Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-01-27 11:09:29 -0500 (Fri, 27 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" | 4465 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" | 4246 |
merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" | 4269 |
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To the developers/maintainers of the FindIT2 package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 668/2162 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
FindIT2 1.5.0 (landing page) Guandong Shang
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: FindIT2 |
Version: 1.5.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FindIT2_1.5.0.tar.gz |
StartedAt: 2023-01-27 01:21:01 -0500 (Fri, 27 Jan 2023) |
EndedAt: 2023-01-27 01:35:42 -0500 (Fri, 27 Jan 2023) |
EllapsedTime: 881.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: FindIT2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FindIT2_1.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/FindIT2.Rcheck’ * using R Under development (unstable) (2023-01-10 r83596) * using platform: x86_64-apple-darwin17.0 (64-bit) * R was compiled by Apple clang version 12.0.0 (clang-1200.0.32.29) GNU Fortran (GCC) 8.2.0 * running under: macOS Mojave 10.14.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FindIT2/DESCRIPTION’ ... OK * this is package ‘FindIT2’ version ‘1.5.0’ * 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 R 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 findIT_regionRP 13.032 0.189 19.042 calcRP_region 10.133 0.188 14.611 calcRP_coverage 6.394 0.543 9.510 calcRP_TFHit 6.497 0.161 9.399 plot_peakGeneCor 6.493 0.049 9.243 enhancerPromoterCor 5.601 0.059 7.476 peakGeneCor 5.172 0.050 7.266 integrate_ChIP_RNA 4.090 0.039 5.875 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FindIT2 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/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) (2023-01-10 r83596) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) 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, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' 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... 2023-01-27 01:32:55 >> some scan range may cross Chr bound, trimming... 2023-01-27 01:32:59 >> preparing weight info... 2023-01-27 01:32:59 >> loading E50h_sampleChr5.bw info... 2023-01-27 01:32:59 ------------ >> extracting and calcluating Chr5 signal... 2023-01-27 01:33:00 >> dealing with Chr5 left gene signal... 2023-01-27 01:33:07 >> norming Chr5RP accoring to the whole Chr RP... 2023-01-27 01:33:08 >> merging all Chr RP together... 2023-01-27 01:33:08 >> done 2023-01-27 01:33:08 >> checking seqlevels match... 2023-01-27 01:33:08 >> 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... 2023-01-27 01:33:08 >> some scan range may cross Chr bound, trimming... 2023-01-27 01:33:11 >> finding overlap peak in gene scan region... 2023-01-27 01:33:11 >> dealing with left peak not your gene scan region... 2023-01-27 01:33:11 >> merging two set peaks... 2023-01-27 01:33:11 >> calculating distance and dealing with gene strand... 2023-01-27 01:33:12 >> merging all info together ... 2023-01-27 01:33:12 >> done 2023-01-27 01:33:12 >> calculating peakCenter to TSS using peak-gene pair... 2023-01-27 01:33:12 >> pre-filling 1356 noAssoc peak gene's RP with 0... 2023-01-27 01:33:14 >> calculating RP using centerToTSS and peak score2023-01-27 01:33:14 >> merging all info together 2023-01-27 01:33:20 >> done 2023-01-27 01:33:22 >> calculating peakCenter to TSS using peak-gene pair... 2023-01-27 01:33:23 >> pre-filling 1356 noAssoc peak gene's RP with 0... 2023-01-27 01:33:25 >> calculating RP using centerToTSS and peak score2023-01-27 01:33:25 >> merging all info together 2023-01-27 01:33:33 >> done 2023-01-27 01:33:34 >> checking seqlevels match... 2023-01-27 01:33:34 >> 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 ------------ annotatePeak using geneScan mode begins >> preparing gene features information and scan region... 