Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:46 -0400 (Tue, 27 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" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: FindIT2 |
Version: 1.11.0 |
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_1.11.0.tar.gz |
StartedAt: 2024-08-27 04:52:23 -0000 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 05:00:11 -0000 (Tue, 27 Aug 2024) |
EllapsedTime: 468.0 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_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/FindIT2.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * 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 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 calcRP_coverage 9.740 0.387 10.146 findIT_regionRP 8.482 0.039 8.540 calcRP_region 6.675 0.072 6.759 plot_peakGeneCor 5.292 0.108 5.411 calcRP_TFHit 4.852 0.152 5.215 * 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-4.4.1/site-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) -- "Race for Your Life" Copyright (C) 2024 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 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 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") >> preparing gene features information... 2024-08-27 04:58:51 >> some scan range may cross Chr bound, trimming... 2024-08-27 04:58:52 >> preparing weight info... 2024-08-27 04:58:52 >> loading E50h_sampleChr5.bw info... 2024-08-27 04:58:52 ------------ >> extracting and calcluating Chr5 signal... 2024-08-27 04:58:52 >> dealing with Chr5 left gene signal... 2024-08-27 04:59:01 >> norming Chr5RP accoring to the whole Chr RP... 2024-08-27 04:59:01 >> merging all Chr RP together... 2024-08-27 04:59:01 >> done 2024-08-27 04:59:01 >> checking seqlevels match... 2024-08-27 04:59:01 >> 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... 2024-08-27 04:59:02 >> some scan range may cross Chr bound, trimming... 2024-08-27 04:59:03 >> finding overlap peak in gene scan region... 2024-08-27 04:59:03 >> dealing with left peak not your gene scan region... 2024-08-27 04:59:03 >> merging two set peaks... 2024-08-27 04:59:03 >> calculating distance and dealing with gene strand... 2024-08-27 04:59:03 >> merging all info together ... 2024-08-27 04:59:03 >> done 2024-08-27 04:59:03 >> calculating peakCenter to TSS using peak-gene pair... 2024-08-27 04:59:03 >> pre-filling 1356 noAssoc peak gene's RP with 0... 2024-08-27 04:59:04 >> calculating RP using centerToTSS and peak score2024-08-27 04:59:04 >> merging all info together 2024-08-27 04:59:07 >> done 2024-08-27 04:59:08 >> calculating peakCenter to TSS using peak-gene pair... 2024-08-27 04:59:08 >> pre-filling 1356 noAssoc peak gene's RP with 0... 2024-08-27 04:59:10 >> calculating RP using centerToTSS and peak score2024-08-27 04:59:10 >> merging all info together 2024-08-27 04:59:13 >> done 2024-08-27 04:59:14 >> checking seqlevels match... 2024-08-27 04:59:14 >> 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... 2024-08-27 04:59:14 >> some scan range may cross Chr bound, trimming... 2024-08-27 04:59:15 >> finding overlap peak in gene scan region... 2024-08-27 04:59:15 >> dealing with left peak not your gene scan region... 2024-08-27 04:59:15 >> merging two set peaks... 2024-08-27 04:59:16 >> calculating distance and dealing with gene strand... 2024-08-27 04:59:16 >> merging all info together ... 2024-08-27 04:59:16 >> done 2024-08-27 04:59:16 >> calculating peakCenter to TSS using peak-gene pair... 2024-08-27 04:59:16 >> calculating RP using centerToTSS and TF hit 2024-08-27 04:59:17 >> merging all info together 2024-08-27 04:59:17 >> done 2024-08-27 04:59:17 >> calculating peakCenter to TSS using peak-gene pair... 2024-08-27 04:59:17 >> calculating RP using centerToTSS and TF hit 2024-08-27 04:59:19 >> merging all info together 2024-08-27 04:59:19 >> done 2024-08-27 04:59:19 >> checking seqlevels match... 