Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:03 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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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 669/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
FindIT2 1.5.0 (landing page) Guandong Shang
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: FindIT2 |
Version: 1.5.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings FindIT2_1.5.0.tar.gz |
StartedAt: 2023-02-07 01:37:35 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 01:46:33 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 537.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: FindIT2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:FindIT2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings FindIT2_1.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/FindIT2.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * 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 calcRP_coverage 9.592 0.666 10.884 findIT_regionRP 9.964 0.036 10.003 calcRP_region 7.257 0.088 8.182 calcRP_TFHit 4.920 0.104 5.538 * 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 ... ‘FindIT2.Rmd’ using ‘UTF-8’... OK NONE * 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-3.17-bioc/R/bin/R CMD INSTALL FindIT2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘FindIT2’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (FindIT2)
FindIT2.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (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... 2023-02-07 01:43:36 >> some scan range may cross Chr bound, trimming... 2023-02-07 01:43:38 >> preparing weight info... 2023-02-07 01:43:38 >> loading E50h_sampleChr5.bw info... 2023-02-07 01:43:38 ------------ >> extracting and calcluating Chr5 signal... 2023-02-07 01:43:39 >> dealing with Chr5 left gene signal... 2023-02-07 01:43:48 >> norming Chr5RP accoring to the whole Chr RP... 2023-02-07 01:43:48 >> merging all Chr RP together... 2023-02-07 01:43:48 >> done 2023-02-07 01:43:48 >> checking seqlevels match... 2023-02-07 01:43:48 >> 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 ------------ annotatePeak using geneScan mode begins >> preparing gene features information and scan region... 2023-02-07 01:43:48 >> some scan range may cross Chr bound, trimming... 2023-02-07 01:43:49 >> finding overlap peak in gene scan region... 2023-02-07 01:43:49 >> dealing with left peak not your gene scan region... 2023-02-07 01:43:49 >> merging two set peaks... 2023-02-07 01:43:50 >> calculating distance and dealing with gene strand... 2023-02-07 01:43:50 >> merging all info together ... 2023-02-07 01:43:50 >> done 2023-02-07 01:43:50 >> calculating peakCenter to TSS using peak-gene pair... 2023-02-07 01:43:50 >> pre-filling 1356 noAssoc peak gene's RP with 0... 2023-02-07 01:43:51 >> calculating RP using centerToTSS and peak score2023-02-07 01:43:51 >> merging all info together 2023-02-07 01:43:54 >> done 2023-02-07 01:43:56 >> calculating peakCenter to TSS using peak-gene pair... 2023-02-07 01:43:56 >> pre-filling 1356 noAssoc peak gene's RP with 0... 2023-02-07 01:43:58 >> calculating RP using centerToTSS and peak score2023-02-07 01:43:58 >> merging all info together 2023-02-07 01:44:02 >> done 2023-02-07 01:44:02 >> checking seqlevels match... 2023-02-07 01:44:03 >> 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... 2023-02-07 01:44:03 >> some scan range may cross Chr bound, trimming... 2023-02-07 01:44:04 >> finding overlap peak in gene scan region... 2023-02-07 01:44:04 >> dealing with left peak not your gene scan region... 2023-02-07 01:44:04 >> merging two set peaks... 2023-02-07 01:44:04 >> calculating distance and dealing with gene strand... 2023-02-07 01:44:04 >> merging all info together ... 