| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:06 -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 preciseTAD package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/preciseTAD.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 1450/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| preciseTAD 1.4.0 (landing page) Mikhail Dozmorov
| 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: preciseTAD |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:preciseTAD.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings preciseTAD_1.4.0.tar.gz |
| StartedAt: 2022-04-13 00:45:03 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 01:03:22 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 1099.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: preciseTAD.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:preciseTAD.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings preciseTAD_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/preciseTAD.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 'preciseTAD/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'preciseTAD' version '1.4.0'
* 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 whether package 'preciseTAD' 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 ... NOTE
Found the following CITATION file in a non-standard place:
CITATION.cff
Most likely 'inst/CITATION' should be used instead.
* 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 LazyData ... 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
preciseTAD 53.94 3.14 57.08
TADrandomForest 26.05 1.13 27.19
TADrfe 13.12 0.23 13.35
createTADdata 7.16 0.05 7.20
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
preciseTAD 57.78 2.45 60.27
TADrandomForest 27.43 0.28 27.77
TADrfe 14.69 0.11 14.80
createTADdata 7.54 0.07 7.61
* 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: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/preciseTAD.Rcheck/00check.log'
for details.
preciseTAD.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/preciseTAD_1.4.0.tar.gz && rm -rf preciseTAD.buildbin-libdir && mkdir preciseTAD.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=preciseTAD.buildbin-libdir preciseTAD_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL preciseTAD_1.4.0.zip && rm preciseTAD_1.4.0.tar.gz preciseTAD_1.4.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
19 3737k 19 735k 0 0 791k 0 0:00:04 --:--:-- 0:00:04 790k
48 3737k 48 1815k 0 0 941k 0 0:00:03 0:00:01 0:00:02 941k
89 3737k 89 3356k 0 0 1145k 0 0:00:03 0:00:02 0:00:01 1145k
100 3737k 100 3737k 0 0 1200k 0 0:00:03 0:00:03 --:--:-- 1200k
install for i386
* installing *source* package 'preciseTAD' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'preciseTAD'
finding HTML links ... done
TADrandomForest html
finding level-2 HTML links ... done
TADrfe html
arrowhead_gm12878_5kb html
bedToGRangesList html
binary_func html
count_func html
createTADdata html
distance_func html
extractBoundaries html
juicer_func html
percent_func html
preciseTAD html
signal_func html
tfbsList html
