Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1504/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
partCNV 1.4.0 (landing page) Ziyi Li
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | 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: 1.4.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:partCNV.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings partCNV_1.4.0.tar.gz |
StartedAt: 2024-12-20 04:28:29 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 04:35:53 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 443.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: partCNV.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:partCNV.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings partCNV_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/partCNV.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'partCNV/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'partCNV' version '1.4.0' * 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 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 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 11.20 1.97 13.83 partCNVH 10.71 0.98 11.78 partCNV 8.07 0.81 9.07 GetExprCountCyto 7.38 0.92 8.64 * 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 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-3.20-bioc/meat/partCNV.Rcheck/00check.log' for details.
partCNV.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL partCNV ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 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. > # 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: 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 Negative: 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 PC_ 5 Positive: 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 Negative: 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 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: 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 Negative: 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 PC_ 5 Positive: 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 Negative: 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 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 49.79 5.71 56.29
partCNV.Rcheck/partCNV-Ex.timings
name | user | system | elapsed | |
GetCytoLocation | 11.20 | 1.97 | 13.83 | |
GetExprCountCyto | 7.38 | 0.92 | 8.64 | |
Hg38_gtf | 0.10 | 0.02 | 0.11 | |
NormalizeCounts | 1.89 | 0.13 | 2.02 | |
SimData | 0.48 | 0.03 | 0.51 | |
SimDataSce | 0.11 | 0.00 | 0.11 | |
partCNV | 8.07 | 0.81 | 9.07 | |
partCNVH | 10.71 | 0.98 | 11.78 | |