Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-16 11:40 -0400 (Fri, 16 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4420 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
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 706/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
FindIT2 1.11.0 (landing page) Guandong Shang
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the FindIT2 package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FindIT2.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: FindIT2 |
Version: 1.11.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FindIT2.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings FindIT2_1.11.0.tar.gz |
StartedAt: 2024-08-16 00:45:30 -0400 (Fri, 16 Aug 2024) |
EndedAt: 2024-08-16 00:51:56 -0400 (Fri, 16 Aug 2024) |
EllapsedTime: 386.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: FindIT2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FindIT2.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings FindIT2_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/FindIT2.Rcheck' * using R version 4.4.1 (2024-06-14 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 'FindIT2/DESCRIPTION' ... OK * this is package 'FindIT2' version '1.11.0' * 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 'FindIT2' 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * 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 calcRP_region 7.73 0.06 11.37 findIT_regionRP 6.94 0.17 7.11 calcRP_TFHit 2.94 0.14 7.51 * 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: OK
FindIT2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL FindIT2 ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'FindIT2' ... ** 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 (FindIT2)
FindIT2.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 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. > library(testthat) > library(FindIT2) Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb > if (!requireNamespace("TxDb.Athaliana.BioMart.plantsmart28")) { + stop("unable to load TxDb.Athaliana.BioMart.plantsmart28") + } Loading required namespace: TxDb.Athaliana.BioMart.plantsmart28 > > test_check("FindIT2") >> checking seqlevels match... 2024-08-16 12:50:41 AM >> your peak_GR seqlevel:Chr5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... Good, your Chrs in peak_GR is all in Txdb ------------ annotatePeak using geneScan mode begins >> preparing gene features information and scan region... 2024-08-16 12:50:41 AM >> some scan range may cross Chr bound, trimming... 2024-08-16 12:50:42 AM >> finding overlap peak in gene scan region... 2024-08-16 12:50:43 AM >> dealing with left peak not your gene scan region... 2024-08-16 12:50:43 AM >> merging two set peaks... 2024-08-16 12:50:43 AM >> calculating distance and dealing with gene strand... 2024-08-16 12:50:43 AM >> merging all info together ... 2024-08-16 12:50:43 AM >> done 2024-08-16 12:50:43 AM >> calculating peakCenter to TSS using peak-gene pair... 2024-08-16 12:50:43 AM >> pre-filling 1356 noAssoc peak gene's RP with 0... 2024-08-16 12:50:44 AM >> calculating RP using centerToTSS and peak score2024-08-16 12:50:44 AM >> merging all info together 2024-08-16 12:50:47 AM >> done 2024-08-16 12:50:48 AM >> calculating peakCenter to TSS using peak-gene pair... 2024-08-16 12:50:49 AM >> pre-filling 1356 noAssoc peak gene's RP with 0... 2024-08-16 12:50:50 AM >> calculating RP using centerToTSS and peak score2024-08-16 12:50:50 AM >> merging all info together 2024-08-16 12:50:53 AM >> done 2024-08-16 12:50:53 AM >> checking seqlevels match... 2024-08-16 12:50:53 AM >> your peak_GR seqlevel:Chr5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... Good, your Chrs in peak_GR is all in Txdb ------------ annotatePeak using geneScan mode begins >> preparing gene features information and scan region... 