Ziyi Li
| Snapshot Date: 2024-11-20 13:40 -0500 (Wed, 20 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/partCNV |
| git_branch: devel |
| git_last_commit: 91c5b22 |
| git_last_commit_date: 2024-10-29 11:21:21 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-21 11:33 -0500 (Thu, 21 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4742 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4456 |
| 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 1493/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| partCNV 1.5.0 (landing page) Ziyi Li
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
|
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. |
| Package: partCNV |
| Version: 1.5.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:partCNV.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings partCNV_1.5.0.tar.gz |
| StartedAt: 2024-11-21 03:54:36 -0500 (Thu, 21 Nov 2024) |
| EndedAt: 2024-11-21 04:04:13 -0500 (Thu, 21 Nov 2024) |
| EllapsedTime: 576.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: partCNV.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:partCNV.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings partCNV_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/partCNV.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘partCNV/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘partCNV’ version ‘1.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘BiocStyle’
All declared Imports should be used.
* 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 7.905 1.277 9.960
partCNVH 7.889 0.646 8.752
partCNV 5.907 0.509 6.633
GetExprCountCyto 5.263 0.863 6.376
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/partCNV.Rcheck/00check.log’
for details.
partCNV.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL partCNV ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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)
partCNV.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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
36.721 3.424 42.267
partCNV.Rcheck/partCNV-Ex.timings
| name | user | system | elapsed | |
| GetCytoLocation | 7.905 | 1.277 | 9.960 | |
| GetExprCountCyto | 5.263 | 0.863 | 6.376 | |
| Hg38_gtf | 0.092 | 0.003 | 0.095 | |
| NormalizeCounts | 1.024 | 0.138 | 1.162 | |
| SimData | 0.404 | 0.002 | 0.406 | |
| SimDataSce | 0.077 | 0.005 | 0.081 | |
| partCNV | 5.907 | 0.509 | 6.633 | |
| partCNVH | 7.889 | 0.646 | 8.752 | |