Guandong Shang
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/FindIT2 |
| git_branch: master |
| git_last_commit: 4c4fab3 |
| git_last_commit_date: 2021-12-28 22:18:58 -0400 (Tue, 28 Dec 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:30 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 645/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FindIT2 1.1.3 (landing page) Guandong Shang
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | 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: 1.1.3 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FindIT2.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings FindIT2_1.1.3.tar.gz |
| StartedAt: 2022-03-17 19:05:43 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:10:22 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 279.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FindIT2.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FindIT2.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings FindIT2_1.1.3.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/FindIT2.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'FindIT2/DESCRIPTION' ... OK * this is package 'FindIT2' version '1.1.3' * 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 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 * 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:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL FindIT2
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-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
converting help for package 'FindIT2'
finding HTML links ... done
ATAC_normCount html
RNADiff_LEC2_GR html
RNA_normCount html
TF_target_database html
calcRP_TFHit html
calcRP_coverage html
calcRP_region html
enhancerPromoterCor html
findIT_MARA html
findIT_TFHit html
findIT_TTPair html
findIT_enrichFisher html
findIT_enrichWilcox html
findIT_regionRP html
getAssocPairNumber html
integrate_ChIP_RNA html
integrate_replicates html
jaccard_findIT_TTpair html
jaccard_findIT_enrichFisher html
loadPeakFile html
mm_geneBound html
mm_geneScan html
mm_nearestGene html
peakGeneCor html
plot_annoDistance html
plot_peakGeneAlias_summary html
plot_peakGeneCor html
test_featureSet html
test_geneSet html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'SGSeq' is missing or broken
done
FindIT2.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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")
>> checking seqlevels match... 2022-03-17 7:09:25 PM
>> 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... 2022-03-17 7:09:25 PM
>> some scan range may cross Chr bound, trimming... 2022-03-17 7:09:26 PM
>> finding overlap peak in gene scan region... 2022-03-17 7:09:26 PM
>> dealing with left peak not your gene scan region... 2022-03-17 7:09:26 PM
>> merging two set peaks... 2022-03-17 7:09:27 PM
>> calculating distance and dealing with gene strand... 2022-03-17 7:09:27 PM
>> merging all info together ... 2022-03-17 7:09:27 PM
>> done 2022-03-17 7:09:27 PM
>> calculating peakCenter to TSS using peak-gene pair... 2022-03-17 7:09:27 PM
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2022-03-17 7:09:28 PM
>> calculating RP using centerToTSS and peak score2022-03-17 7:09:28 PM
>> merging all info together 2022-03-17 7:09:31 PM
>> done 2022-03-17 7:09:31 PM
>> calculating peakCenter to TSS using peak-gene pair... 2022-03-17 7:09:32 PM
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2022-03-17 7:09:33 PM
>> calculating RP using centerToTSS and peak score2022-03-17 7:09:33 PM
>> merging all info together 2022-03-17 7:09:36 PM
>> done 2022-03-17 7:09:36 PM
>> checking seqlevels match... 2022-03-17 7:09:36 PM
>> 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... 2022-03-17 7:09:36 PM