2023-01-27 01:33:35 >> some scan range may cross Chr bound, trimming... 2023-01-27 01:33:37 >> finding overlap peak in gene scan region... 2023-01-27 01:33:37 >> dealing with left peak not your gene scan region... 2023-01-27 01:33:37 >> merging two set peaks... 2023-01-27 01:33:37 >> calculating distance and dealing with gene strand... 2023-01-27 01:33:37 >> merging all info together ... 2023-01-27 01:33:38 >> done 2023-01-27 01:33:38 >> calculating peakCenter to TSS using peak-gene pair... 2023-01-27 01:33:38 >> calculating RP using centerToTSS and TF hit 2023-01-27 01:33:39 >> merging all info together 2023-01-27 01:33:39 >> done 2023-01-27 01:33:40 >> calculating peakCenter to TSS using peak-gene pair... 2023-01-27 01:33:40 >> calculating RP using centerToTSS and TF hit 2023-01-27 01:33:42 >> merging all info together 2023-01-27 01:33:42 >> done 2023-01-27 01:33:42 >> checking seqlevels match... 2023-01-27 01:33:45 >> 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 ------------ annotatePeak using geneScan mode begins >> preparing gene features information and scan region... 2023-01-27 01:33:45 >> some scan range may cross Chr bound, trimming... 2023-01-27 01:33:47 >> finding overlap peak in gene scan region... 2023-01-27 01:33:47 >> dealing with left peak not your gene scan region... 2023-01-27 01:33:47 >> merging two set peaks... 2023-01-27 01:33:47 >> calculating distance and dealing with gene strand... 2023-01-27 01:33:48 >> merging all info together ... 2023-01-27 01:33:48 >> done 2023-01-27 01:33:48 >> calculating peakCenter to TSS using peak-gene pair... 2023-01-27 01:33:48 >> pre-filling 1356 noAssoc peak gene's RP with 0... 2023-01-27 01:33:50 >> calculating RP using centerToTSS and peak score2023-01-27 01:33:50 >> merging all info together 2023-01-27 01:33:56 >> done 2023-01-27 01:33:57 >> extracting RP info from regionRP... 2023-01-27 01:34:00 >> dealing with TF_GR_databse... 2023-01-27 01:34:00 >> calculating percent and p-value... 2023-01-27 01:34:01 >> dealing withE5_0h_R1... 2023-01-27 01:34:01 >> dealing withE5_0h_R2... 2023-01-27 01:34:01 >> dealing withE5_4h_R1... 2023-01-27 01:34:01 >> dealing withE5_4h_R2... 2023-01-27 01:34:01 >> dealing withE5_8h_R1... 2023-01-27 01:34:01 >> dealing withE5_8h_R2... 2023-01-27 01:34:01 >> dealing withE5_16h_R1... 2023-01-27 01:34:01 >> dealing withE5_16h_R2... 2023-01-27 01:34:01 >> dealing withE5_24h_R1... 2023-01-27 01:34:02 >> dealing withE5_24h_R2... 2023-01-27 01:34:02 >> dealing withE5_48h_R1... 2023-01-27 01:34:02 >> dealing withE5_48h_R2... 2023-01-27 01:34:02 >> dealing withE5_48h_R3... 2023-01-27 01:34:02 >> dealing withE5_72h_R1... 2023-01-27 01:34:02 >> dealing withE5_72h_R2... 2023-01-27 01:34:02 >> dealing withE5_72h_R3... 2023-01-27 01:34:02 >> merging all info together... 2023-01-27 01:34:02 >> done 2023-01-27 01:34:03 >> preparing gene features information... 2023-01-27 01:34:03 >> some scan range may cross Chr bound, trimming... 2023-01-27 01:34:05 >> calculating p-value for each TF, which may be time consuming... 2023-01-27 01:34:05 >> merging all info together... 2023-01-27 01:34:05 >> done 2023-01-27 01:34:05 >> dealing with TF_GR_database... 2023-01-27 01:34:06 >> calculating coef and converting into z-score using INT... 2023-01-27 01:34:07 >> dealing with E5_0h_R1... 2023-01-27 01:34:07 >> dealing with E5_0h_R2... 2023-01-27 01:34:07 >> dealing with E5_4h_R1... 2023-01-27 01:34:07 >> dealing with E5_4h_R2... 2023-01-27 01:34:08 >> dealing with E5_8h_R1... 2023-01-27 01:34:08 >> dealing with E5_8h_R2... 2023-01-27 01:34:08 >> dealing with E5_16h_R1... 2023-01-27 01:34:08 >> dealing with E5_16h_R2... 2023-01-27 01:34:08 >> dealing with E5_24h_R1... 2023-01-27 01:34:09 >> dealing with E5_24h_R2... 2023-01-27 01:34:09 >> dealing with E5_48h_R1... 2023-01-27 01:34:09 >> dealing with E5_48h_R2... 2023-01-27 01:34:09 >> dealing with E5_48h_R3... 2023-01-27 01:34:10 >> dealing with E5_72h_R1... 2023-01-27 01:34:10 >> dealing with E5_72h_R2... 2023-01-27 01:34:10 >> dealing with E5_72h_R3... 