Guandong Shang
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/FindIT2 |
| git_branch: RELEASE_3_14 |
| git_last_commit: e395076 |
| git_last_commit_date: 2021-12-28 22:21:52 -0400 (Tue, 28 Dec 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:33 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 642/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FindIT2 1.0.3 (landing page) Guandong Shang
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: FindIT2 |
| Version: 1.0.3 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FindIT2.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings FindIT2_1.0.3.tar.gz |
| StartedAt: 2022-04-12 19:38:30 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 19:47:34 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 544.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FindIT2.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FindIT2.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings FindIT2_1.0.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/FindIT2.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.0.3'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
calcRP_region 6.12 0.41 7.05
findIT_regionRP 6.30 0.03 6.32
calcRP_TFHit 4.71 0.24 41.45
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
calcRP_region 6.75 0.03 6.78
findIT_regionRP 6.70 0.06 6.77
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/FindIT2_1.0.3.tar.gz && rm -rf FindIT2.buildbin-libdir && mkdir FindIT2.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FindIT2.buildbin-libdir FindIT2_1.0.3.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL FindIT2_1.0.3.zip && rm FindIT2_1.0.3.tar.gz FindIT2_1.0.3.zip
###
##############################################################################
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
24 798k 24 194k 0 0 639k 0 0:00:01 --:--:-- 0:00:01 639k
100 798k 100 798k 0 0 916k 0 --:--:-- --:--:-- --:--:-- 916k
install for i386
* 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
install for x64
* installing *source* package 'FindIT2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FindIT2' as FindIT2_1.0.3.zip
* DONE (FindIT2)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'FindIT2' successfully unpacked and MD5 sums checked
|
FindIT2.Rcheck/tests_i386/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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... 2022-04-12 7:45:27 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... 2022-04-12 7:45:27 PM
>> some scan range may cross Chr bound, trimming... 2022-04-12 7:45:29 PM
>> finding overlap peak in gene scan region... 2022-04-12 7:45:29 PM
>> dealing with left peak not your gene scan region... 2022-04-12 7:45:29 PM
>> merging two set peaks... 2022-04-12 7:45:29 PM
>> calculating distance and dealing with gene strand... 2022-04-12 7:45:30 PM
>> merging all info together ... 2022-04-12 7:45:30 PM
>> done 2022-04-12 7:45:30 PM
>> calculating peakCenter to TSS using peak-gene pair... 2022-04-12 7:45:30 PM
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2022-04-12 7:45:30 PM
>> calculating RP using centerToTSS and peak score2022-04-12 7:45:30 PM
>> merging all info together 2022-04-12 7:45:33 PM
>> done 2022-04-12 7:45:34 PM
>> calculating peakCenter to TSS using peak-gene pair... 2022-04-12 7:45:34 PM
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2022-04-12 7:45:35 PM
