| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:47 -0000 (Wed, 01 Mar 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" | 4266 |
| 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 1506/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| preciseTAD 1.9.0 (landing page) Mikhail Dozmorov
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: preciseTAD |
| Version: 1.9.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:preciseTAD.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings preciseTAD_1.9.0.tar.gz |
| StartedAt: 2023-02-28 11:36:14 -0000 (Tue, 28 Feb 2023) |
| EndedAt: 2023-02-28 11:54:42 -0000 (Tue, 28 Feb 2023) |
| EllapsedTime: 1108.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: preciseTAD.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:preciseTAD.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings preciseTAD_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/preciseTAD.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 ‘preciseTAD/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘preciseTAD’ version ‘1.9.0’
* 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 ‘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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
preciseTAD 84.187 1.128 85.326
TADrandomForest 27.452 0.648 28.105
TADrfe 15.216 0.324 15.542
createTADdata 8.221 0.192 8.414
* 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 ...
‘preciseTAD.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/preciseTAD.Rcheck/00check.log’
for details.
preciseTAD.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL preciseTAD ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * 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 *** 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 * DONE (preciseTAD)
preciseTAD.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(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
289.240 5.886 374.797
preciseTAD.Rcheck/preciseTAD-Ex.timings
| name | user | system | elapsed | |
| TADrandomForest | 27.452 | 0.648 | 28.105 | |
| TADrfe | 15.216 | 0.324 | 15.542 | |
| bedToGRangesList | 0.217 | 0.004 | 0.223 | |
| createTADdata | 8.221 | 0.192 | 8.414 | |
| extractBoundaries | 2.922 | 0.012 | 2.935 | |
| preciseTAD | 84.187 | 1.128 | 85.326 | |