2023-01-27 01:34:10 >> merging all info together... 2023-01-27 01:34:11 >> done 2023-01-27 01:34:11 >> checking seqlevels match... 2023-01-27 01:34:11 >> 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... 2023-01-27 01:34:12 >> some scan range may cross Chr bound, trimming... 2023-01-27 01:34:14 >> finding overlap peak in gene scan region... 2023-01-27 01:34:14 >> dealing with left peak not your gene scan region... 2023-01-27 01:34:14 >> merging two set peaks... 2023-01-27 01:34:14 >> calculating distance and dealing with gene strand... 2023-01-27 01:34:14 >> merging all info together ... 2023-01-27 01:34:14 >> done 2023-01-27 01:34:14 >> calculating peakCenter to TSS using peak-gene pair... 2023-01-27 01:34:14 >> calculating RP using centerToTSS and TF hit 2023-01-27 01:34:16 >> merging all info together 2023-01-27 01:34:16 >> done 2023-01-27 01:34:17 >> checking seqlevels match... 2023-01-27 01:34:18 >> your peak_GR seqlevel:5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... >> checking seqlevels match... 2023-01-27 01:34:18 >> your peak_GR seqlevel:Chr5 Chr6... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... >> checking seqlevels match... 2023-01-27 01:34:27 >> 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... 2023-01-27 01:34:27 >> 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... 2023-01-27 01:34:27 >> finding nearest gene and calculating distance... 2023-01-27 01:34:29 >> dealing with gene strand ... 2023-01-27 01:34:29 >> merging all info together ... 2023-01-27 01:34:29 >> done 2023-01-27 01:34:29 >> checking seqlevels match... 2023-01-27 01:34:29 >> 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... 2023-01-27 01:34:30 >> 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 ------------ annotating Peak using nearest gene mode begins >> preparing gene features information... 2023-01-27 01:34:30 >> finding nearest gene and calculating distance... 2023-01-27 01:34:32 >> dealing with gene strand ... 2023-01-27 01:34:32 >> merging all info together ... 2023-01-27 01:34:32 >> done 2023-01-27 01:34:32 >> checking seqlevels match... 2023-01-27 01:34:34 >> 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 >> checking seqlevels match... 2023-01-27 01:34:34 >> 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 ------------ annotating Peak using nearest gene mode begins >> preparing gene features information... 2023-01-27 01:34:35 >> finding nearest gene and calculating distance... 2023-01-27 01:34:36 >> dealing with gene strand ... 2023-01-27 01:34:37 >> merging all info together ... 2023-01-27 01:34:37 >> done 2023-01-27 01:34:37 >> checking seqlevels match... 2023-01-27 01:34:39 >> 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... 2023-01-27 01:34:40 >> 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... 2023-01-27 01:34:40 >> finding nearest gene and calculating distance... 2023-01-27 01:34:42 >> dealing with gene strand ... 2023-01-27 01:34:42 >> merging all info together ... 2023-01-27 01:34:42 >> done 2023-01-27 01:34:42 It seems that there 1 genes have not been annotated by nearestGene mode >> checking seqlevels match... 2023-01-27 01:34:45 >> 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... 2023-01-27 01:34:45 >> 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... 2023-01-27 01:34:45 >> finding nearest gene and calculating distance... 2023-01-27 01:34:47 >> dealing with gene strand ... 2023-01-27 01:34:48 >> merging all info together ... 2023-01-27 01:34:48 >> done 2023-01-27 01:34:48 It seems that there 1 genes have not been annotated by nearestGene mode >> checking seqlevels match... 2023-01-27 01:34:50 >> 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... 2023-01-27 01:34:53 >> 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... 2023-01-27 01:34:55 >> checking seqlevels match... 2023-01-27 01:34:57 >> 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... 2023-01-27 01:35:00 Good, your two matrix colnames matchs >> calculating cor and pvalue, which may be time consuming... 