2024-08-16 12:50:53 AM >> some scan range may cross Chr bound, trimming... 2024-08-16 12:50:54 AM >> finding overlap peak in gene scan region... 2024-08-16 12:50:54 AM >> dealing with left peak not your gene scan region... 2024-08-16 12:50:54 AM >> merging two set peaks... 2024-08-16 12:50:55 AM >> calculating distance and dealing with gene strand... 2024-08-16 12:50:55 AM >> merging all info together ... 2024-08-16 12:50:55 AM >> done 2024-08-16 12:50:55 AM >> calculating peakCenter to TSS using peak-gene pair... 2024-08-16 12:50:55 AM >> calculating RP using centerToTSS and TF hit 2024-08-16 12:50:55 AM >> merging all info together 2024-08-16 12:50:56 AM >> done 2024-08-16 12:50:56 AM >> calculating peakCenter to TSS using peak-gene pair... 2024-08-16 12:50:56 AM >> calculating RP using centerToTSS and TF hit 2024-08-16 12:50:57 AM >> merging all info together 2024-08-16 12:50:57 AM >> done 2024-08-16 12:50:57 AM >> checking seqlevels match... 2024-08-16 12:50:58 AM >> your peak_GR seqlevel:Chr5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... Good, your Chrs in peak_GR is all in Txdb ------------ annotatePeak using geneScan mode begins >> preparing gene features information and scan region... 2024-08-16 12:50:58 AM >> some scan range may cross Chr bound, trimming... 2024-08-16 12:50:59 AM >> finding overlap peak in gene scan region... 2024-08-16 12:50:59 AM >> dealing with left peak not your gene scan region... 2024-08-16 12:50:59 AM >> merging two set peaks... 2024-08-16 12:50:59 AM >> calculating distance and dealing with gene strand... 2024-08-16 12:50:59 AM >> merging all info together ... 2024-08-16 12:50:59 AM >> done 2024-08-16 12:50:59 AM >> calculating peakCenter to TSS using peak-gene pair... 2024-08-16 12:50:59 AM >> pre-filling 1356 noAssoc peak gene's RP with 0... 2024-08-16 12:51:01 AM >> calculating RP using centerToTSS and peak score2024-08-16 12:51:01 AM >> merging all info together 2024-08-16 12:51:03 AM >> done 2024-08-16 12:51:03 AM >> extracting RP info from regionRP... 2024-08-16 12:51:04 AM >> dealing with TF_GR_databse... 2024-08-16 12:51:04 AM >> calculating percent and p-value... 2024-08-16 12:51:04 AM >> dealing withE5_0h_R1... 2024-08-16 12:51:04 AM >> dealing withE5_0h_R2... 2024-08-16 12:51:04 AM >> dealing withE5_4h_R1... 2024-08-16 12:51:05 AM >> dealing withE5_4h_R2... 2024-08-16 12:51:05 AM >> dealing withE5_8h_R1... 2024-08-16 12:51:05 AM >> dealing withE5_8h_R2... 2024-08-16 12:51:05 AM >> dealing withE5_16h_R1... 2024-08-16 12:51:05 AM >> dealing withE5_16h_R2... 2024-08-16 12:51:05 AM >> dealing withE5_24h_R1... 2024-08-16 12:51:05 AM >> dealing withE5_24h_R2... 2024-08-16 12:51:05 AM >> dealing withE5_48h_R1... 2024-08-16 12:51:05 AM >> dealing withE5_48h_R2... 2024-08-16 12:51:05 AM >> dealing withE5_48h_R3... 2024-08-16 12:51:05 AM >> dealing withE5_72h_R1... 2024-08-16 12:51:05 AM >> dealing withE5_72h_R2... 2024-08-16 12:51:05 AM >> dealing withE5_72h_R3... 2024-08-16 12:51:05 AM >> merging all info together... 2024-08-16 12:51:05 AM >> done 2024-08-16 12:51:06 AM >> preparing gene features information... 2024-08-16 12:51:06 AM >> some scan range may cross Chr bound, trimming... 2024-08-16 12:51:07 AM >> calculating p-value for each TF, which may be time consuming... 2024-08-16 12:51:07 AM >> merging all info together... 2024-08-16 12:51:07 AM >> done 2024-08-16 12:51:07 AM >> dealing with TF_GR_database... 2024-08-16 12:51:07 AM >> calculating coef and converting into z-score using INT... 2024-08-16 12:51:07 AM >> dealing with E5_0h_R1... 2024-08-16 12:51:07 AM >> dealing with E5_0h_R2... 2024-08-16 12:51:08 AM >> dealing with E5_4h_R1... 2024-08-16 12:51:08 AM >> dealing with E5_4h_R2... 