Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-23 12:07 -0400 (Tue, 23 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4816 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4605 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4549 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4560 |
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 729/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
FindIT2 1.15.1 (landing page) Guandong Shang
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: FindIT2 |
Version: 1.15.1 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings FindIT2_1.15.1.tar.gz |
StartedAt: 2025-09-23 07:18:26 -0000 (Tue, 23 Sep 2025) |
EndedAt: 2025-09-23 07:25:52 -0000 (Tue, 23 Sep 2025) |
EllapsedTime: 445.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: FindIT2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings FindIT2_1.15.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/FindIT2.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FindIT2/DESCRIPTION’ ... OK * this is package ‘FindIT2’ version ‘1.15.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 22 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘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 loading without being on the library search path ... 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 findIT_regionRP 8.449 0.196 8.667 calcRP_coverage 6.658 0.579 7.254 calcRP_region 6.112 0.120 6.248 * 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: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL FindIT2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘FindIT2’ ... ** this is package ‘FindIT2’ version ‘1.15.1’ ** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-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. > library(testthat) > library(FindIT2) Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 Loading required package: Seqinfo > if (!requireNamespace("TxDb.Athaliana.BioMart.plantsmart28")) { + stop("unable to load TxDb.Athaliana.BioMart.plantsmart28") + } Loading required namespace: TxDb.Athaliana.BioMart.plantsmart28 > > test_check("FindIT2") >> preparing gene features information... 2025-09-23 07:24:36 >> some scan range may cross Chr bound, trimming... 2025-09-23 07:24:37 >> preparing weight info... 2025-09-23 07:24:37 >> loading E50h_sampleChr5.bw info... 2025-09-23 07:24:37 ------------ >> extracting and calcluating Chr5 signal... 2025-09-23 07:24:37 >> dealing with Chr5 left gene signal... 2025-09-23 07:24:43 >> norming Chr5RP accoring to the whole Chr RP... 2025-09-23 07:24:43 >> merging all Chr RP together... 2025-09-23 07:24:43 >> done 2025-09-23 07:24:43 >> checking seqlevels match... 2025-09-23 07:24:43 >> 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... 2025-09-23 07:24:44 >> some scan range may cross Chr bound, trimming... 2025-09-23 07:24:45 >> finding overlap peak in gene scan region... 2025-09-23 07:24:45 >> dealing with left peak not your gene scan region... 2025-09-23 07:24:45 >> merging two set peaks... 2025-09-23 07:24:45 >> calculating distance and dealing with gene strand... 2025-09-23 07:24:45 >> merging all info together ... 2025-09-23 07:24:45 >> done 2025-09-23 07:24:45 >> calculating peakCenter to TSS using peak-gene pair... 2025-09-23 07:24:45 >> pre-filling 1356 noAssoc peak gene's RP with 0... 2025-09-23 07:24:46 >> calculating RP using centerToTSS and peak score2025-09-23 07:24:46 >> merging all info together 2025-09-23 07:24:49 >> done 2025-09-23 07:24:50 >> calculating peakCenter to TSS using peak-gene pair... 2025-09-23 07:24:50 >> pre-filling 1356 noAssoc peak gene's RP with 0... 2025-09-23 07:24:52 >> calculating RP using centerToTSS and peak score2025-09-23 07:24:52 >> merging all info together 2025-09-23 07:24:55 >> done 2025-09-23 07:24:56 >> checking seqlevels match... 