2023-01-27 01:35:04 >> merging all info together... 2023-01-27 01:35:04 >> done 2023-01-27 01:35:04 >> checking seqlevels match... 2023-01-27 01:35:04 >> 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... 2023-01-27 01:35:05 >> checking seqlevels match... 2023-01-27 01:35:05 >> 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... 2023-01-27 01:35:07 >> there are 85 gene have scaned promoter >> using scanEnhancer parameter to scan Enhancer for each gene... 2023-01-27 01:35:08 >> checking seqlevels match... 2023-01-27 01:35:08 >> 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... 2023-01-27 01:35:10 >> calculating cor and pvalue, which may be time consuming... 2023-01-27 01:35:10 >> merging all info together... 2023-01-27 01:35:11 >> done 2023-01-27 01:35:11 Good, your two matrix colnames matchs >> calculating cor and pvalue, which may be time consuming... 2023-01-27 01:35:11 >> merging all info together... 2023-01-27 01:35:11 >> done 2023-01-27 01:35:11 >> checking seqlevels match... 2023-01-27 01:35:12 >> 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... 2023-01-27 01:35:12 >> some scan range may cross Chr bound, trimming... 2023-01-27 01:35:14 >> finding overlap peak in gene scan region... 2023-01-27 01:35:14 >> dealing with left peak not your gene scan region... 2023-01-27 01:35:14 >> merging two set peaks... 2023-01-27 01:35:15 >> calculating distance and dealing with gene strand... 2023-01-27 01:35:15 >> merging all info together ... 2023-01-27 01:35:15 >> done 2023-01-27 01:35:15 Good, your two matrix colnames matchs >> calculating cor and pvalue, which may be time consuming... 2023-01-27 01:35:19 >> merging all info together... 2023-01-27 01:35:19 >> done 2023-01-27 01:35:19 >> checking seqlevels match... 2023-01-27 01:35:19 >> 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 >> using scanPromoter parameter to scan promoter for each gene... 2023-01-27 01:35:19 >> checking seqlevels match... 2023-01-27 01:35:19 >> 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 >> some scan range may cross Chr bound, trimming... 2023-01-27 01:35:22 >> there are 85 gene have scaned promoter >> using scanEnhancer parameter to scan Enhancer for each gene... 2023-01-27 01:35:23 >> checking seqlevels match... 2023-01-27 01:35:23 >> 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 >> some scan range may cross Chr bound, trimming... 2023-01-27 01:35:25 >> calculating cor and pvalue, which may be time consuming... 2023-01-27 01:35:25 >> merging all info together... 2023-01-27 01:35:26 >> done 2023-01-27 01:35:26 Joining, by = "feature_id" Joining, by = "feature_id" `geom_smooth()` using formula = 'y ~ x' Joining, by = "feature_id" Joining, by = "feature_id" `geom_smooth()` using formula = 'y ~ x' [ FAIL 0 | WARN 0 | SKIP 0 | PASS 65 ] > > proc.time() user system elapsed 129.346 2.540 186.349
FindIT2.Rcheck/FindIT2-Ex.timings
name | user | system | elapsed | |
TF_target_database | 0.000 | 0.000 | 0.001 | |
calcRP_TFHit | 6.497 | 0.161 | 9.399 | |
calcRP_coverage | 6.394 | 0.543 | 9.510 | |
calcRP_region | 10.133 | 0.188 | 14.611 | |
enhancerPromoterCor | 5.601 | 0.059 | 7.476 | |
findIT_MARA | 0.924 | 0.010 | 1.155 | |
findIT_TFHit | 1.972 | 0.058 | 2.715 | |
findIT_TTPair | 0.202 | 0.008 | 0.292 | |
findIT_enrichFisher | 0.344 | 0.005 | 0.487 | |
findIT_enrichWilcox | 0.394 | 0.006 | 0.568 | |
findIT_regionRP | 13.032 | 0.189 | 19.042 | |
getAssocPairNumber | 2.302 | 0.024 | 3.416 | |
integrate_ChIP_RNA | 4.090 | 0.039 | 5.875 | |
integrate_replicates | 0.004 | 0.001 | 0.004 | |
jaccard_findIT_TTpair | 0.284 | 0.008 | 0.410 | |
jaccard_findIT_enrichFisher | 0.462 | 0.005 | 0.658 | |
loadPeakFile | 0.122 | 0.001 | 0.175 | |
mm_geneBound | 2.325 | 0.019 | 3.299 | |
mm_geneScan | 2.403 | 0.022 | 3.292 | |
mm_nearestGene | 2.083 | 0.029 | 2.932 | |
peakGeneCor | 5.172 | 0.050 | 7.266 | |
plot_annoDistance | 2.826 | 0.031 | 3.896 | |
plot_peakGeneAlias_summary | 2.711 | 0.029 | 3.701 | |
plot_peakGeneCor | 6.493 | 0.049 | 9.243 | |
test_geneSet | 0.000 | 0.001 | 0.001 | |