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This page was generated on 2024-04-17 11:38:02 -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 1501/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
partCNV 1.0.0  (landing page)
Ziyi Li
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/partCNV
git_branch: RELEASE_3_18
git_last_commit: 4075147
git_last_commit_date: 2023-10-24 11:49:24 -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 partCNV on merida1


To the developers/maintainers of the partCNV package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/partCNV.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: partCNV
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:partCNV.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings partCNV_1.0.0.tar.gz
StartedAt: 2024-04-16 06:44:01 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 06:56:07 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 726.4 seconds
RetCode: 0
Status:   OK  
CheckDir: partCNV.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:partCNV.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings partCNV_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/partCNV.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 ‘partCNV/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘partCNV’ version ‘1.0.0’
* package encoding: UTF-8
* 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 ‘partCNV’ 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
GetCytoLocation: no visible global function definition for ‘data’
GetExprCountCyto: no visible global function definition for ‘data’
Undefined global functions or variables:
  data
Consider adding
  importFrom("utils", "data")
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
GetCytoLocation  14.880  1.997  24.445
partCNVH         13.710  0.813  15.959
partCNV          10.716  0.748  12.670
GetExprCountCyto  9.754  1.690  12.568
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/partCNV.Rcheck/00check.log’
for details.

Installation output

partCNV.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘partCNV’ ...
** using staged installation
** R
** data
** 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 (partCNV)