2024-08-16 12:51:08 AM >> dealing with E5_8h_R1... 2024-08-16 12:51:09 AM >> dealing with E5_8h_R2... 2024-08-16 12:51:09 AM >> dealing with E5_16h_R1... 2024-08-16 12:51:09 AM >> dealing with E5_16h_R2... 2024-08-16 12:51:09 AM >> dealing with E5_24h_R1... 2024-08-16 12:51:09 AM >> dealing with E5_24h_R2... 2024-08-16 12:51:09 AM >> dealing with E5_48h_R1... 2024-08-16 12:51:09 AM >> dealing with E5_48h_R2... 2024-08-16 12:51:09 AM >> dealing with E5_48h_R3... 2024-08-16 12:51:09 AM >> dealing with E5_72h_R1... 2024-08-16 12:51:09 AM >> dealing with E5_72h_R2... 2024-08-16 12:51:09 AM >> dealing with E5_72h_R3... 2024-08-16 12:51:09 AM >> merging all info together... 2024-08-16 12:51:10 AM >> done 2024-08-16 12:51:10 AM >> checking seqlevels match... 2024-08-16 12:51:10 AM >> your peak_GR seqlevel:Chr5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... Good, your Chrs in peak_GR is all in Txdb ------------ annotatePeak using geneScan mode begins >> preparing gene features information and scan region... 2024-08-16 12:51:10 AM >> some scan range may cross Chr bound, trimming... 2024-08-16 12:51:11 AM >> finding overlap peak in gene scan region... 2024-08-16 12:51:11 AM >> dealing with left peak not your gene scan region... 2024-08-16 12:51:11 AM >> merging two set peaks... 2024-08-16 12:51:11 AM >> calculating distance and dealing with gene strand... 2024-08-16 12:51:11 AM >> merging all info together ... 2024-08-16 12:51:11 AM >> done 2024-08-16 12:51:11 AM >> calculating peakCenter to TSS using peak-gene pair... 2024-08-16 12:51:11 AM >> calculating RP using centerToTSS and TF hit 2024-08-16 12:51:12 AM >> merging all info together 2024-08-16 12:51:12 AM >> done 2024-08-16 12:51:12 AM >> checking seqlevels match... 2024-08-16 12:51:13 AM >> your peak_GR seqlevel:5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... >> checking seqlevels match... 2024-08-16 12:51:13 AM >> your peak_GR seqlevel:Chr5 Chr6... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... >> checking seqlevels match... 2024-08-16 12:51:17 AM >> your peak_GR seqlevel:Chr5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... Good, your Chrs in peak_GR is all in Txdb >> checking seqlevels match... 2024-08-16 12:51:17 AM >> your peak_GR seqlevel:Chr5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... Good, your Chrs in peak_GR is all in Txdb ------------ annotating Peak using nearest gene mode begins >> preparing gene features information... 2024-08-16 12:51:17 AM >> finding nearest gene and calculating distance... 2024-08-16 12:51:18 AM >> dealing with gene strand ... 2024-08-16 12:51:18 AM >> merging all info together ... 2024-08-16 12:51:18 AM >> done 2024-08-16 12:51:18 AM >> checking seqlevels match... 2024-08-16 12:51:18 AM >> your peak_GR seqlevel:Chr5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... Good, your Chrs in peak_GR is all in Txdb >> checking seqlevels match... 2024-08-16 12:51:18 AM >> your peak_GR seqlevel:Chr5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... Good, your Chrs in peak_GR is all in Txdb ------------ annotating Peak using nearest gene mode begins >> preparing gene features information... 2024-08-16 12:51:19 AM >> finding nearest gene and calculating distance... 2024-08-16 12:51:20 AM >> dealing with gene strand ... 2024-08-16 12:51:20 AM >> merging all info together ... 2024-08-16 12:51:20 AM >> done 2024-08-16 12:51:20 AM >> checking seqlevels match... 2024-08-16 12:51:21 AM >> your peak_GR seqlevel:Chr5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... Good, your Chrs in peak_GR is all in Txdb >> checking seqlevels match... 2024-08-16 12:51:21 AM >> your peak_GR seqlevel:Chr5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... Good, your Chrs in peak_GR is all in Txdb ------------ annotating Peak using nearest gene mode begins >> preparing gene features information... 