2023-02-07 01:44:04 >> done 2023-02-07 01:44:04 >> calculating peakCenter to TSS using peak-gene pair... 2023-02-07 01:44:04 >> calculating RP using centerToTSS and TF hit 2023-02-07 01:44:05 >> merging all info together 2023-02-07 01:44:05 >> done 2023-02-07 01:44:05 >> calculating peakCenter to TSS using peak-gene pair... 2023-02-07 01:44:06 >> calculating RP using centerToTSS and TF hit 2023-02-07 01:44:06 >> merging all info together 2023-02-07 01:44:07 >> done 2023-02-07 01:44:07 >> checking seqlevels match... 2023-02-07 01:44:08 >> 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... 2023-02-07 01:44:08 >> some scan range may cross Chr bound, trimming... 2023-02-07 01:44:09 >> finding overlap peak in gene scan region... 2023-02-07 01:44:09 >> dealing with left peak not your gene scan region... 2023-02-07 01:44:09 >> merging two set peaks... 2023-02-07 01:44:09 >> calculating distance and dealing with gene strand... 2023-02-07 01:44:09 >> merging all info together ... 2023-02-07 01:44:09 >> done 2023-02-07 01:44:09 >> calculating peakCenter to TSS using peak-gene pair... 2023-02-07 01:44:09 >> pre-filling 1356 noAssoc peak gene's RP with 0... 2023-02-07 01:44:10 >> calculating RP using centerToTSS and peak score2023-02-07 01:44:10 >> merging all info together 2023-02-07 01:44:14 >> done 2023-02-07 01:44:14 >> extracting RP info from regionRP... 2023-02-07 01:44:16 >> dealing with TF_GR_databse... 2023-02-07 01:44:16 >> calculating percent and p-value... 2023-02-07 01:44:16 >> dealing withE5_0h_R1... 2023-02-07 01:44:16 >> dealing withE5_0h_R2... 2023-02-07 01:44:16 >> dealing withE5_4h_R1... 2023-02-07 01:44:16 >> dealing withE5_4h_R2... 2023-02-07 01:44:17 >> dealing withE5_8h_R1... 2023-02-07 01:44:17 >> dealing withE5_8h_R2... 2023-02-07 01:44:17 >> dealing withE5_16h_R1... 2023-02-07 01:44:17 >> dealing withE5_16h_R2... 2023-02-07 01:44:17 >> dealing withE5_24h_R1... 2023-02-07 01:44:17 >> dealing withE5_24h_R2... 2023-02-07 01:44:17 >> dealing withE5_48h_R1... 2023-02-07 01:44:17 >> dealing withE5_48h_R2... 2023-02-07 01:44:17 >> dealing withE5_48h_R3... 2023-02-07 01:44:17 >> dealing withE5_72h_R1... 2023-02-07 01:44:17 >> dealing withE5_72h_R2... 2023-02-07 01:44:17 >> dealing withE5_72h_R3... 2023-02-07 01:44:18 >> merging all info together... 2023-02-07 01:44:18 >> done 2023-02-07 01:44:18 >> preparing gene features information... 2023-02-07 01:44:18 >> some scan range may cross Chr bound, trimming... 2023-02-07 01:44:19 >> calculating p-value for each TF, which may be time consuming... 2023-02-07 01:44:19 >> merging all info together... 2023-02-07 01:44:19 >> done 2023-02-07 01:44:19 >> dealing with TF_GR_database... 2023-02-07 01:44:20 >> calculating coef and converting into z-score using INT... 2023-02-07 01:44:20 >> dealing with E5_0h_R1... 2023-02-07 01:44:20 >> dealing with E5_0h_R2... 2023-02-07 01:44:20 >> dealing with E5_4h_R1... 2023-02-07 01:44:20 >> dealing with E5_4h_R2... 2023-02-07 01:44:20 >> dealing with E5_8h_R1... 2023-02-07 01:44:20 >> dealing with E5_8h_R2... 2023-02-07 01:44:20 >> dealing with E5_16h_R1... 2023-02-07 01:44:21 >> dealing with E5_16h_R2... 2023-02-07 01:44:21 >> dealing with E5_24h_R1... 2023-02-07 01:44:21 >> dealing with E5_24h_R2... 2023-02-07 01:44:21 >> dealing with E5_48h_R1... 2023-02-07 01:44:21 >> dealing with E5_48h_R2... 2023-02-07 01:44:21 >> dealing with E5_48h_R3... 2023-02-07 01:44:21 >> dealing with E5_72h_R1... 2023-02-07 01:44:21 >> dealing with E5_72h_R2... 2023-02-07 01:44:21 >> dealing with E5_72h_R3... 2023-02-07 01:44:21 >> merging all info together... 2023-02-07 01:44:22 >> done 2023-02-07 01:44:22 >> checking seqlevels match... 2023-02-07 01:44:22 >> 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... 2023-02-07 01:44:22 >> some scan range may cross Chr bound, trimming... 2023-02-07 01:44:23 >> finding overlap peak in gene scan region... 