2025-09-23 07:24:56 >> 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... 2025-09-23 07:24:56 >> some scan range may cross Chr bound, trimming... 2025-09-23 07:24:57 >> finding overlap peak in gene scan region... 2025-09-23 07:24:57 >> dealing with left peak not your gene scan region... 2025-09-23 07:24:57 >> merging two set peaks... 2025-09-23 07:24:58 >> calculating distance and dealing with gene strand... 2025-09-23 07:24:58 >> merging all info together ... 2025-09-23 07:24:58 >> done 2025-09-23 07:24:58 >> calculating peakCenter to TSS using peak-gene pair... 2025-09-23 07:24:58 >> calculating RP using centerToTSS and TF hit 2025-09-23 07:24:58 >> merging all info together 2025-09-23 07:24:59 >> done 2025-09-23 07:24:59 >> calculating peakCenter to TSS using peak-gene pair... 2025-09-23 07:24:59 >> calculating RP using centerToTSS and TF hit 2025-09-23 07:24:59 >> merging all info together 2025-09-23 07:24:59 >> done 2025-09-23 07:25:00 >> checking seqlevels match... 2025-09-23 07:25:01 >> 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... 2025-09-23 07:25:01 >> some scan range may cross Chr bound, trimming... 2025-09-23 07:25:01 >> finding overlap peak in gene scan region... 2025-09-23 07:25:02 >> dealing with left peak not your gene scan region... 2025-09-23 07:25:02 >> merging two set peaks... 2025-09-23 07:25:02 >> calculating distance and dealing with gene strand... 2025-09-23 07:25:02 >> merging all info together ... 2025-09-23 07:25:02 >> done 2025-09-23 07:25:02 >> calculating peakCenter to TSS using peak-gene pair... 2025-09-23 07:25:02 >> pre-filling 1356 noAssoc peak gene's RP with 0... 2025-09-23 07:25:03 >> calculating RP using centerToTSS and peak score2025-09-23 07:25:03 >> merging all info together 2025-09-23 07:25:06 >> done 2025-09-23 07:25:06 >> extracting RP info from regionRP... 2025-09-23 07:25:07 >> dealing with TF_GR_databse... 2025-09-23 07:25:07 >> calculating percent and p-value... 2025-09-23 07:25:07 >> dealing withE5_0h_R1... 2025-09-23 07:25:07 >> dealing withE5_0h_R2... 2025-09-23 07:25:07 >> dealing withE5_4h_R1... 2025-09-23 07:25:07 >> dealing withE5_4h_R2... 2025-09-23 07:25:07 >> dealing withE5_8h_R1... 2025-09-23 07:25:07 >> dealing withE5_8h_R2... 2025-09-23 07:25:07 >> dealing withE5_16h_R1... 2025-09-23 07:25:07 >> dealing withE5_16h_R2... 2025-09-23 07:25:08 >> dealing withE5_24h_R1... 2025-09-23 07:25:08 >> dealing withE5_24h_R2... 2025-09-23 07:25:08 >> dealing withE5_48h_R1... 2025-09-23 07:25:08 >> dealing withE5_48h_R2... 2025-09-23 07:25:08 >> dealing withE5_48h_R3... 2025-09-23 07:25:08 >> dealing withE5_72h_R1... 2025-09-23 07:25:08 >> dealing withE5_72h_R2... 2025-09-23 07:25:08 >> dealing withE5_72h_R3... 2025-09-23 07:25:08 >> merging all info together... 2025-09-23 07:25:08 >> done 2025-09-23 07:25:08 >> preparing gene features information... 2025-09-23 07:25:09 >> some scan range may cross Chr bound, trimming... 2025-09-23 07:25:09 >> calculating p-value for each TF, which may be time consuming... 2025-09-23 07:25:09 >> merging all info together... 2025-09-23 07:25:10 >> done 2025-09-23 07:25:10 >> dealing with TF_GR_database... 2025-09-23 07:25:10 >> calculating coef and converting into z-score using INT... 2025-09-23 07:25:10 >> dealing with E5_0h_R1... 2025-09-23 07:25:10 >> dealing with E5_0h_R2... 2025-09-23 07:25:10 >> dealing with E5_4h_R1... 2025-09-23 07:25:10 >> dealing with E5_4h_R2... 2025-09-23 07:25:10 >> dealing with E5_8h_R1... 2025-09-23 07:25:10 >> dealing with E5_8h_R2... 2025-09-23 07:25:11 >> dealing with E5_16h_R1... 2025-09-23 07:25:11 >> dealing with E5_16h_R2... 2025-09-23 07:25:11 >> dealing with E5_24h_R1... 2025-09-23 07:25:11 >> dealing with E5_24h_R2... 2025-09-23 07:25:11 >> dealing with E5_48h_R1... 2025-09-23 07:25:11 >> dealing with E5_48h_R2... 2025-09-23 07:25:11 >> dealing with E5_48h_R3... 