>> calculating RP using centerToTSS and peak score2022-04-12 7:45:35 PM
>> merging all info together 2022-04-12 7:45:37 PM
>> done 2022-04-12 7:45:38 PM
>> checking seqlevels match... 2022-04-12 7:45:38 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... 2022-04-12 7:45:38 PM
>> some scan range may cross Chr bound, trimming... 2022-04-12 7:45:39 PM
>> finding overlap peak in gene scan region... 2022-04-12 7:45:39 PM
>> dealing with left peak not your gene scan region... 2022-04-12 7:45:39 PM
>> merging two set peaks... 2022-04-12 7:45:39 PM
>> calculating distance and dealing with gene strand... 2022-04-12 7:45:39 PM
>> merging all info together ... 2022-04-12 7:45:39 PM
>> done 2022-04-12 7:45:39 PM
>> calculating peakCenter to TSS using peak-gene pair... 2022-04-12 7:45:39 PM
>> calculating RP using centerToTSS and TF hit 2022-04-12 7:45:40 PM
>> merging all info together 2022-04-12 7:45:40 PM
>> done 2022-04-12 7:45:40 PM
>> calculating peakCenter to TSS using peak-gene pair... 2022-04-12 7:45:40 PM
>> calculating RP using centerToTSS and TF hit 2022-04-12 7:45:40 PM
>> merging all info together 2022-04-12 7:45:40 PM
>> done 2022-04-12 7:45:40 PM
>> checking seqlevels match... 2022-04-12 7:45:47 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... 2022-04-12 7:45:47 PM
>> some scan range may cross Chr bound, trimming... 2022-04-12 7:45:47 PM
>> finding overlap peak in gene scan region... 2022-04-12 7:45:47 PM
>> dealing with left peak not your gene scan region... 2022-04-12 7:45:47 PM
>> merging two set peaks... 2022-04-12 7:45:48 PM
>> calculating distance and dealing with gene strand... 2022-04-12 7:45:48 PM
>> merging all info together ... 2022-04-12 7:45:48 PM
>> done 2022-04-12 7:45:48 PM
>> calculating peakCenter to TSS using peak-gene pair... 2022-04-12 7:45:48 PM
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2022-04-12 7:45:48 PM
>> calculating RP using centerToTSS and peak score2022-04-12 7:45:48 PM
>> merging all info together 2022-04-12 7:45:50 PM
>> done 2022-04-12 7:45:50 PM
>> extracting RP info from regionRP... 2022-04-12 7:45:51 PM
>> dealing with TF_GR_databse... 2022-04-12 7:45:51 PM
>> calculating percent and p-value... 2022-04-12 7:45:51 PM
>> dealing withE5_0h_R1... 2022-04-12 7:45:51 PM
>> dealing withE5_0h_R2... 2022-04-12 7:45:51 PM
>> dealing withE5_4h_R1... 2022-04-12 7:45:51 PM
>> dealing withE5_4h_R2... 2022-04-12 7:45:51 PM
>> dealing withE5_8h_R1... 2022-04-12 7:45:51 PM
>> dealing withE5_8h_R2... 2022-04-12 7:45:51 PM
>> dealing withE5_16h_R1... 2022-04-12 7:45:51 PM
>> dealing withE5_16h_R2... 2022-04-12 7:45:51 PM
>> dealing withE5_24h_R1... 2022-04-12 7:45:51 PM
>> dealing withE5_24h_R2... 2022-04-12 7:45:52 PM
>> dealing withE5_48h_R1... 2022-04-12 7:45:52 PM
>> dealing withE5_48h_R2... 2022-04-12 7:45:52 PM
>> dealing withE5_48h_R3... 2022-04-12 7:45:52 PM
>> dealing withE5_72h_R1... 2022-04-12 7:45:52 PM
>> dealing withE5_72h_R2... 2022-04-12 7:45:52 PM
>> dealing withE5_72h_R3... 2022-04-12 7:45:52 PM
>> merging all info together... 2022-04-12 7:45:52 PM
>> done 2022-04-12 7:45:52 PM
>> preparing gene features information... 2022-04-12 7:45:52 PM
>> some scan range may cross Chr bound, trimming... 2022-04-12 7:45:53 PM
>> calculating p-value for each TF, which may be time consuming... 2022-04-12 7:45:53 PM
>> merging all info together... 2022-04-12 7:45:53 PM
>> done 2022-04-12 7:45:53 PM
