Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 709/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
FindIT2 1.13.0 (landing page) Guandong Shang
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 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: 1.13.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings FindIT2_1.13.0.tar.gz |
StartedAt: 2024-12-23 22:02:34 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 22:09:02 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 387.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: FindIT2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings FindIT2_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/FindIT2.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘FindIT2/DESCRIPTION’ ... OK * this is package ‘FindIT2’ version ‘1.13.0’ * 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 5.299 0.088 5.387 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
FindIT2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL FindIT2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > 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: 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... 2024-12-23 22:07:14 >> some scan range may cross Chr bound, trimming... 2024-12-23 22:07:15 >> preparing weight info... 2024-12-23 22:07:15 >> loading E50h_sampleChr5.bw info... 2024-12-23 22:07:15 ------------ >> extracting and calcluating Chr5 signal... 2024-12-23 22:07:15 >> dealing with Chr5 left gene signal... 2024-12-23 22:07:18 >> norming Chr5RP accoring to the whole Chr RP... 2024-12-23 22:07:18 >> merging all Chr RP together... 2024-12-23 22:07:18 >> done 2024-12-23 22:07:18 >> checking seqlevels match... 2024-12-23 22:07:18 >> 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... 2024-12-23 22:07:18 >> some scan range may cross Chr bound, trimming... 2024-12-23 22:07:19 >> finding overlap peak in gene scan region... 2024-12-23 22:07:19 >> dealing with left peak not your gene scan region... 2024-12-23 22:07:19 >> merging two set peaks... 2024-12-23 22:07:19 >> calculating distance and dealing with gene strand... 2024-12-23 22:07:19 >> merging all info together ... 2024-12-23 22:07:19 >> done 2024-12-23 22:07:19 >> calculating peakCenter to TSS using peak-gene pair... 2024-12-23 22:07:19 >> pre-filling 1356 noAssoc peak gene's RP with 0... 2024-12-23 22:07:20 >> calculating RP using centerToTSS and peak score2024-12-23 22:07:20 >> merging all info together 2024-12-23 22:07:22 >> done 2024-12-23 22:07:23 >> calculating peakCenter to TSS using peak-gene pair... 2024-12-23 22:07:23 >> pre-filling 1356 noAssoc peak gene's RP with 0... 2024-12-23 22:07:23 >> calculating RP using centerToTSS and peak score2024-12-23 22:07:23 >> merging all info together 2024-12-23 22:07:27 >> done 2024-12-23 22:07:27 >> checking seqlevels match... 2024-12-23 22:07:27 >> 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 ------------ annotatePeak using geneScan mode begins >> preparing gene features information and scan region... 2024-12-23 22:07:27 >> some scan range may cross Chr bound, trimming... 2024-12-23 22:07:28 >> finding overlap peak in gene scan region... 2024-12-23 22:07:28 >> dealing with left peak not your gene scan region... 2024-12-23 22:07:28 >> merging two set peaks... 2024-12-23 22:07:28 >> calculating distance and dealing with gene strand... 2024-12-23 22:07:28 >> merging all info together ... 2024-12-23 22:07:28 >> done 2024-12-23 22:07:28 >> calculating peakCenter to TSS using peak-gene pair... 2024-12-23 22:07:28 >> calculating RP using centerToTSS and TF hit 2024-12-23 22:07:29 >> merging all info together 2024-12-23 22:07:29 >> done 2024-12-23 22:07:29 >> calculating peakCenter to TSS using peak-gene pair... 2024-12-23 22:07:29 >> calculating RP using centerToTSS and TF hit 2024-12-23 22:07:30 >> merging all info together 2024-12-23 22:07:30 >> done 2024-12-23 22:07:30 >> checking seqlevels match... 