2024-08-27 04:59:20 >> 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 ------------ annotatePeak using geneScan mode begins >> preparing gene features information and scan region... 2024-08-27 04:59:20 >> some scan range may cross Chr bound, trimming... 2024-08-27 04:59:21 >> finding overlap peak in gene scan region... 2024-08-27 04:59:21 >> dealing with left peak not your gene scan region... 2024-08-27 04:59:21 >> merging two set peaks... 2024-08-27 04:59:21 >> calculating distance and dealing with gene strand... 2024-08-27 04:59:21 >> merging all info together ... 2024-08-27 04:59:21 >> done 2024-08-27 04:59:21 >> calculating peakCenter to TSS using peak-gene pair... 2024-08-27 04:59:21 >> pre-filling 1356 noAssoc peak gene's RP with 0... 2024-08-27 04:59:22 >> calculating RP using centerToTSS and peak score2024-08-27 04:59:22 >> merging all info together 2024-08-27 04:59:25 >> done 2024-08-27 04:59:26 >> extracting RP info from regionRP... 2024-08-27 04:59:27 >> dealing with TF_GR_databse... 2024-08-27 04:59:27 >> calculating percent and p-value... 2024-08-27 04:59:27 >> dealing withE5_0h_R1... 2024-08-27 04:59:27 >> dealing withE5_0h_R2... 2024-08-27 04:59:27 >> dealing withE5_4h_R1... 2024-08-27 04:59:27 >> dealing withE5_4h_R2... 2024-08-27 04:59:27 >> dealing withE5_8h_R1... 2024-08-27 04:59:27 >> dealing withE5_8h_R2... 2024-08-27 04:59:27 >> dealing withE5_16h_R1... 2024-08-27 04:59:27 >> dealing withE5_16h_R2... 2024-08-27 04:59:27 >> dealing withE5_24h_R1... 2024-08-27 04:59:27 >> dealing withE5_24h_R2... 2024-08-27 04:59:27 >> dealing withE5_48h_R1... 2024-08-27 04:59:27 >> dealing withE5_48h_R2... 2024-08-27 04:59:27 >> dealing withE5_48h_R3... 2024-08-27 04:59:28 >> dealing withE5_72h_R1... 2024-08-27 04:59:28 >> dealing withE5_72h_R2... 2024-08-27 04:59:28 >> dealing withE5_72h_R3... 2024-08-27 04:59:28 >> merging all info together... 2024-08-27 04:59:28 >> done 2024-08-27 04:59:28 >> preparing gene features information... 2024-08-27 04:59:28 >> some scan range may cross Chr bound, trimming... 2024-08-27 04:59:29 >> calculating p-value for each TF, which may be time consuming... 2024-08-27 04:59:29 >> merging all info together... 2024-08-27 04:59:29 >> done 2024-08-27 04:59:29 >> dealing with TF_GR_database... 2024-08-27 04:59:29 >> calculating coef and converting into z-score using INT... 2024-08-27 04:59:30 >> dealing with E5_0h_R1... 2024-08-27 04:59:30 >> dealing with E5_0h_R2... 2024-08-27 04:59:30 >> dealing with E5_4h_R1... 2024-08-27 04:59:30 >> dealing with E5_4h_R2... 2024-08-27 04:59:30 >> dealing with E5_8h_R1... 2024-08-27 04:59:30 >> dealing with E5_8h_R2... 2024-08-27 04:59:30 >> dealing with E5_16h_R1... 2024-08-27 04:59:30 >> dealing with E5_16h_R2... 2024-08-27 04:59:30 >> dealing with E5_24h_R1... 2024-08-27 04:59:31 >> dealing with E5_24h_R2... 2024-08-27 04:59:31 >> dealing with E5_48h_R1... 2024-08-27 04:59:31 >> dealing with E5_48h_R2... 2024-08-27 04:59:31 >> dealing with E5_48h_R3... 2024-08-27 04:59:31 >> dealing with E5_72h_R1... 2024-08-27 04:59:31 >> dealing with E5_72h_R2... 2024-08-27 04:59:31 >> dealing with E5_72h_R3... 2024-08-27 04:59:31 >> merging all info together... 2024-08-27 04:59:31 >> done 2024-08-27 04:59:32 >> checking seqlevels match... 2024-08-27 04:59:32 >> 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... 2024-08-27 04:59:32 >> some scan range may cross Chr bound, trimming... 2024-08-27 04:59:33 >> finding overlap peak in gene scan region... 