| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-29 16:33:47 -0000 (Sun, 29 Jan 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" | 4021 |
| 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 | ||||
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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
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| 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: 2023-01-28 22:58:09 -0000 (Sat, 28 Jan 2023) |
| EndedAt: 2023-01-28 23:06:02 -0000 (Sat, 28 Jan 2023) |
| EllapsedTime: 473.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: FindIT2.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### 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 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
Warning message:
In utils::packageDescription(basename(dir), dirname(dir)) :
no package 'FindIT2' was found
* 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 loading without being on the library search path ... WARNING
Error in library(FindIT2, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") :
there is no package called ‘FindIT2’
Execution halted
It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* 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 ... SKIPPED
* 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: 2 WARNINGs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/FindIT2.Rcheck/00check.log’
for details.
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/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) (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... 2023-01-28 23:02:48
>> some scan range may cross Chr bound, trimming... 2023-01-28 23:02:50
>> preparing weight info... 2023-01-28 23:02:50
>> loading E50h_sampleChr5.bw info... 2023-01-28 23:02:50
------------
>> extracting and calcluating Chr5 signal... 2023-01-28 23:02:51
>> dealing with Chr5 left gene signal... 2023-01-28 23:03:00
>> norming Chr5RP accoring to the whole Chr RP... 2023-01-28 23:03:00
>> merging all Chr RP together... 2023-01-28 23:03:00
>> done 2023-01-28 23:03:00
>> checking seqlevels match... 2023-01-28 23:03:00
>> 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2023-01-28 23:03:00
>> some scan range may cross Chr bound, trimming... 2023-01-28 23:03:01
>> finding overlap peak in gene scan region... 2023-01-28 23:03:01
>> dealing with left peak not your gene scan region... 2023-01-28 23:03:01
>> merging two set peaks... 2023-01-28 23:03:02
>> calculating distance and dealing with gene strand... 2023-01-28 23:03:02
>> merging all info together ... 2023-01-28 23:03:02
>> done 2023-01-28 23:03:02
>> calculating peakCenter to TSS using peak-gene pair... 2023-01-28 23:03:02
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2023-01-28 23:03:03
>> calculating RP using centerToTSS and peak score2023-01-28 23:03:03
>> merging all info together 2023-01-28 23:03:06
>> done 2023-01-28 23:03:07
>> calculating peakCenter to TSS using peak-gene pair... 2023-01-28 23:03:07
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2023-01-28 23:03:08
>> calculating RP using centerToTSS and peak score2023-01-28 23:03:08
>> merging all info together 2023-01-28 23:03:12
>> done 2023-01-28 23:03:13
>> checking seqlevels match... 2023-01-28 23:03:13
>> 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... 2023-01-28 23:03:13
>> some scan range may cross Chr bound, trimming... 2023-01-28 23:03:14
>> finding overlap peak in gene scan region... 2023-01-28 23:03:14
>> dealing with left peak not your gene scan region... 2023-01-28 23:03:14
>> merging two set peaks... 2023-01-28 23:03:15
>> calculating distance and dealing with gene strand... 2023-01-28 23:03:15
>> merging all info together ... 2023-01-28 23:03:15
>> done 2023-01-28 23:03:15
>> calculating peakCenter to TSS using peak-gene pair... 2023-01-28 23:03:15
>> calculating RP using centerToTSS and TF hit 2023-01-28 23:03:16
>> merging all info together 2023-01-28 23:03:16
>> done 2023-01-28 23:03:16
>> calculating peakCenter to TSS using peak-gene pair... 2023-01-28 23:03:16
>> calculating RP using centerToTSS and TF hit 2023-01-28 23:03:17
>> merging all info together 2023-01-28 23:03:17
>> done 2023-01-28 23:03:17
>> checking seqlevels match... 2023-01-28 23:03:18
>> 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... 2023-01-28 23:03:18
>> some scan range may cross Chr bound, trimming... 2023-01-28 23:03:19