>> dealing with TF_GR_database... 2022-04-12 7:45:53 PM
>> calculating coef and converting into z-score using INT... 2022-04-12 7:45:53 PM
>> dealing withE5_0h_R1... 2022-04-12 7:45:53 PM
>> dealing withE5_0h_R2... 2022-04-12 7:45:53 PM
>> dealing withE5_4h_R1... 2022-04-12 7:45:53 PM
>> dealing withE5_4h_R2... 2022-04-12 7:45:53 PM
>> dealing withE5_8h_R1... 2022-04-12 7:45:54 PM
>> dealing withE5_8h_R2... 2022-04-12 7:45:54 PM
>> dealing withE5_16h_R1... 2022-04-12 7:45:54 PM
>> dealing withE5_16h_R2... 2022-04-12 7:45:54 PM
>> dealing withE5_24h_R1... 2022-04-12 7:45:54 PM
>> dealing withE5_24h_R2... 2022-04-12 7:45:54 PM
>> dealing withE5_48h_R1... 2022-04-12 7:45:54 PM
>> dealing withE5_48h_R2... 2022-04-12 7:45:54 PM
>> dealing withE5_48h_R3... 2022-04-12 7:45:54 PM
>> dealing withE5_72h_R1... 2022-04-12 7:45:54 PM
>> dealing withE5_72h_R2... 2022-04-12 7:45:54 PM
>> dealing withE5_72h_R3... 2022-04-12 7:45:54 PM
>> merging all info together... 2022-04-12 7:45:54 PM
>> done 2022-04-12 7:45:54 PM
>> checking seqlevels match... 2022-04-12 7:45:55 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... 2022-04-12 7:45:55 PM
>> some scan range may cross Chr bound, trimming... 2022-04-12 7:45:55 PM
>> finding overlap peak in gene scan region... 2022-04-12 7:45:55 PM
>> dealing with left peak not your gene scan region... 2022-04-12 7:45:55 PM
>> merging two set peaks... 2022-04-12 7:45:55 PM
>> calculating distance and dealing with gene strand... 2022-04-12 7:45:56 PM
>> merging all info together ... 2022-04-12 7:45:56 PM
>> done 2022-04-12 7:45:56 PM
>> calculating peakCenter to TSS using peak-gene pair... 2022-04-12 7:45:56 PM
>> calculating RP using centerToTSS and TF hit 2022-04-12 7:45:56 PM
>> merging all info together 2022-04-12 7:45:56 PM
>> done 2022-04-12 7:45:56 PM
>> checking seqlevels match... 2022-04-12 7:45:57 PM
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2022-04-12 7:45:57 PM
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2022-04-12 7:46:00 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... 2022-04-12 7:46:00 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... 2022-04-12 7:46:00 PM
>> finding nearest gene and calculating distance... 2022-04-12 7:46:00 PM
>> dealing with gene strand ... 2022-04-12 7:46:01 PM
>> merging all info together ... 2022-04-12 7:46:01 PM
>> done 2022-04-12 7:46:01 PM
>> checking seqlevels match... 2022-04-12 7:46:01 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
>> checking seqlevels match... 2022-04-12 7:46:01 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2022-04-12 7:46:01 PM
>> finding nearest gene and calculating distance... 2022-04-12 7:46:02 PM
>> dealing with gene strand ... 2022-04-12 7:46:02 PM
>> merging all info together ... 2022-04-12 7:46:02 PM
>> done 2022-04-12 7:46:02 PM
>> checking seqlevels match... 2022-04-12 7:46:03 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... 2022-04-12 7:46:03 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... 2022-04-12 7:46:03 PM
>> finding nearest gene and calculating distance... 2022-04-12 7:46:04 PM
>> dealing with gene strand ... 2022-04-12 7:46:04 PM
>> merging all info together ... 2022-04-12 7:46:04 PM
>> done 2022-04-12 7:46:04 PM
>> checking seqlevels match... 2022-04-12 7:46:05 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