>> some scan range may cross Chr bound, trimming... 2022-03-17 7:09:37 PM
>> finding overlap peak in gene scan region... 2022-03-17 7:09:37 PM
>> dealing with left peak not your gene scan region... 2022-03-17 7:09:37 PM
>> merging two set peaks... 2022-03-17 7:09:37 PM
>> calculating distance and dealing with gene strand... 2022-03-17 7:09:37 PM
>> merging all info together ... 2022-03-17 7:09:37 PM
>> done 2022-03-17 7:09:37 PM
>> calculating peakCenter to TSS using peak-gene pair... 2022-03-17 7:09:37 PM
>> calculating RP using centerToTSS and TF hit 2022-03-17 7:09:38 PM
>> merging all info together 2022-03-17 7:09:38 PM
>> done 2022-03-17 7:09:38 PM
>> calculating peakCenter to TSS using peak-gene pair... 2022-03-17 7:09:38 PM
>> calculating RP using centerToTSS and TF hit 2022-03-17 7:09:38 PM
>> merging all info together 2022-03-17 7:09:38 PM
>> done 2022-03-17 7:09:39 PM
>> checking seqlevels match... 2022-03-17 7:09:39 PM
>> 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... 2022-03-17 7:09:39 PM
>> some scan range may cross Chr bound, trimming... 2022-03-17 7:09:40 PM
>> finding overlap peak in gene scan region... 2022-03-17 7:09:40 PM
>> dealing with left peak not your gene scan region... 2022-03-17 7:09:40 PM
>> merging two set peaks... 2022-03-17 7:09:40 PM
>> calculating distance and dealing with gene strand... 2022-03-17 7:09:40 PM
>> merging all info together ... 2022-03-17 7:09:40 PM
>> done 2022-03-17 7:09:40 PM
>> calculating peakCenter to TSS using peak-gene pair... 2022-03-17 7:09:40 PM
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2022-03-17 7:09:41 PM
>> calculating RP using centerToTSS and peak score2022-03-17 7:09:41 PM
>> merging all info together 2022-03-17 7:09:43 PM
>> done 2022-03-17 7:09:43 PM
>> extracting RP info from regionRP... 2022-03-17 7:09:43 PM
>> dealing with TF_GR_databse... 2022-03-17 7:09:43 PM
>> calculating percent and p-value... 2022-03-17 7:09:43 PM
>> dealing withE5_0h_R1... 2022-03-17 7:09:43 PM
>> dealing withE5_0h_R2... 2022-03-17 7:09:44 PM
>> dealing withE5_4h_R1... 2022-03-17 7:09:44 PM
>> dealing withE5_4h_R2... 2022-03-17 7:09:44 PM
>> dealing withE5_8h_R1... 2022-03-17 7:09:44 PM
>> dealing withE5_8h_R2... 2022-03-17 7:09:44 PM
>> dealing withE5_16h_R1... 2022-03-17 7:09:44 PM
>> dealing withE5_16h_R2... 2022-03-17 7:09:44 PM
>> dealing withE5_24h_R1... 2022-03-17 7:09:44 PM
>> dealing withE5_24h_R2... 2022-03-17 7:09:44 PM
>> dealing withE5_48h_R1... 2022-03-17 7:09:44 PM
>> dealing withE5_48h_R2... 2022-03-17 7:09:44 PM
>> dealing withE5_48h_R3... 2022-03-17 7:09:44 PM
>> dealing withE5_72h_R1... 2022-03-17 7:09:44 PM
>> dealing withE5_72h_R2... 2022-03-17 7:09:44 PM
>> dealing withE5_72h_R3... 2022-03-17 7:09:44 PM
>> merging all info together... 2022-03-17 7:09:44 PM
>> done 2022-03-17 7:09:44 PM
>> preparing gene features information... 2022-03-17 7:09:44 PM
>> some scan range may cross Chr bound, trimming... 2022-03-17 7:09:45 PM
>> calculating p-value for each TF, which may be time consuming... 2022-03-17 7:09:45 PM
>> merging all info together... 2022-03-17 7:09:45 PM
>> done 2022-03-17 7:09:45 PM
>> dealing with TF_GR_database... 2022-03-17 7:09:45 PM
>> calculating coef and converting into z-score using INT... 2022-03-17 7:09:45 PM
>> dealing withE5_0h_R1... 2022-03-17 7:09:45 PM
>> dealing withE5_0h_R2... 2022-03-17 7:09:45 PM
>> dealing withE5_4h_R1... 2022-03-17 7:09:45 PM
>> dealing withE5_4h_R2... 2022-03-17 7:09:46 PM
>> dealing withE5_8h_R1... 2022-03-17 7:09:46 PM
>> dealing withE5_8h_R2... 2022-03-17 7:09:46 PM
>> dealing withE5_16h_R1... 2022-03-17 7:09:46 PM
>> dealing withE5_16h_R2... 2022-03-17 7:09:46 PM
>> dealing withE5_24h_R1... 2022-03-17 7:09:46 PM
>> dealing withE5_24h_R2... 2022-03-17 7:09:46 PM