2024-08-16 12:51:21 AM >> finding nearest gene and calculating distance... 2024-08-16 12:51:22 AM >> dealing with gene strand ... 2024-08-16 12:51:22 AM >> merging all info together ... 2024-08-16 12:51:22 AM >> done 2024-08-16 12:51:22 AM >> checking seqlevels match... 2024-08-16 12:51:23 AM >> your peak_GR seqlevel:Chr5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... Good, your Chrs in peak_GR is all in Txdb >> checking seqlevels match... 2024-08-16 12:51:23 AM >> your peak_GR seqlevel:Chr5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... Good, your Chrs in peak_GR is all in Txdb ------------ annotating Peak using nearest gene mode begins >> preparing gene features information... 2024-08-16 12:51:23 AM >> finding nearest gene and calculating distance... 2024-08-16 12:51:25 AM >> dealing with gene strand ... 2024-08-16 12:51:25 AM >> merging all info together ... 2024-08-16 12:51:25 AM >> done 2024-08-16 12:51:25 AM It seems that there 1 genes have not been annotated by nearestGene mode >> checking seqlevels match... 2024-08-16 12:51:26 AM >> your peak_GR seqlevel:Chr5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... Good, your Chrs in peak_GR is all in Txdb >> checking seqlevels match... 2024-08-16 12:51:26 AM >> your peak_GR seqlevel:Chr5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... Good, your Chrs in peak_GR is all in Txdb ------------ annotating Peak using nearest gene mode begins >> preparing gene features information... 2024-08-16 12:51:26 AM >> finding nearest gene and calculating distance... 2024-08-16 12:51:27 AM >> dealing with gene strand ... 2024-08-16 12:51:28 AM >> merging all info together ... 2024-08-16 12:51:28 AM >> done 2024-08-16 12:51:28 AM It seems that there 1 genes have not been annotated by nearestGene mode >> checking seqlevels match... 2024-08-16 12:51:29 AM >> your peak_GR seqlevel:Chr5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... Good, your Chrs in peak_GR is all in Txdb >> checking seqlevels match... 2024-08-16 12:51:30 AM >> your peak_GR seqlevel:Chr5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... Good, your Chrs in peak_GR is all in Txdb >> some scan range may cross Chr bound, trimming... 2024-08-16 12:51:32 AM >> checking seqlevels match... 2024-08-16 12:51:33 AM >> your peak_GR seqlevel:Chr5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... Good, your Chrs in peak_GR is all in Txdb >> some scan range may cross Chr bound, trimming... 2024-08-16 12:51:34 AM Good, your two matrix colnames matchs >> calculating cor and pvalue, which may be time consuming... 2024-08-16 12:51:35 AM >> merging all info together... 2024-08-16 12:51:35 AM >> done 2024-08-16 12:51:35 AM >> checking seqlevels match... 2024-08-16 12:51:35 AM >> your peak_GR seqlevel:Chr5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... Good, your Chrs in peak_GR is all in Txdb >> using scanPromoter parameter to scan promoter for each gene... 2024-08-16 12:51:35 AM >> checking seqlevels match... 2024-08-16 12:51:36 AM >> your peak_GR seqlevel:Chr5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... Good, your Chrs in peak_GR is all in Txdb >> some scan range may cross Chr bound, trimming... 2024-08-16 12:51:37 AM >> there are 85 gene have scaned promoter >> using scanEnhancer parameter to scan Enhancer for each gene... 2024-08-16 12:51:37 AM >> checking seqlevels match... 2024-08-16 12:51:37 AM >> your peak_GR seqlevel:Chr5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... Good, your Chrs in peak_GR is all in Txdb >> some scan range may cross Chr bound, trimming... 2024-08-16 12:51:38 AM >> calculating cor and pvalue, which may be time consuming... 