>> checking seqlevels match... 2022-04-12 7:46:05 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2022-04-12 7:46:05 PM
>> finding nearest gene and calculating distance... 2022-04-12 7:46:05 PM
>> dealing with gene strand ... 2022-04-12 7:46:05 PM
>> merging all info together ... 2022-04-12 7:46:05 PM
>> done 2022-04-12 7:46:05 PM
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2022-04-12 7:46:06 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
>> checking seqlevels match... 2022-04-12 7:46:06 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2022-04-12 7:46:06 PM
>> finding nearest gene and calculating distance... 2022-04-12 7:46:07 PM
>> dealing with gene strand ... 2022-04-12 7:46:07 PM
>> merging all info together ... 2022-04-12 7:46:07 PM
>> done 2022-04-12 7:46:07 PM
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2022-04-12 7:46:08 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
>> checking seqlevels match... 2022-04-12 7:46:09 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... 2022-04-12 7:46:10 PM
>> checking seqlevels match... 2022-04-12 7:46:11 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... 2022-04-12 7:46:12 PM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2022-04-12 7:46:13 PM
>> merging all info together... 2022-04-12 7:46:13 PM
>> done 2022-04-12 7:46:13 PM
>> checking seqlevels match... 2022-04-12 7:46:13 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... 2022-04-12 7:46:13 PM
>> checking seqlevels match... 2022-04-12 7:46:13 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... 2022-04-12 7:46:14 PM
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2022-04-12 7:46:14 PM
>> checking seqlevels match... 2022-04-12 7:46:14 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... 2022-04-12 7:46:15 PM
>> calculating cor and pvalue, which may be time consuming... 2022-04-12 7:46:15 PM
>> merging all info together... 2022-04-12 7:46:15 PM
>> done 2022-04-12 7:46:15 PM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2022-04-12 7:46:15 PM
>> merging all info together... 2022-04-12 7:46:15 PM
>> done 2022-04-12 7:46:16 PM
>> checking seqlevels match... 2022-04-12 7:46:16 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... 2022-04-12 7:46:16 PM
>> some scan range may cross Chr bound, trimming... 2022-04-12 7:46:17 PM
>> finding overlap peak in gene scan region... 2022-04-12 7:46:17 PM
>> dealing with left peak not your gene scan region... 2022-04-12 7:46:17 PM
>> merging two set peaks... 2022-04-12 7:46:17 PM
>> calculating distance and dealing with gene strand... 2022-04-12 7:46:18 PM
>> merging all info together ... 2022-04-12 7:46:18 PM
>> done 2022-04-12 7:46:18 PM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2022-04-12 7:46:18 PM
>> merging all info together... 2022-04-12 7:46:18 PM
>> done 2022-04-12 7:46:18 PM
>> checking seqlevels match... 2022-04-12 7:46:18 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... 2022-04-12 7:46:19 PM
>> checking seqlevels match... 2022-04-12 7:46:19 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... 2022-04-12 7:46:19 PM
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2022-04-12 7:46:20 PM
>> checking seqlevels match... 2022-04-12 7:46:20 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... 2022-04-12 7:46:20 PM
>> calculating cor and pvalue, which may be time consuming... 2022-04-12 7:46:21 PM
>> merging all info together... 2022-04-12 7:46:21 PM