>> dealing withE5_48h_R1... 2022-03-17 7:09:46 PM
>> dealing withE5_48h_R2... 2022-03-17 7:09:46 PM
>> dealing withE5_48h_R3... 2022-03-17 7:09:46 PM
>> dealing withE5_72h_R1... 2022-03-17 7:09:46 PM
>> dealing withE5_72h_R2... 2022-03-17 7:09:46 PM
>> dealing withE5_72h_R3... 2022-03-17 7:09:46 PM
>> merging all info together... 2022-03-17 7:09:46 PM
>> done 2022-03-17 7:09:47 PM
>> checking seqlevels match... 2022-03-17 7:09:47 PM
>> 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... 2022-03-17 7:09:47 PM
>> some scan range may cross Chr bound, trimming... 2022-03-17 7:09:47 PM
>> finding overlap peak in gene scan region... 2022-03-17 7:09:47 PM
>> dealing with left peak not your gene scan region... 2022-03-17 7:09:47 PM
>> merging two set peaks... 2022-03-17 7:09:47 PM
>> calculating distance and dealing with gene strand... 2022-03-17 7:09:48 PM
>> merging all info together ... 2022-03-17 7:09:48 PM
>> done 2022-03-17 7:09:48 PM
>> calculating peakCenter to TSS using peak-gene pair... 2022-03-17 7:09:48 PM
>> calculating RP using centerToTSS and TF hit 2022-03-17 7:09:48 PM
>> merging all info together 2022-03-17 7:09:48 PM
>> done 2022-03-17 7:09:48 PM
>> checking seqlevels match... 2022-03-17 7:09:49 PM
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2022-03-17 7:09:49 PM
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2022-03-17 7:09:51 PM
>> 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... 2022-03-17 7:09:51 PM
>> 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... 2022-03-17 7:09:51 PM
>> finding nearest gene and calculating distance... 2022-03-17 7:09:52 PM
>> dealing with gene strand ... 2022-03-17 7:09:52 PM
>> merging all info together ... 2022-03-17 7:09:52 PM
>> done 2022-03-17 7:09:52 PM
>> checking seqlevels match... 2022-03-17 7:09:52 PM
>> 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... 2022-03-17 7:09:52 PM
>> 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... 2022-03-17 7:09:52 PM
>> finding nearest gene and calculating distance... 2022-03-17 7:09:53 PM
>> dealing with gene strand ... 2022-03-17 7:09:53 PM
>> merging all info together ... 2022-03-17 7:09:53 PM
>> done 2022-03-17 7:09:53 PM
>> checking seqlevels match... 2022-03-17 7:09:54 PM
>> 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... 2022-03-17 7:09:54 PM
>> 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... 2022-03-17 7:09:54 PM
>> finding nearest gene and calculating distance... 2022-03-17 7:09:55 PM
>> dealing with gene strand ... 2022-03-17 7:09:55 PM
>> merging all info together ... 2022-03-17 7:09:55 PM
>> done 2022-03-17 7:09:55 PM
>> checking seqlevels match... 2022-03-17 7:09:56 PM
>> 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... 2022-03-17 7:09:56 PM
>> 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... 2022-03-17 7:09:56 PM
>> finding nearest gene and calculating distance... 2022-03-17 7:09:57 PM
>> dealing with gene strand ... 2022-03-17 7:09:57 PM
>> merging all info together ... 2022-03-17 7:09:57 PM
>> done 2022-03-17 7:09:57 PM
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2022-03-17 7:09:58 PM
>> 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... 2022-03-17 7:09:58 PM
>> 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... 2022-03-17 7:09:58 PM
>> finding nearest gene and calculating distance... 2022-03-17 7:09:59 PM
>> dealing with gene strand ... 2022-03-17 7:09:59 PM
>> merging all info together ... 2022-03-17 7:09:59 PM
>> done 2022-03-17 7:09:59 PM
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2022-03-17 7:09:59 PM
>> 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... 2022-03-17 7:10:01 PM
>> 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... 2022-03-17 7:10:02 PM