>> finding overlap peak in gene scan region... 2023-01-28 23:03:19
>> dealing with left peak not your gene scan region... 2023-01-28 23:03:19
>> merging two set peaks... 2023-01-28 23:03:19
>> calculating distance and dealing with gene strand... 2023-01-28 23:03:20
>> merging all info together ... 2023-01-28 23:03:20
>> done 2023-01-28 23:03:20
>> calculating peakCenter to TSS using peak-gene pair... 2023-01-28 23:03:20
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2023-01-28 23:03:21
>> calculating RP using centerToTSS and peak score2023-01-28 23:03:21
>> merging all info together 2023-01-28 23:03:24
>> done 2023-01-28 23:03:24
>> extracting RP info from regionRP... 2023-01-28 23:03:26
>> dealing with TF_GR_databse... 2023-01-28 23:03:26
>> calculating percent and p-value... 2023-01-28 23:03:26
>> dealing withE5_0h_R1... 2023-01-28 23:03:26
>> dealing withE5_0h_R2... 2023-01-28 23:03:26
>> dealing withE5_4h_R1... 2023-01-28 23:03:26
>> dealing withE5_4h_R2... 2023-01-28 23:03:26
>> dealing withE5_8h_R1... 2023-01-28 23:03:27
>> dealing withE5_8h_R2... 2023-01-28 23:03:27
>> dealing withE5_16h_R1... 2023-01-28 23:03:27
>> dealing withE5_16h_R2... 2023-01-28 23:03:27
>> dealing withE5_24h_R1... 2023-01-28 23:03:27
>> dealing withE5_24h_R2... 2023-01-28 23:03:27
>> dealing withE5_48h_R1... 2023-01-28 23:03:27
>> dealing withE5_48h_R2... 2023-01-28 23:03:27
>> dealing withE5_48h_R3... 2023-01-28 23:03:27
>> dealing withE5_72h_R1... 2023-01-28 23:03:27
>> dealing withE5_72h_R2... 2023-01-28 23:03:27
>> dealing withE5_72h_R3... 2023-01-28 23:03:27
>> merging all info together... 2023-01-28 23:03:27
>> done 2023-01-28 23:03:27
>> preparing gene features information... 2023-01-28 23:03:28
>> some scan range may cross Chr bound, trimming... 2023-01-28 23:03:29
>> calculating p-value for each TF, which may be time consuming... 2023-01-28 23:03:29
>> merging all info together... 2023-01-28 23:03:29
>> done 2023-01-28 23:03:29
>> dealing with TF_GR_database... 2023-01-28 23:03:29
>> calculating coef and converting into z-score using INT... 2023-01-28 23:03:29
>> dealing with E5_0h_R1... 2023-01-28 23:03:29
>> dealing with E5_0h_R2... 2023-01-28 23:03:30
>> dealing with E5_4h_R1... 2023-01-28 23:03:30
>> dealing with E5_4h_R2... 2023-01-28 23:03:30
>> dealing with E5_8h_R1... 2023-01-28 23:03:30
>> dealing with E5_8h_R2... 2023-01-28 23:03:30
>> dealing with E5_16h_R1... 2023-01-28 23:03:30
>> dealing with E5_16h_R2... 2023-01-28 23:03:30
>> dealing with E5_24h_R1... 2023-01-28 23:03:30
>> dealing with E5_24h_R2... 2023-01-28 23:03:30
>> dealing with E5_48h_R1... 2023-01-28 23:03:31
>> dealing with E5_48h_R2... 2023-01-28 23:03:31
>> dealing with E5_48h_R3... 2023-01-28 23:03:31
>> dealing with E5_72h_R1... 2023-01-28 23:03:31
>> dealing with E5_72h_R2... 2023-01-28 23:03:31
>> dealing with E5_72h_R3... 2023-01-28 23:03:31
>> merging all info together... 2023-01-28 23:03:31
>> done 2023-01-28 23:03:31
>> checking seqlevels match... 2023-01-28 23:03:31
>> 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... 2023-01-28 23:03:32
>> some scan range may cross Chr bound, trimming... 2023-01-28 23:03:33
>> finding overlap peak in gene scan region... 2023-01-28 23:03:33
>> dealing with left peak not your gene scan region... 2023-01-28 23:03:33
>> merging two set peaks... 2023-01-28 23:03:33
>> calculating distance and dealing with gene strand... 2023-01-28 23:03:33
>> merging all info together ... 2023-01-28 23:03:33
>> done 2023-01-28 23:03:33
>> calculating peakCenter to TSS using peak-gene pair... 2023-01-28 23:03:33
>> calculating RP using centerToTSS and TF hit 2023-01-28 23:03:34
>> merging all info together 2023-01-28 23:03:34
>> done 2023-01-28 23:03:34
>> checking seqlevels match... 2023-01-28 23:03:35
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2023-01-28 23:03:35
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2023-01-28 23:03:39
>> 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... 2023-01-28 23:03:39
>> 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2023-01-28 23:03:39
>> finding nearest gene and calculating distance... 2023-01-28 23:03:40
>> dealing with gene strand ... 2023-01-28 23:03:40
>> merging all info together ... 2023-01-28 23:03:40
>> done 2023-01-28 23:03:40
>> checking seqlevels match... 2023-01-28 23:03:40
>> 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... 2023-01-28 23:03:41
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2023-01-28 23:03:41