*** copying figures
** 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 'preciseTAD' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'preciseTAD' as preciseTAD_1.4.0.zip
* DONE (preciseTAD)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'preciseTAD' successfully unpacked and MD5 sums checked
|
preciseTAD.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(preciseTAD)
>
> test_check("preciseTAD")
+ Fold1: mtry= 2, ntree=500, nodesize=1
- Fold1: mtry= 2, ntree=500, nodesize=1
+ Fold1: mtry= 5, ntree=500, nodesize=1
- Fold1: mtry= 5, ntree=500, nodesize=1
+ Fold1: mtry= 8, ntree=500, nodesize=1
- Fold1: mtry= 8, ntree=500, nodesize=1
+ Fold1: mtry=10, ntree=500, nodesize=1
- Fold1: mtry=10, ntree=500, nodesize=1
+ Fold1: mtry=13, ntree=500, nodesize=1
- Fold1: mtry=13, ntree=500, nodesize=1
+ Fold1: mtry=16, ntree=500, nodesize=1
- Fold1: mtry=16, ntree=500, nodesize=1
+ Fold1: mtry=18, ntree=500, nodesize=1
- Fold1: mtry=18, ntree=500, nodesize=1
+ Fold1: mtry=21, ntree=500, nodesize=1
- Fold1: mtry=21, ntree=500, nodesize=1
+ Fold1: mtry=24, ntree=500, nodesize=1
- Fold1: mtry=24, ntree=500, nodesize=1
+ Fold1: mtry=26, ntree=500, nodesize=1
- Fold1: mtry=26, ntree=500, nodesize=1
+ Fold2: mtry= 2, ntree=500, nodesize=1
- Fold2: mtry= 2, ntree=500, nodesize=1
+ Fold2: mtry= 5, ntree=500, nodesize=1
- Fold2: mtry= 5, ntree=500, nodesize=1
+ Fold2: mtry= 8, ntree=500, nodesize=1
- Fold2: mtry= 8, ntree=500, nodesize=1
+ Fold2: mtry=10, ntree=500, nodesize=1
- Fold2: mtry=10, ntree=500, nodesize=1
+ Fold2: mtry=13, ntree=500, nodesize=1
- Fold2: mtry=13, ntree=500, nodesize=1
+ Fold2: mtry=16, ntree=500, nodesize=1
- Fold2: mtry=16, ntree=500, nodesize=1
+ Fold2: mtry=18, ntree=500, nodesize=1
- Fold2: mtry=18, ntree=500, nodesize=1
+ Fold2: mtry=21, ntree=500, nodesize=1
- Fold2: mtry=21, ntree=500, nodesize=1
+ Fold2: mtry=24, ntree=500, nodesize=1
- Fold2: mtry=24, ntree=500, nodesize=1
+ Fold2: mtry=26, ntree=500, nodesize=1
- Fold2: mtry=26, ntree=500, nodesize=1
+ Fold3: mtry= 2, ntree=500, nodesize=1
- Fold3: mtry= 2, ntree=500, nodesize=1
+ Fold3: mtry= 5, ntree=500, nodesize=1
- Fold3: mtry= 5, ntree=500, nodesize=1
+ Fold3: mtry= 8, ntree=500, nodesize=1
- Fold3: mtry= 8, ntree=500, nodesize=1
+ Fold3: mtry=10, ntree=500, nodesize=1
- Fold3: mtry=10, ntree=500, nodesize=1
+ Fold3: mtry=13, ntree=500, nodesize=1
- Fold3: mtry=13, ntree=500, nodesize=1
+ Fold3: mtry=16, ntree=500, nodesize=1
- Fold3: mtry=16, ntree=500, nodesize=1
+ Fold3: mtry=18, ntree=500, nodesize=1
- Fold3: mtry=18, ntree=500, nodesize=1
+ Fold3: mtry=21, ntree=500, nodesize=1
- Fold3: mtry=21, ntree=500, nodesize=1
+ Fold3: mtry=24, ntree=500, nodesize=1
- Fold3: mtry=24, ntree=500, nodesize=1
+ Fold3: mtry=26, ntree=500, nodesize=1
- Fold3: mtry=26, ntree=500, nodesize=1
Aggregating results
Selecting tuning parameters
Fitting mtry = 2, ntree = 500, nodesize = 1 on full training set
+(rfe) fit Fold1 size: 26
-(rfe) fit Fold1 size: 26
+(rfe) imp Fold1
-(rfe) imp Fold1
+(rfe) fit Fold1 size: 16
-(rfe) fit Fold1 size: 16
+(rfe) fit Fold1 size: 8
-(rfe) fit Fold1 size: 8
+(rfe) fit Fold1 size: 4