2025-09-23 07:25:11 >> dealing with E5_72h_R1... 2025-09-23 07:25:11 >> dealing with E5_72h_R2... 2025-09-23 07:25:11 >> dealing with E5_72h_R3... 2025-09-23 07:25:12 >> merging all info together... 2025-09-23 07:25:12 >> done 2025-09-23 07:25:12 >> checking seqlevels match... 2025-09-23 07:25:12 >> 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... 2025-09-23 07:25:12 >> some scan range may cross Chr bound, trimming... 2025-09-23 07:25:13 >> finding overlap peak in gene scan region... 2025-09-23 07:25:13 >> dealing with left peak not your gene scan region... 2025-09-23 07:25:13 >> merging two set peaks... 2025-09-23 07:25:13 >> calculating distance and dealing with gene strand... 2025-09-23 07:25:13 >> merging all info together ... 2025-09-23 07:25:13 >> done 2025-09-23 07:25:13 >> calculating peakCenter to TSS using peak-gene pair... 2025-09-23 07:25:13 >> calculating RP using centerToTSS and TF hit 2025-09-23 07:25:14 >> merging all info together 2025-09-23 07:25:14 >> done 2025-09-23 07:25:14 >> checking seqlevels match... 2025-09-23 07:25:15 >> your peak_GR seqlevel:5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... >> checking seqlevels match... 2025-09-23 07:25:15 >> your peak_GR seqlevel:Chr5 Chr6... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... >> checking seqlevels match... 2025-09-23 07:25:19 >> 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... 2025-09-23 07:25:19 >> 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... 2025-09-23 07:25:19 >> finding nearest gene and calculating distance... 2025-09-23 07:25:20 >> dealing with gene strand ... 2025-09-23 07:25:20 >> merging all info together ... 2025-09-23 07:25:20 >> done 2025-09-23 07:25:20 >> checking seqlevels match... 2025-09-23 07:25:20 >> 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... 2025-09-23 07:25:20 >> 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... 2025-09-23 07:25:21 >> finding nearest gene and calculating distance... 2025-09-23 07:25:21 >> dealing with gene strand ... 2025-09-23 07:25:22 >> merging all info together ... 2025-09-23 07:25:22 >> done 2025-09-23 07:25:22 >> checking seqlevels match... 2025-09-23 07:25:23 >> 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... 2025-09-23 07:25:23 >> 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... 2025-09-23 07:25:23 >> finding nearest gene and calculating distance... 2025-09-23 07:25:24 >> dealing with gene strand ... 2025-09-23 07:25:24 >> merging all info together ... 2025-09-23 07:25:24 >> done 2025-09-23 07:25:24 >> checking seqlevels match... 2025-09-23 07:25:25 >> 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... 2025-09-23 07:25:25 >> 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... 2025-09-23 07:25:25 >> finding nearest gene and calculating distance... 2025-09-23 07:25:26 >> dealing with gene strand ... 2025-09-23 07:25:26 >> merging all info together ... 2025-09-23 07:25:26 >> done 2025-09-23 07:25:26 It seems that there 1 genes have not been annotated by nearestGene mode >> checking seqlevels match... 2025-09-23 07:25:27 >> 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... 2025-09-23 07:25:27 >> 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... 2025-09-23 07:25:27 >> finding nearest gene and calculating distance... 2025-09-23 07:25:28 >> dealing with gene strand ... 2025-09-23 07:25:28 >> merging all info together ... 2025-09-23 07:25:28 >> done 2025-09-23 07:25:29 It seems that there 1 genes have not been annotated by nearestGene mode >> checking seqlevels match... 2025-09-23 07:25:30 >> 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... 2025-09-23 07:25:31 >> 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... 2025-09-23 07:25:32 >> checking seqlevels match... 2025-09-23 07:25:34 >> 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... 