>> finding nearest gene and calculating distance... 2023-01-28 23:03:43
>> dealing with gene strand ... 2023-01-28 23:03:43
>> merging all info together ... 2023-01-28 23:03:43
>> done 2023-01-28 23:03:43
>> checking seqlevels match... 2023-01-28 23:03:44
>> 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... 2023-01-28 23:03:44
>> 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... 2023-01-28 23:03:44
>> finding nearest gene and calculating distance... 2023-01-28 23:03:45
>> dealing with gene strand ... 2023-01-28 23:03:45
>> merging all info together ... 2023-01-28 23:03:45
>> done 2023-01-28 23:03:45
>> checking seqlevels match... 2023-01-28 23:03:46
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> checking seqlevels match... 2023-01-28 23:03:46
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2023-01-28 23:03:46
>> finding nearest gene and calculating distance... 2023-01-28 23:03:47
>> dealing with gene strand ... 2023-01-28 23:03:48
>> merging all info together ... 2023-01-28 23:03:48
>> done 2023-01-28 23:03:48
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2023-01-28 23:03:49
>> 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... 2023-01-28 23:03:49
>> 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... 2023-01-28 23:03:49
>> finding nearest gene and calculating distance... 2023-01-28 23:03:50
>> dealing with gene strand ... 2023-01-28 23:03:50
>> merging all info together ... 2023-01-28 23:03:50
>> done 2023-01-28 23:03:50
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2023-01-28 23:03:51
>> 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... 2023-01-28 23:03:53
>> 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... 2023-01-28 23:03:54
>> checking seqlevels match... 2023-01-28 23:03:55
>> 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... 2023-01-28 23:03:56
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2023-01-28 23:03:57
>> merging all info together... 2023-01-28 23:03:58
>> done 2023-01-28 23:03:58
>> checking seqlevels match... 2023-01-28 23:03:58
>> 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
>> using scanPromoter parameter to scan promoter for each gene... 2023-01-28 23:03:58
>> checking seqlevels match... 2023-01-28 23:03:58
>> 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
>> some scan range may cross Chr bound, trimming... 2023-01-28 23:03:59
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2023-01-28 23:03:59
>> checking seqlevels match... 2023-01-28 23:03:59
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming... 2023-01-28 23:04:00
>> calculating cor and pvalue, which may be time consuming... 2023-01-28 23:04:01
>> merging all info together... 2023-01-28 23:04:01
>> done 2023-01-28 23:04:01
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2023-01-28 23:04:01
>> merging all info together... 2023-01-28 23:04:01
>> done 2023-01-28 23:04:01
>> checking seqlevels match... 2023-01-28 23:04:01
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2023-01-28 23:04:01
>> some scan range may cross Chr bound, trimming... 2023-01-28 23:04:02
>> finding overlap peak in gene scan region... 2023-01-28 23:04:02
>> dealing with left peak not your gene scan region... 2023-01-28 23:04:02
>> merging two set peaks... 2023-01-28 23:04:03
>> calculating distance and dealing with gene strand... 2023-01-28 23:04:03
>> merging all info together ... 2023-01-28 23:04:03
>> done 2023-01-28 23:04:03
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2023-01-28 23:04:04
>> merging all info together... 2023-01-28 23:04:04
>> done 2023-01-28 23:04:04
>> checking seqlevels match... 2023-01-28 23:04:04
>> 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... 2023-01-28 23:04:05
>> checking seqlevels match... 2023-01-28 23:04:05
>> 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... 2023-01-28 23:04:06
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2023-01-28 23:04:06
>> checking seqlevels match... 2023-01-28 23:04:06
>> your peak_GR seqlevel:Chr5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
Good, your Chrs in peak_GR is all in Txdb
>> some scan range may cross Chr bound, trimming... 2023-01-28 23:04:07
>> calculating cor and pvalue, which may be time consuming... 2023-01-28 23:04:07
>> merging all info together... 2023-01-28 23:04:08
>> done 2023-01-28 23:04:08
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
94.887 1.170 96.314