2023-02-07 01:44:23 >> dealing with left peak not your gene scan region... 2023-02-07 01:44:23 >> merging two set peaks... 2023-02-07 01:44:23 >> calculating distance and dealing with gene strand... 2023-02-07 01:44:23 >> merging all info together ... 2023-02-07 01:44:23 >> done 2023-02-07 01:44:23 >> calculating peakCenter to TSS using peak-gene pair... 2023-02-07 01:44:23 >> calculating RP using centerToTSS and TF hit 2023-02-07 01:44:24 >> merging all info together 2023-02-07 01:44:24 >> done 2023-02-07 01:44:24 >> checking seqlevels match... 2023-02-07 01:44:25 >> your peak_GR seqlevel:5... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... >> checking seqlevels match... 2023-02-07 01:44:25 >> your peak_GR seqlevel:Chr5 Chr6... >> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC... >> checking seqlevels match... 2023-02-07 01:44:30 >> 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... 2023-02-07 01:44:30 >> 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... 2023-02-07 01:44:30 >> finding nearest gene and calculating distance... 2023-02-07 01:44:31 >> dealing with gene strand ... 2023-02-07 01:44:32 >> merging all info together ... 2023-02-07 01:44:32 >> done 2023-02-07 01:44:32 >> checking seqlevels match... 2023-02-07 01:44:32 >> 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 >> checking seqlevels match... 2023-02-07 01:44:32 >> 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 ------------ annotating Peak using nearest gene mode begins >> preparing gene features information... 2023-02-07 01:44:32 >> finding nearest gene and calculating distance... 2023-02-07 01:44:33 >> dealing with gene strand ... 2023-02-07 01:44:33 >> merging all info together ... 2023-02-07 01:44:33 >> done 2023-02-07 01:44:33 >> checking seqlevels match... 2023-02-07 01:44:34 >> 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... 2023-02-07 01:44:34 >> 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... 2023-02-07 01:44:34 >> finding nearest gene and calculating distance... 2023-02-07 01:44:35 >> dealing with gene strand ... 2023-02-07 01:44:35 >> merging all info together ... 2023-02-07 01:44:35 >> done 2023-02-07 01:44:35 >> checking seqlevels match... 2023-02-07 01:44:37 >> 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 >> checking seqlevels match... 2023-02-07 01:44:38 >> 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 ------------ annotating Peak using nearest gene mode begins >> preparing gene features information... 2023-02-07 01:44:38 >> finding nearest gene and calculating distance... 2023-02-07 01:44:39 >> dealing with gene strand ... 2023-02-07 01:44:39 >> merging all info together ... 2023-02-07 01:44:39 >> done 2023-02-07 01:44:39 It seems that there 1 genes have not been annotated by nearestGene mode >> checking seqlevels match... 2023-02-07 01:44:40 >> 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... 2023-02-07 01:44:40 >> 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... 2023-02-07 01:44:40 >> finding nearest gene and calculating distance... 2023-02-07 01:44:41 >> dealing with gene strand ... 2023-02-07 01:44:41 >> merging all info together ... 2023-02-07 01:44:41 >> done 2023-02-07 01:44:41 It seems that there 1 genes have not been annotated by nearestGene mode >> checking seqlevels match... 2023-02-07 01:44:42 >> 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 >> checking seqlevels match... 2023-02-07 01:44:43 >> 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... 2023-02-07 01:44:45 >> checking seqlevels match... 2023-02-07 01:44:45 >> 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 >> some scan range may cross Chr bound, trimming... 2023-02-07 01:44:46 Good, your two matrix colnames matchs >> calculating cor and pvalue, which may be time consuming... 2023-02-07 01:44:48 >> merging all info together... 