2025-09-23 07:25:35 Good, your two matrix colnames matchs >> calculating cor and pvalue, which may be time consuming... 2025-09-23 07:25:36 >> merging all info together... 2025-09-23 07:25:36 >> done 2025-09-23 07:25:37 >> checking seqlevels match... 2025-09-23 07:25:37 >> 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... 2025-09-23 07:25:37 >> checking seqlevels match... 2025-09-23 07:25:37 >> 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... 2025-09-23 07:25:38 >> there are 85 gene have scaned promoter >> using scanEnhancer parameter to scan Enhancer for each gene... 2025-09-23 07:25:38 >> checking seqlevels match... 2025-09-23 07:25:38 >> 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... 2025-09-23 07:25:39 >> calculating cor and pvalue, which may be time consuming... 2025-09-23 07:25:39 >> merging all info together... 2025-09-23 07:25:39 >> done 2025-09-23 07:25:39 Good, your two matrix colnames matchs >> calculating cor and pvalue, which may be time consuming... 2025-09-23 07:25:40 >> merging all info together... 2025-09-23 07:25:40 >> done 2025-09-23 07:25:40 >> checking seqlevels match... 2025-09-23 07:25:40 >> 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... 2025-09-23 07:25:40 >> some scan range may cross Chr bound, trimming... 2025-09-23 07:25:41 >> finding overlap peak in gene scan region... 2025-09-23 07:25:41 >> dealing with left peak not your gene scan region... 2025-09-23 07:25:41 >> merging two set peaks... 2025-09-23 07:25:41 >> calculating distance and dealing with gene strand... 2025-09-23 07:25:41 >> merging all info together ... 2025-09-23 07:25:41 >> done 2025-09-23 07:25:41 Good, your two matrix colnames matchs >> calculating cor and pvalue, which may be time consuming... 2025-09-23 07:25:43 >> merging all info together... 2025-09-23 07:25:43 >> done 2025-09-23 07:25:43 >> checking seqlevels match... 2025-09-23 07:25:43 >> 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... 2025-09-23 07:25:43 >> checking seqlevels match... 2025-09-23 07:25:43 >> 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... 2025-09-23 07:25:44 >> there are 85 gene have scaned promoter >> using scanEnhancer parameter to scan Enhancer for each gene... 2025-09-23 07:25:44 >> checking seqlevels match... 2025-09-23 07:25:44 >> 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... 2025-09-23 07:25:45 >> calculating cor and pvalue, which may be time consuming... 2025-09-23 07:25:46 >> merging all info together... 2025-09-23 07:25:46 >> done 2025-09-23 07:25:46 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 65 ] > > proc.time() user system elapsed 85.942 1.622 87.780
FindIT2.Rcheck/FindIT2-Ex.timings
name | user | system | elapsed | |
TF_target_database | 0 | 0 | 0 | |
calcRP_TFHit | 4.091 | 0.163 | 4.426 | |
calcRP_coverage | 6.658 | 0.579 | 7.254 | |
calcRP_region | 6.112 | 0.120 | 6.248 | |
enhancerPromoterCor | 3.262 | 0.040 | 3.309 | |
findIT_MARA | 0.585 | 0.007 | 0.595 | |
findIT_TFHit | 1.122 | 0.000 | 1.125 | |
findIT_TTPair | 0.095 | 0.000 | 0.095 | |
findIT_enrichFisher | 0.215 | 0.000 | 0.215 | |
findIT_enrichWilcox | 0.244 | 0.003 | 0.249 | |
findIT_regionRP | 8.449 | 0.196 | 8.667 | |
getAssocPairNumber | 1.472 | 0.012 | 1.488 | |
integrate_ChIP_RNA | 2.587 | 0.036 | 2.630 | |
integrate_replicates | 0.003 | 0.000 | 0.003 | |
jaccard_findIT_TTpair | 0.129 | 0.004 | 0.134 | |
jaccard_findIT_enrichFisher | 0.282 | 0.000 | 0.283 | |
loadPeakFile | 0.084 | 0.000 | 0.084 | |
mm_geneBound | 1.539 | 0.020 | 1.564 | |
mm_geneScan | 1.528 | 0.000 | 1.532 | |
mm_nearestGene | 1.381 | 0.016 | 1.400 | |
peakGeneCor | 3.121 | 0.024 | 3.154 | |
plot_annoDistance | 2.263 | 0.012 | 2.282 | |
plot_peakGeneAlias_summary | 1.752 | 0.012 | 1.773 | |
plot_peakGeneCor | 4.353 | 0.016 | 4.381 | |
test_geneSet | 0.001 | 0.000 | 0.001 | |