Tests output

partCNV.Rcheck/tests/testthat.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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(partCNV)
> 
> test_check("partCNV")
loading from cache
require("GenomicRanges")
Interested region: chr20:28100001-51200000.
A total of 381 genes are located in this region.
loading from cache
Interested region: chr20:25600000-49800000.
A total of 368 genes are located in this region.
loading from cache
Interested region: chr20:28100001-51200000.
A total of 381 genes are located in this region.
loading from cache
Interested region: chr20:28100001-51200000.
A total of 381 genes are located in this region.
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
PC_ 1 
Positive:  RBM39, STK4, ZFAS1, YWHAB, SCAND1, ROMO1, PTPN1, RPN2, RAB5IF, DYNLRB1 
	   NORAD, OSER1, ASXL1, DDX27, RALY, SNHG17, SRSF6, COMMD7, MAPRE1, PREX1 
	   PHF20, NCOA3, CHMP4B, SLC35C2, CHD6, ARFGEF2, BLCAP, CBFA2T2, EIF2S2, UBE2V1 
Negative:  UBE2C, TGM2, TPX2, RIPOR3, NFS1, DNTTIP1, POFUT1, PLTP, DSN1, LINC01597 
	   AL031666.3, AL031667.3, PXMP4, SDC4, MYBL2, RALY-AS1, ZNF341, PIGU, BCL2L1, HM13-AS1 
	   RBM12, TP53RK, OSER1-DT, TOMM34, E2F1, MYH7B, CSE1L, ACTL10, TOP1, AL023803.3 
PC_ 2 
Positive:  MYBL2, TPX2, EIF2S2, ROMO1, DYNLRB1, STAU1, ERGIC3, CSE1L, AHCY, SCAND1 
	   TOP1, YWHAB, ZMYND8, UBE2C, RPN2, EIF6, UBE2V1, SRSF6, ZFAS1, RBL1 
	   E2F1, PKIG, RAB5IF, FAM83D, SERINC3, DPM1, DSN1, ID1, IFT52, RALY 
Negative:  STK4, PREX1, NCOA3, CEBPB, FO393401.1, PTPN1, SAMHD1, CHD6, ITCH, CD40 
	   PPP1R16B, SLC35C2, OSER1, RALGAPB, ZNF335, SLC9A8, ZNFX1, TMEM189, NDRG3, DLGAP4 
	   MMP24OS, NOL4L, LINC00494, KCNG1, TP53INP2, SYS1, PLCG1-AS1, ELMO2, TRPC4AP, AL133342.1 
PC_ 3 
Positive:  TTPAL, FAM83D, BCL2L1, RIPOR3, ZNF335, TTI1, DHX35, SERINC3, GSS, RPRD1B 
	   PLAGL2, NDRG3, TPX2, CTSA, UBE2C, TGM2, SAMHD1, PIGT, RBL1, ACTR5 
	   AL035071.1, TMEM189, IFT52, DLGAP4, RNF114, CEP250, SLA2, PLCG1-AS1, RALGAPB, B4GALT5 
Negative:  CD40, ZFAS1, PKIG, NCOA3, BCAS4, SNHG11, KCNG1, LINC00494, RBM39, EDEM2 
	   LINC01597, ERGIC3, FO393401.1, RALY, TGIF2, DYNLRB1, SLC9A8, CHMP4B, CPNE1, PHF20 
	   RAB5IF, UQCC1, PTPN1, CTNNBL1, MOCS3, SCAND1, HM13, TOMM34, SOGA1, AL035106.1 
PC_ 4 
Positive:  CD40, LINC00494, KCNG1, NCOA3, ARFGEF2, TTI1, FAM83D, PKIG, TTPAL, ASXL1 
	   MAP1LC3A, SOGA1, PTPN1, TOP1, DHX35, MYBL2, MAPRE1, RBL1, ACTR5, RBM12 
	   PCIF1, CEP250, MANBAL, NORAD, PIGU, ZSWIM1, DSN1, PLAGL2, RIPOR3, TGM2 
Negative:  ELMO2, RPN2, SAMHD1, PABPC1L, ID1, YWHAB, CEBPB, NOL4L, EIF6, TMEM189 
	   DNTTIP1, PLCG1, HM13, NDRG3, TM9SF4, ZFAS1, DLGAP4, BLCAP, SLC12A5, RALGAPB 
	   TOMM34, PLCG1-AS1, PIGT, PREX1, COMMD7, TP53INP2, MMP24OS, CPNE1, AL035106.1, AHCY 
PC_ 5 
Positive:  BLCAP, DBNDD2, PABPC1L, SPATA2, UQCC1, ELMO2, MAP1LC3A, ID1, KCNG1, DLGAP4 
	   AHCY, NCOA5, MANBAL, SYS1, AL035071.1, LINC00494, OSER1, CBFA2T2, PKIG, DNTTIP1 
	   PXMP4, DNMT3B, TGIF2, PIGU, RALGAPB, TRPC4AP, SNHG17, ZHX3, PHF20, CD40 
Negative:  PREX1, STAU1, UBE2V1, SLA2, TTPAL, STK4, ARFGEF2, RBM39, CEBPB, SAMHD1 
	   PLCG1, ZNFX1, ZMYND8, TOP1, AL133342.1, RBL1, L3MBTL1, YWHAB, SULF2, NOL4L 
	   BCAS4, NORAD, ASXL1, SNTA1, CHD6, PTPN1, TM9SF4, CHMP4B, SRSF6, DHX35 
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 400
Number of edges: 14975

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9990
Number of communities: 1
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 400
Number of edges: 14975

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9890
Number of communities: 1
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 400
Number of edges: 14975

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9790
Number of communities: 1
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 400
Number of edges: 14975

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9690
Number of communities: 1
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 400
Number of edges: 14975

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9590
Number of communities: 1
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 400
Number of edges: 14975

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9490
Number of communities: 1
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 400
Number of edges: 14975

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9390
Number of communities: 1
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 400
Number of edges: 14975

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9290
Number of communities: 1
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 400
Number of edges: 14975