2024-12-23 22:07:30 >> 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 ------------ annotatePeak using geneScan mode begins >> preparing gene features information and scan region... 2024-12-23 22:07:30 >> some scan range may cross Chr bound, trimming... 2024-12-23 22:07:31 >> finding overlap peak in gene scan region... 2024-12-23 22:07:31 >> dealing with left peak not your gene scan region... 2024-12-23 22:07:31 >> merging two set peaks... 2024-12-23 22:07:31 >> calculating distance and dealing with gene strand... 2024-12-23 22:07:31 >> merging all info together ... 2024-12-23 22:07:31 >> done 2024-12-23 22:07:31 >> calculating peakCenter to TSS using peak-gene pair... 2024-12-23 22:07:31 >> pre-filling 1356 noAssoc peak gene's RP with 0... 2024-12-23 22:07:32 >> calculating RP using centerToTSS and peak score2024-12-23 22:07:32 >> merging all info together 2024-12-23 22:07:34 >> done 2024-12-23 22:07:34 >> extracting RP info from regionRP... 2024-12-23 22:07:35 >> dealing with TF_GR_databse... 2024-12-23 22:07:35 >> calculating percent and p-value... 2024-12-23 22:07:35 >> dealing withE5_0h_R1... 2024-12-23 22:07:35 >> dealing withE5_0h_R2... 2024-12-23 22:07:35 >> dealing withE5_4h_R1... 2024-12-23 22:07:35 >> dealing withE5_4h_R2... 2024-12-23 22:07:35 >> dealing withE5_8h_R1... 2024-12-23 22:07:35 >> dealing withE5_8h_R2... 2024-12-23 22:07:35 >> dealing withE5_16h_R1... 2024-12-23 22:07:35 >> dealing withE5_16h_R2... 2024-12-23 22:07:35 >> dealing withE5_24h_R1... 2024-12-23 22:07:35 >> dealing withE5_24h_R2... 2024-12-23 22:07:35 >> dealing withE5_48h_R1... 2024-12-23 22:07:35 >> dealing withE5_48h_R2... 2024-12-23 22:07:35 >> dealing withE5_48h_R3... 2024-12-23 22:07:35 >> dealing withE5_72h_R1... 2024-12-23 22:07:35 >> dealing withE5_72h_R2... 2024-12-23 22:07:35 >> dealing withE5_72h_R3... 2024-12-23 22:07:35 >> merging all info together... 2024-12-23 22:07:35 >> done 2024-12-23 22:07:35 >> preparing gene features information... 2024-12-23 22:07:36 >> some scan range may cross Chr bound, trimming... 2024-12-23 22:07:36 >> calculating p-value for each TF, which may be time consuming... 2024-12-23 22:07:36 >> merging all info together... 2024-12-23 22:07:36 >> done 2024-12-23 22:07:36 >> dealing with TF_GR_database... 2024-12-23 22:07:36 >> calculating coef and converting into z-score using INT... 2024-12-23 22:07:37 >> dealing with E5_0h_R1... 2024-12-23 22:07:37 >> dealing with E5_0h_R2... 2024-12-23 22:07:37 >> dealing with E5_4h_R1... 2024-12-23 22:07:37 >> dealing with E5_4h_R2... 2024-12-23 22:07:37 >> dealing with E5_8h_R1... 2024-12-23 22:07:37 >> dealing with E5_8h_R2... 2024-12-23 22:07:37 >> dealing with E5_16h_R1... 2024-12-23 22:07:37 >> dealing with E5_16h_R2... 2024-12-23 22:07:37 >> dealing with E5_24h_R1... 2024-12-23 22:07:37 >> dealing with E5_24h_R2... 2024-12-23 22:07:37 >> dealing with E5_48h_R1... 2024-12-23 22:07:37 >> dealing with E5_48h_R2... 2024-12-23 22:07:37 >> dealing with E5_48h_R3... 2024-12-23 22:07:37 >> dealing with E5_72h_R1... 2024-12-23 22:07:37 >> dealing with E5_72h_R2... 2024-12-23 22:07:37 >> dealing with E5_72h_R3... 2024-12-23 22:07:37 >> merging all info together... 2024-12-23 22:07:38 >> done 2024-12-23 22:07:38 >> checking seqlevels match... 2024-12-23 22:07:38 >> 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 ------------ annotatePeak using geneScan mode begins >> preparing gene features information and scan region... 2024-12-23 22:07:38 >> some scan range may cross Chr bound, trimming... 2024-12-23 22:07:39 >> finding overlap peak in gene scan region... 