2024-08-16 12:51:38 AM >> merging all info together... 2024-08-16 12:51:38 AM >> done 2024-08-16 12:51:39 AM Good, your two matrix colnames matchs >> calculating cor and pvalue, which may be time consuming... 2024-08-16 12:51:39 AM >> merging all info together... 2024-08-16 12:51:39 AM >> done 2024-08-16 12:51:39 AM >> checking seqlevels match... 2024-08-16 12:51:39 AM >> your peak_GR seqlevel:Chr5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... Good, your Chrs in peak_GR is all in Txdb ------------ annotatePeak using geneScan mode begins >> preparing gene features information and scan region... 2024-08-16 12:51:39 AM >> some scan range may cross Chr bound, trimming... 2024-08-16 12:51:40 AM >> finding overlap peak in gene scan region... 2024-08-16 12:51:40 AM >> dealing with left peak not your gene scan region... 2024-08-16 12:51:40 AM >> merging two set peaks... 2024-08-16 12:51:40 AM >> calculating distance and dealing with gene strand... 2024-08-16 12:51:40 AM >> merging all info together ... 2024-08-16 12:51:40 AM >> done 2024-08-16 12:51:40 AM Good, your two matrix colnames matchs >> calculating cor and pvalue, which may be time consuming... 2024-08-16 12:51:42 AM >> merging all info together... 2024-08-16 12:51:42 AM >> done 2024-08-16 12:51:42 AM >> checking seqlevels match... 2024-08-16 12:51:42 AM >> your peak_GR seqlevel:Chr5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... Good, your Chrs in peak_GR is all in Txdb >> using scanPromoter parameter to scan promoter for each gene... 2024-08-16 12:51:42 AM >> checking seqlevels match... 2024-08-16 12:51:42 AM >> your peak_GR seqlevel:Chr5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... Good, your Chrs in peak_GR is all in Txdb >> some scan range may cross Chr bound, trimming... 2024-08-16 12:51:43 AM >> there are 85 gene have scaned promoter >> using scanEnhancer parameter to scan Enhancer for each gene... 2024-08-16 12:51:43 AM >> checking seqlevels match... 2024-08-16 12:51:43 AM >> your peak_GR seqlevel:Chr5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... Good, your Chrs in peak_GR is all in Txdb >> some scan range may cross Chr bound, trimming... 2024-08-16 12:51:44 AM >> calculating cor and pvalue, which may be time consuming... 2024-08-16 12:51:45 AM >> merging all info together... 2024-08-16 12:51:45 AM >> done 2024-08-16 12:51:45 AM Joining with `by = join_by(feature_id)` Joining with `by = join_by(feature_id)` `geom_smooth()` using formula = 'y ~ x' Joining with `by = join_by(feature_id)` Joining with `by = join_by(feature_id)` `geom_smooth()` using formula = 'y ~ x' [ FAIL 0 | WARN 0 | SKIP 0 | PASS 63 ] > > proc.time() user system elapsed 75.04 2.84 79.12
FindIT2.Rcheck/FindIT2-Ex.timings
name | user | system | elapsed | |
TF_target_database | 0 | 0 | 0 | |
calcRP_TFHit | 2.94 | 0.14 | 7.51 | |
calcRP_coverage | 0.04 | 0.02 | 0.06 | |
calcRP_region | 7.73 | 0.06 | 11.37 | |
enhancerPromoterCor | 3.10 | 0.22 | 3.33 | |
findIT_MARA | 0.59 | 0.06 | 0.67 | |
findIT_TFHit | 0.98 | 0.06 | 1.06 | |
findIT_TTPair | 0.16 | 0.05 | 0.20 | |
findIT_enrichFisher | 0.25 | 0.02 | 0.27 | |
findIT_enrichWilcox | 0.21 | 0.00 | 0.22 | |
findIT_regionRP | 6.94 | 0.17 | 7.11 | |
getAssocPairNumber | 1.47 | 0.08 | 1.54 | |
integrate_ChIP_RNA | 2.80 | 0.11 | 2.90 | |
integrate_replicates | 0 | 0 | 0 | |
jaccard_findIT_TTpair | 0.11 | 0.13 | 0.24 | |
jaccard_findIT_enrichFisher | 0.25 | 0.01 | 0.26 | |
loadPeakFile | 0.08 | 0.00 | 0.08 | |
mm_geneBound | 1.58 | 0.02 | 1.59 | |
mm_geneScan | 1.66 | 0.06 | 1.72 | |
mm_nearestGene | 1.50 | 0.09 | 1.59 | |
peakGeneCor | 3.37 | 0.17 | 3.55 | |
plot_annoDistance | 1.88 | 0.11 | 2.00 | |
plot_peakGeneAlias_summary | 1.75 | 0.08 | 1.84 | |
plot_peakGeneCor | 3.99 | 0.27 | 4.25 | |
test_geneSet | 0 | 0 | 0 | |