>> done 2022-04-12 7:46:21 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
58.34 1.78 64.48
|
FindIT2.Rcheck/tests_x64/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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... 2022-04-12 7:46:33 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... 2022-04-12 7:46:33 PM
>> some scan range may cross Chr bound, trimming... 2022-04-12 7:46:34 PM
>> finding overlap peak in gene scan region... 2022-04-12 7:46:34 PM
>> dealing with left peak not your gene scan region... 2022-04-12 7:46:34 PM
>> merging two set peaks... 2022-04-12 7:46:35 PM
>> calculating distance and dealing with gene strand... 2022-04-12 7:46:35 PM
>> merging all info together ... 2022-04-12 7:46:35 PM
>> done 2022-04-12 7:46:35 PM
>> calculating peakCenter to TSS using peak-gene pair... 2022-04-12 7:46:35 PM
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2022-04-12 7:46:36 PM
>> calculating RP using centerToTSS and peak score2022-04-12 7:46:36 PM
>> merging all info together 2022-04-12 7:46:39 PM
>> done 2022-04-12 7:46:40 PM
>> calculating peakCenter to TSS using peak-gene pair... 2022-04-12 7:46:40 PM
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2022-04-12 7:46:41 PM
>> calculating RP using centerToTSS and peak score2022-04-12 7:46:41 PM
>> merging all info together 2022-04-12 7:46:44 PM
>> done 2022-04-12 7:46:44 PM
>> checking seqlevels match... 2022-04-12 7:46:45 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... 2022-04-12 7:46:45 PM
>> some scan range may cross Chr bound, trimming... 2022-04-12 7:46:46 PM
>> finding overlap peak in gene scan region... 2022-04-12 7:46:46 PM
>> dealing with left peak not your gene scan region... 2022-04-12 7:46:46 PM
>> merging two set peaks... 2022-04-12 7:46:46 PM
>> calculating distance and dealing with gene strand... 2022-04-12 7:46:46 PM
>> merging all info together ... 2022-04-12 7:46:46 PM
>> done 2022-04-12 7:46:46 PM
>> calculating peakCenter to TSS using peak-gene pair... 2022-04-12 7:46:46 PM
>> calculating RP using centerToTSS and TF hit 2022-04-12 7:46:47 PM
>> merging all info together 2022-04-12 7:46:47 PM
>> done 2022-04-12 7:46:47 PM
>> calculating peakCenter to TSS using peak-gene pair... 2022-04-12 7:46:47 PM
>> calculating RP using centerToTSS and TF hit 2022-04-12 7:46:48 PM
>> merging all info together 2022-04-12 7:46:48 PM
>> done 2022-04-12 7:46:48 PM
>> checking seqlevels match... 2022-04-12 7:46:49 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... 2022-04-12 7:46:49 PM
>> some scan range may cross Chr bound, trimming... 2022-04-12 7:46:49 PM
>> finding overlap peak in gene scan region... 2022-04-12 7:46:49 PM
>> dealing with left peak not your gene scan region... 2022-04-12 7:46:49 PM
>> merging two set peaks... 2022-04-12 7:46:50 PM
>> calculating distance and dealing with gene strand... 2022-04-12 7:46:50 PM
>> merging all info together ... 2022-04-12 7:46:50 PM
>> done 2022-04-12 7:46:50 PM
>> calculating peakCenter to TSS using peak-gene pair... 2022-04-12 7:46:50 PM
>> pre-filling 1356 noAssoc peak gene's RP with 0... 2022-04-12 7:46:50 PM
>> calculating RP using centerToTSS and peak score2022-04-12 7:46:50 PM
>> merging all info together 2022-04-12 7:46:53 PM
>> done 2022-04-12 7:46:53 PM
>> extracting RP info from regionRP... 2022-04-12 7:46:54 PM
>> dealing with TF_GR_databse... 2022-04-12 7:46:54 PM