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9201
Number of communities: 2
Elapsed time: 0 seconds
qi = 0.229937938120215
diff_p = 88.7338431716195
0.41
qi = 0.211865678741964
diff_p = 1.08462786133086
0.4225
qi = 0.212544318328912
diff_p = 7.04508104151934
0.4025
qi = 0.211457139924986
diff_p = 3.66870107638065
0.4
qi = 0.211320732302255
diff_p = 2.45592669820758
0.3875
qi = 0.210636967429884
diff_p = 1.60104507775815
0.385
qi = 0.210499866478258
diff_p = 2.2172901450684
0.38
qi = 0.210225313556707
diff_p = 1.6196923581697
0.3725
qi = 0.209812600830449
diff_p = 0.336266856490941
0.375
qi = 0.209950290037766
diff_p = 0.300486865798939
0.37
qi = 0.209674792800335
diff_p = 0.348032435355523
0.375
qi = 0.209950290037766
diff_p = 0.11802890558157
0.37
qi = 0.209674792800335
diff_p = 0.344247325972077
0.37
loading from cache
Interested region: chr20:28100001-51200000.
A total of 381 genes are located in this region.
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
PC_ 1 
Positive:  RBM39, STK4, ZFAS1, YWHAB, SCAND1, ROMO1, PTPN1, RPN2, RAB5IF, DYNLRB1 
	   NORAD, OSER1, ASXL1, DDX27, RALY, SNHG17, SRSF6, COMMD7, MAPRE1, PREX1 
	   PHF20, NCOA3, CHMP4B, SLC35C2, CHD6, ARFGEF2, BLCAP, CBFA2T2, EIF2S2, UBE2V1 
Negative:  UBE2C, TGM2, TPX2, RIPOR3, NFS1, DNTTIP1, POFUT1, PLTP, DSN1, LINC01597 
	   AL031666.3, AL031667.3, PXMP4, SDC4, MYBL2, RALY-AS1, ZNF341, PIGU, BCL2L1, HM13-AS1 
	   RBM12, TP53RK, OSER1-DT, TOMM34, E2F1, MYH7B, CSE1L, ACTL10, TOP1, AL023803.3 
PC_ 2 
Positive:  MYBL2, TPX2, EIF2S2, ROMO1, DYNLRB1, STAU1, ERGIC3, CSE1L, AHCY, SCAND1 
	   TOP1, YWHAB, ZMYND8, UBE2C, RPN2, EIF6, UBE2V1, SRSF6, ZFAS1, RBL1 
	   E2F1, PKIG, RAB5IF, FAM83D, SERINC3, DPM1, DSN1, ID1, IFT52, RALY 
Negative:  STK4, PREX1, NCOA3, CEBPB, FO393401.1, PTPN1, SAMHD1, CHD6, ITCH, CD40 
	   PPP1R16B, SLC35C2, OSER1, RALGAPB, ZNF335, SLC9A8, ZNFX1, TMEM189, NDRG3, DLGAP4 
	   MMP24OS, NOL4L, LINC00494, KCNG1, TP53INP2, SYS1, PLCG1-AS1, ELMO2, TRPC4AP, AL133342.1 
PC_ 3 
Positive:  TTPAL, FAM83D, BCL2L1, RIPOR3, ZNF335, TTI1, DHX35, SERINC3, GSS, RPRD1B 
	   PLAGL2, NDRG3, TPX2, CTSA, UBE2C, TGM2, SAMHD1, PIGT, RBL1, ACTR5 
	   AL035071.1, TMEM189, IFT52, DLGAP4, RNF114, CEP250, SLA2, PLCG1-AS1, RALGAPB, B4GALT5 
Negative:  CD40, ZFAS1, PKIG, NCOA3, BCAS4, SNHG11, KCNG1, LINC00494, RBM39, EDEM2 
	   LINC01597, ERGIC3, FO393401.1, RALY, TGIF2, DYNLRB1, SLC9A8, CHMP4B, CPNE1, PHF20 
	   RAB5IF, UQCC1, PTPN1, CTNNBL1, MOCS3, SCAND1, HM13, TOMM34, SOGA1, AL035106.1 
PC_ 4 
Positive:  CD40, LINC00494, KCNG1, NCOA3, ARFGEF2, TTI1, FAM83D, PKIG, TTPAL, ASXL1 
	   MAP1LC3A, SOGA1, PTPN1, TOP1, DHX35, MYBL2, MAPRE1, RBL1, ACTR5, RBM12 
	   PCIF1, CEP250, MANBAL, NORAD, PIGU, ZSWIM1, DSN1, PLAGL2, RIPOR3, TGM2 
Negative:  ELMO2, RPN2, SAMHD1, PABPC1L, ID1, YWHAB, CEBPB, NOL4L, EIF6, TMEM189 
	   DNTTIP1, PLCG1, HM13, NDRG3, TM9SF4, ZFAS1, DLGAP4, BLCAP, SLC12A5, RALGAPB 
	   TOMM34, PLCG1-AS1, PIGT, PREX1, COMMD7, TP53INP2, MMP24OS, CPNE1, AL035106.1, AHCY 
PC_ 5 
Positive:  BLCAP, DBNDD2, PABPC1L, SPATA2, UQCC1, ELMO2, MAP1LC3A, ID1, KCNG1, DLGAP4 
	   AHCY, NCOA5, MANBAL, SYS1, AL035071.1, LINC00494, OSER1, CBFA2T2, PKIG, DNTTIP1 
	   PXMP4, DNMT3B, TGIF2, PIGU, RALGAPB, TRPC4AP, SNHG17, ZHX3, PHF20, CD40 
Negative:  PREX1, STAU1, UBE2V1, SLA2, TTPAL, STK4, ARFGEF2, RBM39, CEBPB, SAMHD1 
	   PLCG1, ZNFX1, ZMYND8, TOP1, AL133342.1, RBL1, L3MBTL1, YWHAB, SULF2, NOL4L 
	   BCAS4, NORAD, ASXL1, SNTA1, CHD6, PTPN1, TM9SF4, CHMP4B, SRSF6, DHX35 
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 400
Number of edges: 14975