-(rfe) fit Fold1 size: 4
+(rfe) fit Fold1 size: 2
-(rfe) fit Fold1 size: 2
+(rfe) fit Fold2 size: 26
-(rfe) fit Fold2 size: 26
+(rfe) imp Fold2
-(rfe) imp Fold2
+(rfe) fit Fold2 size: 16
-(rfe) fit Fold2 size: 16
+(rfe) fit Fold2 size: 8
-(rfe) fit Fold2 size: 8
+(rfe) fit Fold2 size: 4
-(rfe) fit Fold2 size: 4
+(rfe) fit Fold2 size: 2
-(rfe) fit Fold2 size: 2
+(rfe) fit Fold3 size: 26
-(rfe) fit Fold3 size: 26
+(rfe) imp Fold3
-(rfe) imp Fold3
+(rfe) fit Fold3 size: 16
-(rfe) fit Fold3 size: 16
+(rfe) fit Fold3 size: 8
-(rfe) fit Fold3 size: 8
+(rfe) fit Fold3 size: 4
-(rfe) fit Fold3 size: 4
+(rfe) fit Fold3 size: 2
-(rfe) fit Fold3 size: 2
+(rfe) fit Fold4 size: 26
-(rfe) fit Fold4 size: 26
+(rfe) imp Fold4
-(rfe) imp Fold4
+(rfe) fit Fold4 size: 16
-(rfe) fit Fold4 size: 16
+(rfe) fit Fold4 size: 8
-(rfe) fit Fold4 size: 8
+(rfe) fit Fold4 size: 4
-(rfe) fit Fold4 size: 4
+(rfe) fit Fold4 size: 2
-(rfe) fit Fold4 size: 2
+(rfe) fit Fold5 size: 26
-(rfe) fit Fold5 size: 26
+(rfe) imp Fold5
-(rfe) imp Fold5
+(rfe) fit Fold5 size: 16
-(rfe) fit Fold5 size: 16
+(rfe) fit Fold5 size: 8
-(rfe) fit Fold5 size: 8
+(rfe) fit Fold5 size: 4
-(rfe) fit Fold5 size: 4
+(rfe) fit Fold5 size: 2
-(rfe) fit Fold5 size: 2
+ Fold1: mtry=2, ntree=500, nodesize=1
- Fold1: mtry=2, ntree=500, nodesize=1
+ Fold2: mtry=2, ntree=500, nodesize=1
- Fold2: mtry=2, ntree=500, nodesize=1
+ Fold3: mtry=2, ntree=500, nodesize=1
- Fold3: mtry=2, ntree=500, nodesize=1
Aggregating results
Fitting final model on full training set
[1] "Establishing bp resolution test data using a distance type feature space"
[1] "Establishing probability vector"
[1] "Determining optimal combination of epsilon neighborhood (eps) and minimum number of points (MinPts)"
[1] "Initializing DBSCAN for MinPts=3 and eps=10000"
[1] " preciseTAD identified 13 PTBRs"
[1] " Establishing PTBPs"
[1] " Cluster 1 out of 13"
[1] " Cluster 2 out of 13"
[1] " Cluster 3 out of 13"
[1] " Cluster 4 out of 13"
[1] " Cluster 5 out of 13"
[1] " Cluster 6 out of 13"
[1] " Cluster 7 out of 13"
[1] " Cluster 8 out of 13"
[1] " Cluster 9 out of 13"
[1] " Cluster 10 out of 13"
[1] " Cluster 11 out of 13"
[1] " Cluster 12 out of 13"
[1] " Cluster 13 out of 13"
[1] "Optimal combination of MinPts and eps is = (3, 10000)"
[1] "preciseTAD identified a total of 12897 base pairs whose predictive probability was equal to or exceeded a threshold of 1"
[1] "Initializing DBSCAN for MinPts = 3 and eps = 10000"
[1] "preciseTAD identified 13 PTBRs"
[1] "Establishing PTBPs"
[1] "Cluster 1 out of 13"
[1] "Cluster 2 out of 13"
[1] "Cluster 3 out of 13"
[1] "Cluster 4 out of 13"
[1] "Cluster 5 out of 13"
[1] "Cluster 6 out of 13"
[1] "Cluster 7 out of 13"
[1] "Cluster 8 out of 13"
[1] "Cluster 9 out of 13"
[1] "Cluster 10 out of 13"
[1] "Cluster 11 out of 13"
[1] "Cluster 12 out of 13"
[1] "Cluster 13 out of 13"
+ Fold1: mtry=2, ntree=500, nodesize=1
- Fold1: mtry=2, ntree=500, nodesize=1
+ Fold2: mtry=2, ntree=500, nodesize=1
- Fold2: mtry=2, ntree=500, nodesize=1
+ Fold3: mtry=2, ntree=500, nodesize=1
- Fold3: mtry=2, ntree=500, nodesize=1
Aggregating results