>> calculating percent and p-value... 2022-04-12 7:46:54 PM
>> dealing withE5_0h_R1... 2022-04-12 7:46:54 PM
>> dealing withE5_0h_R2... 2022-04-12 7:46:54 PM
>> dealing withE5_4h_R1... 2022-04-12 7:46:54 PM
>> dealing withE5_4h_R2... 2022-04-12 7:46:54 PM
>> dealing withE5_8h_R1... 2022-04-12 7:46:54 PM
>> dealing withE5_8h_R2... 2022-04-12 7:46:54 PM
>> dealing withE5_16h_R1... 2022-04-12 7:46:54 PM
>> dealing withE5_16h_R2... 2022-04-12 7:46:54 PM
>> dealing withE5_24h_R1... 2022-04-12 7:46:54 PM
>> dealing withE5_24h_R2... 2022-04-12 7:46:54 PM
>> dealing withE5_48h_R1... 2022-04-12 7:46:54 PM
>> dealing withE5_48h_R2... 2022-04-12 7:46:54 PM
>> dealing withE5_48h_R3... 2022-04-12 7:46:54 PM
>> dealing withE5_72h_R1... 2022-04-12 7:46:55 PM
>> dealing withE5_72h_R2... 2022-04-12 7:46:55 PM
>> dealing withE5_72h_R3... 2022-04-12 7:46:55 PM
>> merging all info together... 2022-04-12 7:46:55 PM
>> done 2022-04-12 7:46:55 PM
>> preparing gene features information... 2022-04-12 7:46:55 PM
>> some scan range may cross Chr bound, trimming... 2022-04-12 7:46:56 PM
>> calculating p-value for each TF, which may be time consuming... 2022-04-12 7:46:56 PM
>> merging all info together... 2022-04-12 7:46:56 PM
>> done 2022-04-12 7:46:56 PM
>> dealing with TF_GR_database... 2022-04-12 7:46:56 PM
>> calculating coef and converting into z-score using INT... 2022-04-12 7:46:56 PM
>> dealing withE5_0h_R1... 2022-04-12 7:46:56 PM
>> dealing withE5_0h_R2... 2022-04-12 7:46:57 PM
>> dealing withE5_4h_R1... 2022-04-12 7:46:57 PM
>> dealing withE5_4h_R2... 2022-04-12 7:46:57 PM
>> dealing withE5_8h_R1... 2022-04-12 7:46:57 PM
>> dealing withE5_8h_R2... 2022-04-12 7:46:57 PM
>> dealing withE5_16h_R1... 2022-04-12 7:46:57 PM
>> dealing withE5_16h_R2... 2022-04-12 7:46:57 PM
>> dealing withE5_24h_R1... 2022-04-12 7:46:57 PM
>> dealing withE5_24h_R2... 2022-04-12 7:46:57 PM
>> dealing withE5_48h_R1... 2022-04-12 7:46:57 PM
>> dealing withE5_48h_R2... 2022-04-12 7:46:58 PM
>> dealing withE5_48h_R3... 2022-04-12 7:46:58 PM
>> dealing withE5_72h_R1... 2022-04-12 7:46:58 PM
>> dealing withE5_72h_R2... 2022-04-12 7:46:58 PM
>> dealing withE5_72h_R3... 2022-04-12 7:46:58 PM
>> merging all info together... 2022-04-12 7:46:58 PM
>> done 2022-04-12 7:46:58 PM
>> checking seqlevels match... 2022-04-12 7:46:58 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
------------
annotatePeak using geneScan mode begins
>> preparing gene features information and scan region... 2022-04-12 7:46:58 PM
>> some scan range may cross Chr bound, trimming... 2022-04-12 7:46:59 PM
>> finding overlap peak in gene scan region... 2022-04-12 7:46:59 PM
>> dealing with left peak not your gene scan region... 2022-04-12 7:46:59 PM
>> merging two set peaks... 2022-04-12 7:46:59 PM
>> calculating distance and dealing with gene strand... 2022-04-12 7:46:59 PM
>> merging all info together ... 2022-04-12 7:46:59 PM
>> done 2022-04-12 7:46:59 PM
>> calculating peakCenter to TSS using peak-gene pair... 2022-04-12 7:46:59 PM
>> calculating RP using centerToTSS and TF hit 2022-04-12 7:47:00 PM
>> merging all info together 2022-04-12 7:47:00 PM
>> done 2022-04-12 7:47:00 PM
>> checking seqlevels match... 2022-04-12 7:47:01 PM
>> your peak_GR seqlevel:5...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2022-04-12 7:47:01 PM
>> your peak_GR seqlevel:Chr5 Chr6...
>> your Txdb seqlevel:Chr1 Chr2 Chr3 Chr4 Chr5 ChrM ChrC...