2024-12-23 22:07:39 >> dealing with left peak not your gene scan region... 2024-12-23 22:07:39 >> merging two set peaks... 2024-12-23 22:07:39 >> calculating distance and dealing with gene strand... 2024-12-23 22:07:39 >> merging all info together ... 2024-12-23 22:07:39 >> done 2024-12-23 22:07:39 >> calculating peakCenter to TSS using peak-gene pair... 2024-12-23 22:07:39 >> calculating RP using centerToTSS and TF hit 2024-12-23 22:07:39 >> merging all info together 2024-12-23 22:07:39 >> done 2024-12-23 22:07:39 >> checking seqlevels match... 2024-12-23 22:07:40 >> your peak_GR seqlevel:5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... >> checking seqlevels match... 2024-12-23 22:07:40 >> your peak_GR seqlevel:Chr5 Chr6... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... >> checking seqlevels match... 2024-12-23 22:07:43 >> 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 >> checking seqlevels match... 2024-12-23 22:07:43 >> 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 ------------ annotating Peak using nearest gene mode begins >> preparing gene features information... 2024-12-23 22:07:43 >> finding nearest gene and calculating distance... 2024-12-23 22:07:43 >> dealing with gene strand ... 2024-12-23 22:07:43 >> merging all info together ... 2024-12-23 22:07:43 >> done 2024-12-23 22:07:43 >> checking seqlevels match... 2024-12-23 22:07:44 >> 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... 2024-12-23 22:07:44 >> 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... 2024-12-23 22:07:44 >> finding nearest gene and calculating distance... 2024-12-23 22:07:44 >> dealing with gene strand ... 2024-12-23 22:07:44 >> merging all info together ... 2024-12-23 22:07:44 >> done 2024-12-23 22:07:44 >> checking seqlevels match... 2024-12-23 22:07:45 >> 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... 2024-12-23 22:07:45 >> 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... 2024-12-23 22:07:45 >> finding nearest gene and calculating distance... 2024-12-23 22:07:47 >> dealing with gene strand ... 2024-12-23 22:07:47 >> merging all info together ... 2024-12-23 22:07:47 >> done 2024-12-23 22:07:47 >> checking seqlevels match... 2024-12-23 22:07:47 >> 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... 2024-12-23 22:07:48 >> 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 ------------ annotating Peak using nearest gene mode begins >> preparing gene features information... 2024-12-23 22:07:48 >> finding nearest gene and calculating distance... 2024-12-23 22:07:48 >> dealing with gene strand ... 2024-12-23 22:07:48 >> merging all info together ... 2024-12-23 22:07:48 >> done 2024-12-23 22:07:48 It seems that there 1 genes have not been annotated by nearestGene mode >> checking seqlevels match... 2024-12-23 22:07:49 >> 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 >> checking seqlevels match... 2024-12-23 22:07:49 >> 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... 2024-12-23 22:07:49 >> finding nearest gene and calculating distance... 2024-12-23 22:07:50 >> dealing with gene strand ... 2024-12-23 22:07:50 >> merging all info together ... 2024-12-23 22:07:50 >> done 2024-12-23 22:07:50 It seems that there 1 genes have not been annotated by nearestGene mode >> checking seqlevels match... 2024-12-23 22:07:51 >> 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... 2024-12-23 22:07:51 >> 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 >> some scan range may cross Chr bound, trimming... 2024-12-23 22:07:52 >> checking seqlevels match... 2024-12-23 22:07:53 >> 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... 2024-12-23 22:07:53 Good, your two matrix colnames matchs >> calculating cor and pvalue, which may be time consuming... 