Fitting final model on full training set
[1] "Establishing bp resolution test data using a distance type feature space"
[1] "Establishing probability vector"
[1] "Determining optimal combination of epsilon neighborhood (eps) and minimum number of points (MinPts)"
[1] "Initializing DBSCAN for MinPts=1000 and eps=5000"
[1] " preciseTAD identified 14 PTBRs"
[1] " Establishing PTBPs"
[1] " Cluster 1 out of 14"
[1] " Cluster 2 out of 14"
[1] " Cluster 3 out of 14"
[1] " Cluster 4 out of 14"
[1] " Cluster 5 out of 14"
[1] " Cluster 6 out of 14"
[1] " Cluster 7 out of 14"
[1] " Cluster 8 out of 14"
[1] " Cluster 9 out of 14"
[1] " Cluster 10 out of 14"
[1] " Cluster 11 out of 14"
[1] " Cluster 12 out of 14"
[1] " Cluster 13 out of 14"
[1] " Cluster 14 out of 14"
[1] "Optimal combination of MinPts and eps is = (1000, 5000)"
[1] "preciseTAD identified a total of 59929 base pairs whose predictive probability was equal to or exceeded a threshold of 0.99"
[1] "Initializing DBSCAN for MinPts = 1000 and eps = 5000"
[1] "preciseTAD identified 14 PTBRs"
[1] "Establishing PTBPs"
[1] "Cluster 1 out of 14"
[1] "Cluster 2 out of 14"
[1] "Cluster 3 out of 14"
[1] "Cluster 4 out of 14"
[1] "Cluster 5 out of 14"
[1] "Cluster 6 out of 14"
[1] "Cluster 7 out of 14"
[1] "Cluster 8 out of 14"
[1] "Cluster 9 out of 14"
[1] "Cluster 10 out of 14"
[1] "Cluster 11 out of 14"
[1] "Cluster 12 out of 14"
[1] "Cluster 13 out of 14"
[1] "Cluster 14 out of 14"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
>
> proc.time()
user system elapsed
183.82 14.57 252.40
|
preciseTAD.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(preciseTAD)
>
> test_check("preciseTAD")
+ Fold1: mtry= 2, ntree=500, nodesize=1
- Fold1: mtry= 2, ntree=500, nodesize=1
+ Fold1: mtry= 5, ntree=500, nodesize=1
- Fold1: mtry= 5, ntree=500, nodesize=1
+ Fold1: mtry= 8, ntree=500, nodesize=1
- Fold1: mtry= 8, ntree=500, nodesize=1
+ Fold1: mtry=10, ntree=500, nodesize=1
- Fold1: mtry=10, ntree=500, nodesize=1
+ Fold1: mtry=13, ntree=500, nodesize=1
- Fold1: mtry=13, ntree=500, nodesize=1
+ Fold1: mtry=16, ntree=500, nodesize=1
- Fold1: mtry=16, ntree=500, nodesize=1
+ Fold1: mtry=18, ntree=500, nodesize=1
- Fold1: mtry=18, ntree=500, nodesize=1
+ Fold1: mtry=21, ntree=500, nodesize=1
- Fold1: mtry=21, ntree=500, nodesize=1
+ Fold1: mtry=24, ntree=500, nodesize=1
- Fold1: mtry=24, ntree=500, nodesize=1
+ Fold1: mtry=26, ntree=500, nodesize=1
- Fold1: mtry=26, ntree=500, nodesize=1
+ Fold2: mtry= 2, ntree=500, nodesize=1
- Fold2: mtry= 2, ntree=500, nodesize=1
+ Fold2: mtry= 5, ntree=500, nodesize=1
- Fold2: mtry= 5, ntree=500, nodesize=1
+ Fold2: mtry= 8, ntree=500, nodesize=1
- Fold2: mtry= 8, ntree=500, nodesize=1
+ Fold2: mtry=10, ntree=500, nodesize=1
- Fold2: mtry=10, ntree=500, nodesize=1
+ Fold2: mtry=13, ntree=500, nodesize=1
- Fold2: mtry=13, ntree=500, nodesize=1
+ Fold2: mtry=16, ntree=500, nodesize=1
- Fold2: mtry=16, ntree=500, nodesize=1
+ Fold2: mtry=18, ntree=500, nodesize=1
- Fold2: mtry=18, ntree=500, nodesize=1
+ Fold2: mtry=21, ntree=500, nodesize=1
- Fold2: mtry=21, ntree=500, nodesize=1