>> checking seqlevels match... 2022-04-12 7:47:05 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
>> checking seqlevels match... 2022-04-12 7:47:05 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2022-04-12 7:47:05 PM
>> finding nearest gene and calculating distance... 2022-04-12 7:47:05 PM
>> dealing with gene strand ... 2022-04-12 7:47:06 PM
>> merging all info together ... 2022-04-12 7:47:06 PM
>> done 2022-04-12 7:47:06 PM
>> checking seqlevels match... 2022-04-12 7:47:06 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
>> checking seqlevels match... 2022-04-12 7:47:06 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2022-04-12 7:47:06 PM
>> finding nearest gene and calculating distance... 2022-04-12 7:47:06 PM
>> dealing with gene strand ... 2022-04-12 7:47:07 PM
>> merging all info together ... 2022-04-12 7:47:07 PM
>> done 2022-04-12 7:47:07 PM
>> checking seqlevels match... 2022-04-12 7:47:07 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... 2022-04-12 7:47:07 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... 2022-04-12 7:47:07 PM
>> finding nearest gene and calculating distance... 2022-04-12 7:47:08 PM
>> dealing with gene strand ... 2022-04-12 7:47:08 PM
>> merging all info together ... 2022-04-12 7:47:08 PM
>> done 2022-04-12 7:47:08 PM
>> checking seqlevels match... 2022-04-12 7:47:09 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
>> checking seqlevels match... 2022-04-12 7:47:09 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
------------
annotating Peak using nearest gene mode begins
>> preparing gene features information... 2022-04-12 7:47:09 PM
>> finding nearest gene and calculating distance... 2022-04-12 7:47:10 PM
>> dealing with gene strand ... 2022-04-12 7:47:10 PM
>> merging all info together ... 2022-04-12 7:47:10 PM
>> done 2022-04-12 7:47:10 PM
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2022-04-12 7:47:11 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... 2022-04-12 7:47:11 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... 2022-04-12 7:47:11 PM
>> finding nearest gene and calculating distance... 2022-04-12 7:47:11 PM
>> dealing with gene strand ... 2022-04-12 7:47:12 PM
>> merging all info together ... 2022-04-12 7:47:12 PM
>> done 2022-04-12 7:47:12 PM
It seems that there 1 genes have not been annotated by nearestGene mode
>> checking seqlevels match... 2022-04-12 7:47:12 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... 2022-04-12 7:47:13 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... 2022-04-12 7:47:14 PM
>> checking seqlevels match... 2022-04-12 7:47:15 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... 2022-04-12 7:47:15 PM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2022-04-12 7:47:16 PM
>> merging all info together... 2022-04-12 7:47:16 PM
>> done 2022-04-12 7:47:16 PM
>> checking seqlevels match... 2022-04-12 7:47:17 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... 2022-04-12 7:47:17 PM
>> checking seqlevels match... 2022-04-12 7:47:17 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... 2022-04-12 7:47:17 PM
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2022-04-12 7:47:18 PM
>> checking seqlevels match... 2022-04-12 7:47:18 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... 2022-04-12 7:47:18 PM
>> calculating cor and pvalue, which may be time consuming... 2022-04-12 7:47:19 PM
>> merging all info together... 2022-04-12 7:47:19 PM
>> done 2022-04-12 7:47:19 PM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2022-04-12 7:47:19 PM
>> merging all info together... 2022-04-12 7:47:19 PM
>> done 2022-04-12 7:47:19 PM
>> checking seqlevels match... 2022-04-12 7:47:19 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... 2022-04-12 7:47:19 PM
>> some scan range may cross Chr bound, trimming... 2022-04-12 7:47:20 PM
>> finding overlap peak in gene scan region... 2022-04-12 7:47:20 PM
>> dealing with left peak not your gene scan region... 2022-04-12 7:47:20 PM
>> merging two set peaks... 2022-04-12 7:47:20 PM
>> calculating distance and dealing with gene strand... 2022-04-12 7:47:20 PM
>> merging all info together ... 2022-04-12 7:47:20 PM
>> done 2022-04-12 7:47:20 PM
Good, your two matrix colnames matchs
>> calculating cor and pvalue, which may be time consuming... 2022-04-12 7:47:21 PM
>> merging all info together... 2022-04-12 7:47:21 PM
>> done 2022-04-12 7:47:21 PM
>> checking seqlevels match... 2022-04-12 7:47:21 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... 2022-04-12 7:47:21 PM
>> checking seqlevels match... 2022-04-12 7:47:21 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... 2022-04-12 7:47:22 PM
>> there are 85 gene have scaned promoter
>> using scanEnhancer parameter to scan Enhancer for each gene... 2022-04-12 7:47:22 PM
>> checking seqlevels match... 2022-04-12 7:47:22 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... 2022-04-12 7:47:23 PM
>> calculating cor and pvalue, which may be time consuming... 2022-04-12 7:47:23 PM
>> merging all info together... 2022-04-12 7:47:23 PM
>> done 2022-04-12 7:47:24 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
61.18 0.96 62.14
|
|
FindIT2.Rcheck/examples_i386/FindIT2-Ex.timings
|
FindIT2.Rcheck/examples_x64/FindIT2-Ex.timings
|