32.20  377.56 

Example timings

Mergeomics.Rcheck/Mergeomics-Ex.timings

nameusersystemelapsed
MSEA.KDA.onestep000
job.kda0.020.000.01
kda.analyze0.020.000.01
kda.analyze.exec 8.29 0.5611.44
kda.analyze.simulate7.900.568.46
kda.analyze.test8.500.589.10
kda.configure000
kda.finish0.110.020.14
kda.finish.estimate0.050.040.09
kda.finish.save0.060.020.08
kda.finish.summarize0.080.000.08
kda.finish.trim0.060.020.08
kda.prepare8.810.679.48
kda.prepare.overlap000
kda.prepare.screen000
kda.start1.140.171.31
kda.start.edges000
kda.start.identify000
kda.start.modules000
kda2cytoscape0.30.00.3
kda2cytoscape.colorize000
kda2cytoscape.colormap000
kda2cytoscape.drivers0.090.030.14
kda2cytoscape.edges0.110.010.13
kda2cytoscape.exec0.160.060.22
kda2cytoscape.identify000
kda2himmeli0.360.050.72
kda2himmeli.colorize000
kda2himmeli.colormap000
kda2himmeli.drivers0.110.020.14
kda2himmeli.edges0.140.030.17
kda2himmeli.exec0.250.030.28
kda2himmeli.identify0.020.000.02
ssea.analyze5.470.669.34
ssea.analyze.observe3.400.123.55
ssea.analyze.randgenes3.350.113.48
ssea.analyze.randloci2.980.193.19
ssea.analyze.simulate4.520.795.36
ssea.analyze.statistic000
ssea.control3.090.083.20
ssea.finish4.520.775.30
ssea.finish.details5.230.766.06
ssea.finish.fdr4.810.965.80
ssea.finish.genes5.350.656.05
ssea.meta6.210.506.81
ssea.prepare3.320.163.48
ssea.prepare.counts3.230.163.41
ssea.prepare.structure2.860.072.95
ssea.start3.050.103.16
ssea.start.configure0.580.010.61
ssea.start.identify000
ssea.start.relabel3.040.073.14
ssea2kda7.031.258.67
ssea2kda.analyze6.831.568.42
ssea2kda.import5.060.755.83
tool.aggregate000
tool.cluster0.020.010.03
tool.cluster.static000
tool.coalesce0.050.020.07
tool.coalesce.exec0.140.000.14
tool.coalesce.find0.150.000.15
tool.coalesce.merge0.140.000.14
tool.fdr000
tool.fdr.bh000
tool.fdr.empirical000
tool.graph1.610.141.75
tool.graph.degree1.360.081.44
tool.graph.list1.420.031.45
tool.metap0.000.020.02
tool.normalize0.020.000.01
tool.normalize.quality0.010.000.02
tool.overlap000
tool.read0.270.000.26
tool.save000
tool.subgraph0.060.010.08
tool.subgraph.find0.060.020.08
tool.subgraph.search0.110.030.14
tool.subgraph.stats0.100.000.09
tool.translate0.040.000.05
tool.unify000