+ Fold2: mtry=24, ntree=500, nodesize=1
- Fold2: mtry=24, ntree=500, nodesize=1
+ Fold2: mtry=26, ntree=500, nodesize=1
- Fold2: mtry=26, ntree=500, nodesize=1
+ Fold3: mtry= 2, ntree=500, nodesize=1
- Fold3: mtry= 2, ntree=500, nodesize=1
+ Fold3: mtry= 5, ntree=500, nodesize=1
- Fold3: mtry= 5, ntree=500, nodesize=1
+ Fold3: mtry= 8, ntree=500, nodesize=1
- Fold3: mtry= 8, ntree=500, nodesize=1
+ Fold3: mtry=10, ntree=500, nodesize=1
- Fold3: mtry=10, ntree=500, nodesize=1
+ Fold3: mtry=13, ntree=500, nodesize=1
- Fold3: mtry=13, ntree=500, nodesize=1
+ Fold3: mtry=16, ntree=500, nodesize=1
- Fold3: mtry=16, ntree=500, nodesize=1
+ Fold3: mtry=18, ntree=500, nodesize=1
- Fold3: mtry=18, ntree=500, nodesize=1
+ Fold3: mtry=21, ntree=500, nodesize=1
- Fold3: mtry=21, ntree=500, nodesize=1
+ Fold3: mtry=24, ntree=500, nodesize=1
- Fold3: mtry=24, ntree=500, nodesize=1
+ Fold3: mtry=26, ntree=500, nodesize=1
- Fold3: mtry=26, ntree=500, nodesize=1
Aggregating results
Selecting tuning parameters
Fitting mtry = 2, ntree = 500, nodesize = 1 on full training set
+(rfe) fit Fold1 size: 26
-(rfe) fit Fold1 size: 26
+(rfe) imp Fold1
-(rfe) imp Fold1
+(rfe) fit Fold1 size: 16
-(rfe) fit Fold1 size: 16
+(rfe) fit Fold1 size: 8
-(rfe) fit Fold1 size: 8
+(rfe) fit Fold1 size: 4
-(rfe) fit Fold1 size: 4
+(rfe) fit Fold1 size: 2
-(rfe) fit Fold1 size: 2
+(rfe) fit Fold2 size: 26
-(rfe) fit Fold2 size: 26
+(rfe) imp Fold2
-(rfe) imp Fold2
+(rfe) fit Fold2 size: 16
-(rfe) fit Fold2 size: 16
+(rfe) fit Fold2 size: 8
-(rfe) fit Fold2 size: 8
+(rfe) fit Fold2 size: 4
-(rfe) fit Fold2 size: 4
+(rfe) fit Fold2 size: 2
-(rfe) fit Fold2 size: 2
+(rfe) fit Fold3 size: 26
-(rfe) fit Fold3 size: 26
+(rfe) imp Fold3
-(rfe) imp Fold3
+(rfe) fit Fold3 size: 16
-(rfe) fit Fold3 size: 16
+(rfe) fit Fold3 size: 8
-(rfe) fit Fold3 size: 8
+(rfe) fit Fold3 size: 4
-(rfe) fit Fold3 size: 4
+(rfe) fit Fold3 size: 2
-(rfe) fit Fold3 size: 2
+(rfe) fit Fold4 size: 26
-(rfe) fit Fold4 size: 26
+(rfe) imp Fold4
-(rfe) imp Fold4
+(rfe) fit Fold4 size: 16
-(rfe) fit Fold4 size: 16
+(rfe) fit Fold4 size: 8
-(rfe) fit Fold4 size: 8
+(rfe) fit Fold4 size: 4
-(rfe) fit Fold4 size: 4
+(rfe) fit Fold4 size: 2
-(rfe) fit Fold4 size: 2
+(rfe) fit Fold5 size: 26
-(rfe) fit Fold5 size: 26
+(rfe) imp Fold5
-(rfe) imp Fold5
+(rfe) fit Fold5 size: 16
-(rfe) fit Fold5 size: 16
+(rfe) fit Fold5 size: 8
-(rfe) fit Fold5 size: 8
+(rfe) fit Fold5 size: 4
-(rfe) fit Fold5 size: 4
+(rfe) fit Fold5 size: 2
-(rfe) fit Fold5 size: 2
+ Fold1: mtry=2, ntree=500, nodesize=1
- Fold1: mtry=2, ntree=500, nodesize=1
+ Fold2: mtry=2, ntree=500, nodesize=1
- Fold2: mtry=2, ntree=500, nodesize=1
+ Fold3: mtry=2, ntree=500, nodesize=1
- Fold3: mtry=2, ntree=500, nodesize=1
Aggregating results
Fitting final model on full training set
[1] "Establishing bp resolution test data using a distance type feature space"
[1] "Establishing probability vector"
[1] "Determining optimal combination of epsilon neighborhood (eps) and minimum number of points (MinPts)"
[1] "Initializing DBSCAN for MinPts=3 and eps=10000"
[1] " preciseTAD identified 13 PTBRs"