2023-02-07 01:44:48 >> done 2023-02-07 01:44:48 >> checking seqlevels match... 2023-02-07 01:44:48 >> 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 >> using scanPromoter parameter to scan promoter for each gene... 2023-02-07 01:44:49 >> checking seqlevels match... 2023-02-07 01:44:49 >> 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 >> some scan range may cross Chr bound, trimming... 2023-02-07 01:44:50 >> there are 85 gene have scaned promoter >> using scanEnhancer parameter to scan Enhancer for each gene... 2023-02-07 01:44:50 >> checking seqlevels match... 2023-02-07 01:44:50 >> 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 >> some scan range may cross Chr bound, trimming... 2023-02-07 01:44:51 >> calculating cor and pvalue, which may be time consuming... 2023-02-07 01:44:51 >> merging all info together... 2023-02-07 01:44:52 >> done 2023-02-07 01:44:52 Good, your two matrix colnames matchs >> calculating cor and pvalue, which may be time consuming... 2023-02-07 01:44:52 >> merging all info together... 2023-02-07 01:44:52 >> done 2023-02-07 01:44:52 >> checking seqlevels match... 2023-02-07 01:44:52 >> 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 ------------ annotatePeak using geneScan mode begins >> preparing gene features information and scan region... 2023-02-07 01:44:52 >> some scan range may cross Chr bound, trimming... 2023-02-07 01:44:53 >> finding overlap peak in gene scan region... 2023-02-07 01:44:53 >> dealing with left peak not your gene scan region... 2023-02-07 01:44:53 >> merging two set peaks... 2023-02-07 01:44:53 >> calculating distance and dealing with gene strand... 2023-02-07 01:44:53 >> merging all info together ... 2023-02-07 01:44:53 >> done 2023-02-07 01:44:53 Good, your two matrix colnames matchs >> calculating cor and pvalue, which may be time consuming... 2023-02-07 01:44:55 >> merging all info together... 2023-02-07 01:44:55 >> done 2023-02-07 01:44:55 >> checking seqlevels match... 2023-02-07 01:44:55 >> 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... 2023-02-07 01:44:55 >> checking seqlevels match... 2023-02-07 01:44:55 >> 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... 2023-02-07 01:44:56 >> there are 85 gene have scaned promoter >> using scanEnhancer parameter to scan Enhancer for each gene... 2023-02-07 01:44:57 >> checking seqlevels match... 2023-02-07 01:44:57 >> 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... 2023-02-07 01:44:58 >> calculating cor and pvalue, which may be time consuming... 2023-02-07 01:44:58 >> merging all info together... 2023-02-07 01:44:58 >> done 2023-02-07 01:44:58 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 97.261 1.098 98.480
FindIT2.Rcheck/FindIT2-Ex.timings
name | user | system | elapsed | |
TF_target_database | 0 | 0 | 0 | |
calcRP_TFHit | 4.920 | 0.104 | 5.538 | |
calcRP_coverage | 9.592 | 0.666 | 10.884 | |
calcRP_region | 7.257 | 0.088 | 8.182 | |
enhancerPromoterCor | 3.942 | 0.016 | 4.290 | |
findIT_MARA | 0.612 | 0.008 | 0.691 | |
findIT_TFHit | 1.415 | 0.004 | 1.597 | |
findIT_TTPair | 0.159 | 0.000 | 0.159 | |
findIT_enrichFisher | 0.260 | 0.000 | 0.261 | |
findIT_enrichWilcox | 0.268 | 0.000 | 0.269 | |
findIT_regionRP | 9.964 | 0.036 | 10.003 | |
getAssocPairNumber | 1.632 | 0.024 | 1.656 | |
integrate_ChIP_RNA | 2.888 | 0.008 | 2.898 | |
integrate_replicates | 0.002 | 0.000 | 0.003 | |
jaccard_findIT_TTpair | 0.206 | 0.004 | 0.209 | |
jaccard_findIT_enrichFisher | 0.333 | 0.000 | 0.332 | |
loadPeakFile | 0.079 | 0.000 | 0.079 | |
mm_geneBound | 1.678 | 0.008 | 1.686 | |
mm_geneScan | 1.715 | 0.004 | 1.719 | |
mm_nearestGene | 1.539 | 0.008 | 1.547 | |
peakGeneCor | 3.326 | 0.008 | 3.519 | |
plot_annoDistance | 1.998 | 0.000 | 2.000 | |
plot_peakGeneAlias_summary | 1.838 | 0.000 | 1.845 | |
plot_peakGeneCor | 4.207 | 0.008 | 4.218 | |
test_geneSet | 0.000 | 0.000 | 0.001 | |