2024-08-27 04:59:33 >> dealing with left peak not your gene scan region... 2024-08-27 04:59:33 >> merging two set peaks... 2024-08-27 04:59:33 >> calculating distance and dealing with gene strand... 2024-08-27 04:59:33 >> merging all info together ... 2024-08-27 04:59:33 >> done 2024-08-27 04:59:33 >> calculating peakCenter to TSS using peak-gene pair... 2024-08-27 04:59:33 >> calculating RP using centerToTSS and TF hit 2024-08-27 04:59:34 >> merging all info together 2024-08-27 04:59:34 >> done 2024-08-27 04:59:34 >> checking seqlevels match... 2024-08-27 04:59:35 >> your peak_GR seqlevel:5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... >> checking seqlevels match... 2024-08-27 04:59:35 >> your peak_GR seqlevel:Chr5 Chr6... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... >> checking seqlevels match... 2024-08-27 04:59:40 >> 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 >> checking seqlevels match... 2024-08-27 04:59:40 >> 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 ------------ annotating Peak using nearest gene mode begins >> preparing gene features information... 2024-08-27 04:59:40 >> finding nearest gene and calculating distance... 2024-08-27 04:59:41 >> dealing with gene strand ... 2024-08-27 04:59:41 >> merging all info together ... 2024-08-27 04:59:41 >> done 2024-08-27 04:59:41 >> checking seqlevels match... 2024-08-27 04:59:41 >> 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... 2024-08-27 04:59:42 >> 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... 2024-08-27 04:59:42 >> finding nearest gene and calculating distance... 2024-08-27 04:59:43 >> dealing with gene strand ... 2024-08-27 04:59:43 >> merging all info together ... 2024-08-27 04:59:43 >> done 2024-08-27 04:59:43 >> checking seqlevels match... 2024-08-27 04:59:44 >> 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 >> checking seqlevels match... 2024-08-27 04:59:44 >> 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 ------------ annotating Peak using nearest gene mode begins >> preparing gene features information... 2024-08-27 04:59:44 >> finding nearest gene and calculating distance... 2024-08-27 04:59:45 >> dealing with gene strand ... 2024-08-27 04:59:45 >> merging all info together ... 2024-08-27 04:59:45 >> done 2024-08-27 04:59:45 >> checking seqlevels match... 2024-08-27 04:59:46 >> 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... 2024-08-27 04:59:46 >> 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... 2024-08-27 04:59:46 >> finding nearest gene and calculating distance... 2024-08-27 04:59:47 >> dealing with gene strand ... 2024-08-27 04:59:47 >> merging all info together ... 2024-08-27 04:59:47 >> done 2024-08-27 04:59:47 It seems that there 1 genes have not been annotated by nearestGene mode >> checking seqlevels match... 2024-08-27 04:59:48 >> 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... 2024-08-27 04:59:49 >> 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... 2024-08-27 04:59:49 >> finding nearest gene and calculating distance... 2024-08-27 04:59:50 >> dealing with gene strand ... 2024-08-27 04:59:50 >> merging all info together ... 2024-08-27 04:59:50 >> done 2024-08-27 04:59:50 It seems that there 1 genes have not been annotated by nearestGene mode >> checking seqlevels match... 2024-08-27 04:59:51 >> 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... 2024-08-27 04:59:52 >> 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... 2024-08-27 04:59:53 >> checking seqlevels match... 2024-08-27 04:59:54 >> 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... 2024-08-27 04:59:55 Good, your two matrix colnames matchs >> calculating cor and pvalue, which may be time consuming... 