[1] " Establishing PTBPs"
[1] " Cluster 1 out of 13"
[1] " Cluster 2 out of 13"
[1] " Cluster 3 out of 13"
[1] " Cluster 4 out of 13"
[1] " Cluster 5 out of 13"
[1] " Cluster 6 out of 13"
[1] " Cluster 7 out of 13"
[1] " Cluster 8 out of 13"
[1] " Cluster 9 out of 13"
[1] " Cluster 10 out of 13"
[1] " Cluster 11 out of 13"
[1] " Cluster 12 out of 13"
[1] " Cluster 13 out of 13"
[1] "Optimal combination of MinPts and eps is = (3, 10000)"
[1] "preciseTAD identified a total of 12897 base pairs whose predictive probability was equal to or exceeded a threshold of 1"
[1] "Initializing DBSCAN for MinPts = 3 and eps = 10000"
[1] "preciseTAD identified 13 PTBRs"
[1] "Establishing PTBPs"
[1] "Cluster 1 out of 13"
[1] "Cluster 2 out of 13"
[1] "Cluster 3 out of 13"
[1] "Cluster 4 out of 13"
[1] "Cluster 5 out of 13"
[1] "Cluster 6 out of 13"
[1] "Cluster 7 out of 13"
[1] "Cluster 8 out of 13"
[1] "Cluster 9 out of 13"
[1] "Cluster 10 out of 13"
[1] "Cluster 11 out of 13"
[1] "Cluster 12 out of 13"
[1] "Cluster 13 out of 13"
+ Fold1: mtry=2, ntree=500, nodesize=1
- Fold1: mtry=2, ntree=500, nodesize=1
+ Fold2: mtry=2, ntree=500, nodesize=1
- Fold2: mtry=2, ntree=500, nodesize=1
+ Fold3: mtry=2, ntree=500, nodesize=1
- Fold3: mtry=2, ntree=500, nodesize=1
Aggregating results
Fitting final model on full training set
[1] "Establishing bp resolution test data using a distance type feature space"
[1] "Establishing probability vector"
[1] "Determining optimal combination of epsilon neighborhood (eps) and minimum number of points (MinPts)"
[1] "Initializing DBSCAN for MinPts=1000 and eps=5000"
[1] " preciseTAD identified 14 PTBRs"
[1] " Establishing PTBPs"
[1] " Cluster 1 out of 14"
[1] " Cluster 2 out of 14"
[1] " Cluster 3 out of 14"
[1] " Cluster 4 out of 14"
[1] " Cluster 5 out of 14"
[1] " Cluster 6 out of 14"
[1] " Cluster 7 out of 14"
[1] " Cluster 8 out of 14"
[1] " Cluster 9 out of 14"
[1] " Cluster 10 out of 14"
[1] " Cluster 11 out of 14"
[1] " Cluster 12 out of 14"
[1] " Cluster 13 out of 14"
[1] " Cluster 14 out of 14"
[1] "Optimal combination of MinPts and eps is = (1000, 5000)"
[1] "preciseTAD identified a total of 59929 base pairs whose predictive probability was equal to or exceeded a threshold of 0.99"
[1] "Initializing DBSCAN for MinPts = 1000 and eps = 5000"
[1] "preciseTAD identified 14 PTBRs"
[1] "Establishing PTBPs"
[1] "Cluster 1 out of 14"
[1] "Cluster 2 out of 14"
[1] "Cluster 3 out of 14"
[1] "Cluster 4 out of 14"
[1] "Cluster 5 out of 14"
[1] "Cluster 6 out of 14"
[1] "Cluster 7 out of 14"
[1] "Cluster 8 out of 14"
[1] "Cluster 9 out of 14"
[1] "Cluster 10 out of 14"
[1] "Cluster 11 out of 14"
[1] "Cluster 12 out of 14"
[1] "Cluster 13 out of 14"
[1] "Cluster 14 out of 14"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 17 ]
>
> proc.time()
user system elapsed
176.04 12.90 241.53
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preciseTAD.Rcheck/examples_i386/preciseTAD-Ex.timings
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preciseTAD.Rcheck/examples_x64/preciseTAD-Ex.timings
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