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9990
Number of communities: 1
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 400
Number of edges: 14975

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9890
Number of communities: 1
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 400
Number of edges: 14975

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9790
Number of communities: 1
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 400
Number of edges: 14975

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9690
Number of communities: 1
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 400
Number of edges: 14975

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9590
Number of communities: 1
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 400
Number of edges: 14975

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9490
Number of communities: 1
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 400
Number of edges: 14975

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9390
Number of communities: 1
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 400
Number of edges: 14975

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9290
Number of communities: 1
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 400
Number of edges: 14975

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9201
Number of communities: 2
Elapsed time: 0 seconds
qi = 0.229937938120215
diff_p = 88.7338431716195
0.41
qi = 0.211865678741964
diff_p = 1.08462786133086
0.4225
qi = 0.212544318328912
diff_p = 7.04508104151934
0.4025
qi = 0.211457139924986
diff_p = 3.66870107638065
0.4
qi = 0.211320732302255
diff_p = 2.45592669820758
0.3875
qi = 0.210636967429884
diff_p = 1.60104507775815
0.385
qi = 0.210499866478258
diff_p = 2.2172901450684
0.38
qi = 0.210225313556707
diff_p = 1.6196923581697
0.3725
qi = 0.209812600830449
diff_p = 0.336266856490941
0.375
qi = 0.209950290037766
diff_p = 0.300486865798939
0.37
qi = 0.209674792800335
diff_p = 0.348032435355523
0.375
qi = 0.209950290037766
diff_p = 0.11802890558157
0.37
qi = 0.209674792800335
diff_p = 0.344247325972077
0.37
converged at iteration 48 with logLik: -80.91016 
Normalizing layer: counts
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
PC_ 1 
Positive:  TGM2, NFS1, RBM12, SOGA1, DSN1, SNHG11, DHX35, AL023803.3, MROH8, MYH7B 
	   TOP1, CEP250, AL023803.2, TRPC4AP, MANBAL, PPP1R16B, NDRG3, FAM83D, FO393401.1, TTI1 
Negative:  ROMO1, RPN2, RBM39, RAB5IF, SNHG17, PHF20, EIF6, CTNNBL1, ERGIC3, CPNE1 
	   BLCAP, MMP24OS, SAMHD1, RPRD1B, RALGAPB, RBL1, SLA2, EDEM2, UQCC1, ACTR5 
PC_ 2 
Positive:  TOP1, ERGIC3, EIF6, RPN2, RAB5IF, ROMO1, DSN1, CTNNBL1, RBL1, SOGA1 
	   AL023803.2, CPNE1, RBM39, MANBAL, SNHG17, FAM83D, SNHG11, PPP1R16B, NFS1, PHF20 
Negative:  NDRG3, PLCG1-AS1, RALGAPB, SAMHD1, RPRD1B, ACTR5, SLA2, MYH7B, DHX35, CEP250 
	   TTI1, FO393401.1, MMP24OS, EDEM2, RBM12, TGM2, UQCC1, BLCAP, TRPC4AP, MROH8 
PC_ 3 
Positive:  FAM83D, DHX35, RPRD1B, TTI1, RBL1, RBM12, TGM2, ACTR5, TOP1, CEP250 
	   DSN1, ROMO1, MANBAL, ERGIC3, RPN2, SOGA1, MROH8, BLCAP, UQCC1, NFS1 
Negative:  FO393401.1, RALGAPB, SLA2, SNHG11, PPP1R16B, CPNE1, PHF20, SAMHD1, EIF6, MMP24OS 
	   RAB5IF, TRPC4AP, SNHG17, PLCG1-AS1, NDRG3, MYH7B, AL023803.2, CTNNBL1, RBM39, AL023803.3 
PC_ 4 
Positive:  SLA2, RALGAPB, SAMHD1, RAB5IF, FAM83D, CEP250, MMP24OS, ROMO1, RBL1, AL023803.3 
	   AL023803.2, EIF6, MANBAL, TGM2, PPP1R16B, TTI1, DHX35, RPN2, SOGA1, TOP1 
Negative:  EDEM2, ACTR5, UQCC1, TRPC4AP, CPNE1, CTNNBL1, SNHG17, PHF20, DSN1, SNHG11 
	   RPRD1B, PLCG1-AS1, NDRG3, MYH7B, RBM12, ERGIC3, FO393401.1, NFS1, BLCAP, MROH8 
PC_ 5 
Positive:  NDRG3, PLCG1-AS1, ROMO1, ERGIC3, TOP1, MYH7B, RBM12, RALGAPB, ACTR5, RBL1 
	   EIF6, RPN2, DSN1, RBM39, MROH8, CTNNBL1, SAMHD1, DHX35, SNHG17, NFS1 
Negative:  TTI1, MMP24OS, FO393401.1, FAM83D, EDEM2, TRPC4AP, MANBAL, BLCAP, CPNE1, UQCC1 
	   SOGA1, RPRD1B, SLA2, SNHG11, AL023803.3, PHF20, TGM2, RAB5IF, PPP1R16B, CEP250 
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 400
Number of edges: 12627