2024-08-27 04:59:57 >> merging all info together... 2024-08-27 04:59:57 >> done 2024-08-27 04:59:57 >> checking seqlevels match... 2024-08-27 04:59:57 >> 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... 2024-08-27 04:59:57 >> checking seqlevels match... 2024-08-27 04:59:57 >> 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... 2024-08-27 04:59:58 >> there are 85 gene have scaned promoter >> using scanEnhancer parameter to scan Enhancer for each gene... 2024-08-27 04:59:59 >> checking seqlevels match... 2024-08-27 04:59:59 >> 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... 2024-08-27 05:00:00 >> calculating cor and pvalue, which may be time consuming... 2024-08-27 05:00:00 >> merging all info together... 2024-08-27 05:00:00 >> done 2024-08-27 05:00:00 Good, your two matrix colnames matchs >> calculating cor and pvalue, which may be time consuming... 2024-08-27 05:00:00 >> merging all info together... 2024-08-27 05:00:00 >> done 2024-08-27 05:00:01 >> checking seqlevels match... 2024-08-27 05:00:01 >> 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... 2024-08-27 05:00:01 >> some scan range may cross Chr bound, trimming... 2024-08-27 05:00:02 >> finding overlap peak in gene scan region... 2024-08-27 05:00:02 >> dealing with left peak not your gene scan region... 2024-08-27 05:00:02 >> merging two set peaks... 2024-08-27 05:00:02 >> calculating distance and dealing with gene strand... 2024-08-27 05:00:02 >> merging all info together ... 2024-08-27 05:00:02 >> done 2024-08-27 05:00:02 Good, your two matrix colnames matchs >> calculating cor and pvalue, which may be time consuming... 2024-08-27 05:00:04 >> merging all info together... 2024-08-27 05:00:04 >> done 2024-08-27 05:00:04 >> checking seqlevels match... 2024-08-27 05:00:04 >> 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... 2024-08-27 05:00:04 >> checking seqlevels match... 2024-08-27 05:00:04 >> 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... 2024-08-27 05:00:05 >> there are 85 gene have scaned promoter >> using scanEnhancer parameter to scan Enhancer for each gene... 2024-08-27 05:00:05 >> checking seqlevels match... 2024-08-27 05:00:06 >> 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... 2024-08-27 05:00:07 >> calculating cor and pvalue, which may be time consuming... 2024-08-27 05:00:07 >> merging all info together... 2024-08-27 05:00:07 >> done 2024-08-27 05:00:07 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 91.569 2.083 93.836
FindIT2.Rcheck/FindIT2-Ex.timings
name | user | system | elapsed | |
TF_target_database | 0.000 | 0.000 | 0.001 | |
calcRP_TFHit | 4.852 | 0.152 | 5.215 | |
calcRP_coverage | 9.740 | 0.387 | 10.146 | |
calcRP_region | 6.675 | 0.072 | 6.759 | |
enhancerPromoterCor | 3.636 | 0.020 | 3.662 | |
findIT_MARA | 0.599 | 0.000 | 0.600 | |
findIT_TFHit | 1.375 | 0.008 | 1.385 | |
findIT_TTPair | 0.099 | 0.000 | 0.099 | |
findIT_enrichFisher | 0.217 | 0.000 | 0.217 | |
findIT_enrichWilcox | 0.239 | 0.000 | 0.239 | |
findIT_regionRP | 8.482 | 0.039 | 8.540 | |
getAssocPairNumber | 1.658 | 0.004 | 1.666 | |
integrate_ChIP_RNA | 2.905 | 0.016 | 2.928 | |
integrate_replicates | 0.002 | 0.000 | 0.002 | |
jaccard_findIT_TTpair | 0.163 | 0.000 | 0.163 | |
jaccard_findIT_enrichFisher | 0.275 | 0.000 | 0.276 | |
loadPeakFile | 0.079 | 0.000 | 0.079 | |
mm_geneBound | 1.738 | 0.008 | 1.748 | |
mm_geneScan | 1.754 | 0.008 | 1.765 | |
mm_nearestGene | 2.705 | 0.045 | 2.756 | |
peakGeneCor | 3.361 | 0.004 | 3.373 | |
plot_annoDistance | 2.087 | 0.004 | 2.095 | |
plot_peakGeneAlias_summary | 1.904 | 0.000 | 1.908 | |
plot_peakGeneCor | 5.292 | 0.108 | 5.411 | |
test_geneSet | 0 | 0 | 0 | |