Mikhail Dozmorov
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/preciseTAD |
| git_branch: master |
| git_last_commit: 62c257b |
| git_last_commit_date: 2021-10-26 13:02:48 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:20 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the 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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1458/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| preciseTAD 1.5.0 (landing page) Mikhail Dozmorov
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: preciseTAD |
| Version: 1.5.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:preciseTAD.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings preciseTAD_1.5.0.tar.gz |
| StartedAt: 2022-03-17 19:54:55 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:04:01 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 546.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: preciseTAD.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:preciseTAD.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings preciseTAD_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/preciseTAD.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'preciseTAD/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'preciseTAD' 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 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 43.77 6.04 49.81
TADrandomForest 21.27 1.38 22.64
TADrfe 10.98 0.86 11.85
createTADdata 6.48 0.40 6.89
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/preciseTAD.Rcheck/00check.log'
for details.
preciseTAD.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL preciseTAD
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-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
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
* DONE (preciseTAD)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'profileplyr' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'RnBeads' is missing or broken
done
preciseTAD.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(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
144.07 28.79 216.87
preciseTAD.Rcheck/preciseTAD-Ex.timings
| name | user | system | elapsed | |
| TADrandomForest | 21.27 | 1.38 | 22.64 | |
| TADrfe | 10.98 | 0.86 | 11.85 | |
| bedToGRangesList | 0.13 | 0.00 | 0.12 | |
| createTADdata | 6.48 | 0.40 | 6.89 | |
| extractBoundaries | 2.17 | 0.02 | 2.19 | |
| preciseTAD | 43.77 | 6.04 | 49.81 | |