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9990
Number of communities: 1
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 400
Number of edges: 12627

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9890
Number of communities: 1
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 400
Number of edges: 12627

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9790
Number of communities: 1
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 400
Number of edges: 12627

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9690
Number of communities: 1
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 400
Number of edges: 12627

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9590
Number of communities: 1
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 400
Number of edges: 12627

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9490
Number of communities: 1
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 400
Number of edges: 12627

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.9394
Number of communities: 2
Elapsed time: 0 seconds
qi = 0.235518261351573
diff_p = 208.522225971789
0.21
qi = 0.200608566019358
diff_p = 3.86123370768259
0.2525
qi = 0.203083904278474
diff_p = 0.516816900771607
0.245
qi = 0.202650911768908
diff_p = 1.5013173870293
0.245
qi = 0.202650911768908
diff_p = 1.84459622577338
0.24
qi = 0.202361349300245
diff_p = 1.94523975236974
0.235
qi = 0.202071059067909
diff_p = 1.97247143245344
0.23
qi = 0.201780036109746
diff_p = 1.9742424855847
0.2275
qi = 0.201634248639502
diff_p = 1.94882637398603
0.2225
qi = 0.201342120051476
diff_p = 1.91957609656751
0.2225
[ FAIL 0 | WARN 13 | SKIP 0 | PASS 9 ]

[ FAIL 0 | WARN 13 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
 72.787   5.431  86.368

Example timings

partCNV.Rcheck/partCNV-Ex.timings

nameusersystemelapsed
GetCytoLocation14.880 1.99724.445
GetExprCountCyto 9.754 1.69012.568
Hg38_gtf0.1580.0040.170
NormalizeCounts1.5640.0511.682
SimData1.1370.0221.232
SimDataSce0.1320.0140.153
partCNV10.716 0.74812.670
partCNVH13.710 0.81315.959