2024-12-23 22:07:54 >> merging all info together... 2024-12-23 22:07:54 >> done 2024-12-23 22:07:55 >> checking seqlevels match... 2024-12-23 22:07:55 >> 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... 2024-12-23 22:07:55 >> checking seqlevels match... 2024-12-23 22:07:55 >> 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... 2024-12-23 22:07:55 >> there are 85 gene have scaned promoter >> using scanEnhancer parameter to scan Enhancer for each gene... 2024-12-23 22:07:56 >> checking seqlevels match... 2024-12-23 22:07:56 >> 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 >> some scan range may cross Chr bound, trimming... 2024-12-23 22:07:57 >> calculating cor and pvalue, which may be time consuming... 2024-12-23 22:07:57 >> merging all info together... 2024-12-23 22:07:58 >> done 2024-12-23 22:07:58 Good, your two matrix colnames matchs >> calculating cor and pvalue, which may be time consuming... 2024-12-23 22:07:58 >> merging all info together... 2024-12-23 22:07:58 >> done 2024-12-23 22:07:58 >> checking seqlevels match... 2024-12-23 22:07:58 >> 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... 2024-12-23 22:07:58 >> some scan range may cross Chr bound, trimming... 2024-12-23 22:07:59 >> finding overlap peak in gene scan region... 2024-12-23 22:07:59 >> dealing with left peak not your gene scan region... 2024-12-23 22:07:59 >> merging two set peaks... 2024-12-23 22:07:59 >> calculating distance and dealing with gene strand... 2024-12-23 22:07:59 >> merging all info together ... 2024-12-23 22:07:59 >> done 2024-12-23 22:07:59 Good, your two matrix colnames matchs >> calculating cor and pvalue, which may be time consuming... 2024-12-23 22:08:00 >> merging all info together... 2024-12-23 22:08:00 >> done 2024-12-23 22:08:00 >> checking seqlevels match... 2024-12-23 22:08:00 >> 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... 2024-12-23 22:08:00 >> checking seqlevels match... 2024-12-23 22:08:00 >> 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... 2024-12-23 22:08:00 >> there are 85 gene have scaned promoter >> using scanEnhancer parameter to scan Enhancer for each gene... 2024-12-23 22:08:01 >> checking seqlevels match... 2024-12-23 22:08:01 >> 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 >> some scan range may cross Chr bound, trimming... 2024-12-23 22:08:01 >> calculating cor and pvalue, which may be time consuming... 2024-12-23 22:08:02 >> merging all info together... 2024-12-23 22:08:02 >> done 2024-12-23 22:08:02 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 58.430 2.158 60.584
FindIT2.Rcheck/FindIT2-Ex.timings
name | user | system | elapsed | |
TF_target_database | 0.001 | 0.000 | 0.001 | |
calcRP_TFHit | 3.362 | 0.190 | 3.568 | |
calcRP_coverage | 3.307 | 0.206 | 3.513 | |
calcRP_region | 4.231 | 0.050 | 4.281 | |
enhancerPromoterCor | 2.410 | 0.051 | 2.461 | |
findIT_MARA | 0.433 | 0.001 | 0.435 | |
findIT_TFHit | 0.941 | 0.007 | 0.948 | |
findIT_TTPair | 0.068 | 0.002 | 0.070 | |
findIT_enrichFisher | 0.148 | 0.000 | 0.148 | |
findIT_enrichWilcox | 0.164 | 0.002 | 0.166 | |
findIT_regionRP | 5.299 | 0.088 | 5.387 | |
getAssocPairNumber | 1.064 | 0.006 | 1.071 | |
integrate_ChIP_RNA | 1.825 | 0.056 | 1.881 | |
integrate_replicates | 0.002 | 0.000 | 0.002 | |
jaccard_findIT_TTpair | 0.096 | 0.002 | 0.097 | |
jaccard_findIT_enrichFisher | 0.187 | 0.004 | 0.191 | |
loadPeakFile | 0.057 | 0.001 | 0.058 | |
mm_geneBound | 1.083 | 0.008 | 1.092 | |
mm_geneScan | 1.096 | 0.011 | 1.107 | |
mm_nearestGene | 0.998 | 0.013 | 1.011 | |
peakGeneCor | 2.102 | 0.022 | 2.131 | |
plot_annoDistance | 1.403 | 0.023 | 1.434 | |
plot_peakGeneAlias_summary | 1.182 | 0.008 | 1.190 | |
plot_peakGeneCor | 3.451 | 0.174 | 3.629 | |
test_geneSet | 0 | 0 | 0 | |