>> checking seqlevels match... 2022-03-17 7:10:02 PM
>> 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... 2022-03-17 7:10:03 PM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2022-03-17 7:10:04 PM
>> merging all info together... 2022-03-17 7:10:04 PM
>> done 2022-03-17 7:10:04 PM
>> checking seqlevels match... 2022-03-17 7:10:04 PM
>> 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... 2022-03-17 7:10:04 PM
>> checking seqlevels match... 2022-03-17 7:10:04 PM
>> 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... 2022-03-17 7:10:05 PM
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2022-03-17 7:10:05 PM
>> checking seqlevels match... 2022-03-17 7:10:05 PM
>> 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... 2022-03-17 7:10:06 PM
>> calculating cor and pvalue, which may be time consuming... 2022-03-17 7:10:06 PM
>> merging all info together... 2022-03-17 7:10:06 PM
>> done 2022-03-17 7:10:06 PM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2022-03-17 7:10:06 PM
>> merging all info together... 2022-03-17 7:10:06 PM
>> done 2022-03-17 7:10:06 PM
>> checking seqlevels match... 2022-03-17 7:10:06 PM
>> 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... 2022-03-17 7:10:06 PM
>> some scan range may cross Chr bound, trimming... 2022-03-17 7:10:07 PM
>> finding overlap peak in gene scan region... 2022-03-17 7:10:07 PM
>> dealing with left peak not your gene scan region... 2022-03-17 7:10:07 PM
>> merging two set peaks... 2022-03-17 7:10:07 PM
>> calculating distance and dealing with gene strand... 2022-03-17 7:10:07 PM
>> merging all info together ... 2022-03-17 7:10:07 PM
>> done 2022-03-17 7:10:07 PM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2022-03-17 7:10:08 PM
>> merging all info together... 2022-03-17 7:10:08 PM
>> done 2022-03-17 7:10:08 PM
>> checking seqlevels match... 2022-03-17 7:10:08 PM
>> 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... 2022-03-17 7:10:08 PM
>> checking seqlevels match... 2022-03-17 7:10:08 PM
>> 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... 2022-03-17 7:10:08 PM
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2022-03-17 7:10:09 PM
>> checking seqlevels match... 2022-03-17 7:10:09 PM
>> 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... 2022-03-17 7:10:10 PM
>> calculating cor and pvalue, which may be time consuming... 2022-03-17 7:10:10 PM
>> merging all info together... 2022-03-17 7:10:10 PM
>> done 2022-03-17 7:10:10 PM
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 63 ]
>
> proc.time()
user system elapsed
54.29 2.82 57.10
FindIT2.Rcheck/FindIT2-Ex.timings
| name | user | system | elapsed | |
| TF_target_database | 0 | 0 | 0 | |
| calcRP_TFHit | 2.78 | 0.05 | 2.83 | |
| calcRP_coverage | 0.05 | 0.00 | 0.04 | |
| calcRP_region | 4.46 | 0.32 | 4.78 | |
| enhancerPromoterCor | 2.03 | 0.11 | 2.14 | |
| findIT_MARA | 0.36 | 0.00 | 0.36 | |
| findIT_TFHit | 0.72 | 0.02 | 0.73 | |
| findIT_TTPair | 0.06 | 0.06 | 0.13 | |
| findIT_enrichFisher | 0.12 | 0.00 | 0.12 | |
| findIT_enrichWilcox | 0.13 | 0.02 | 0.14 | |
| findIT_regionRP | 4.59 | 0.14 | 4.74 | |
| getAssocPairNumber | 0.89 | 0.03 | 0.92 | |
| integrate_ChIP_RNA | 1.52 | 0.05 | 1.56 | |
| integrate_replicates | 0 | 0 | 0 | |
| jaccard_findIT_TTpair | 0.09 | 0.04 | 0.14 | |
| jaccard_findIT_enrichFisher | 0.16 | 0.00 | 0.16 | |
| loadPeakFile | 0.04 | 0.00 | 0.05 | |
| mm_geneBound | 0.91 | 0.03 | 0.93 | |
| mm_geneScan | 0.89 | 0.00 | 0.89 | |
| mm_nearestGene | 1.42 | 0.08 | 1.50 | |
| peakGeneCor | 1.50 | 0.16 | 1.66 | |
| plot_annoDistance | 0.97 | 0.09 | 1.06 | |
| plot_peakGeneAlias_summary | 0.91 | 0.11 | 1.02 | |
| plot_peakGeneCor | 2.08 | 0.05 | 2.12 | |
| test_geneSet | 0 | 0 | 0 | |