Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:44 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 |
Package 1566/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
preciseTAD 1.15.0 (landing page) Mikhail Dozmorov
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the preciseTAD package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: preciseTAD |
Version: 1.15.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:preciseTAD.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings preciseTAD_1.15.0.tar.gz |
StartedAt: 2024-08-26 22:34:48 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 22:47:12 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 744.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: preciseTAD.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:preciseTAD.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings preciseTAD_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/preciseTAD.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘preciseTAD/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘preciseTAD’ version ‘1.15.0’ * 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 ... NOTE License stub is invalid DCF. * 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 code 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 60.721 3.587 64.687 TADrandomForest 26.432 0.819 27.394 TADrfe 14.630 0.604 15.320 createTADdata 7.479 0.143 7.682 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/preciseTAD.Rcheck/00check.log’ for details.
preciseTAD.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL preciseTAD ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 210.300 13.788 292.141
preciseTAD.Rcheck/preciseTAD-Ex.timings
name | user | system | elapsed | |
TADrandomForest | 26.432 | 0.819 | 27.394 | |
TADrfe | 14.630 | 0.604 | 15.320 | |
bedToGRangesList | 0.184 | 0.004 | 0.189 | |
createTADdata | 7.479 | 0.143 | 7.682 | |
extractBoundaries | 2.107 | 0.027 | 2.152 | |
preciseTAD | 60.721 | 3.587 | 64.687 | |