Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1735/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RgnTX 1.8.0 (landing page) Yue Wang
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the RgnTX package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RgnTX.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: RgnTX |
Version: 1.8.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RgnTX.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RgnTX_1.8.0.tar.gz |
StartedAt: 2024-12-20 04:44:55 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 04:54:12 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 556.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RgnTX.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RgnTX.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RgnTX_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/RgnTX.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘RgnTX/DESCRIPTION’ ... OK * this is package ‘RgnTX’ version ‘1.8.0’ * 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 ‘RgnTX’ 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 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed shiftedZScoreTx 33.129 0.064 33.194 permTestTxIA_customPick 18.620 0.040 18.660 permTestTxIA 18.253 0.037 18.291 permTestTx 16.503 0.088 16.593 permTestTx_customPick 13.848 0.043 13.892 permTestTx_customAll 12.649 0.008 12.657 overlapCountsTxIA 8.848 0.095 8.944 getStopCodon 6.729 0.041 6.771 distanceTx 6.487 0.177 6.664 overlapWidthTx 5.786 0.031 5.817 randomizeFeaturesTx 5.445 0.031 5.477 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
RgnTX.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL RgnTX ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘RgnTX’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (RgnTX)
RgnTX.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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(RgnTX) > > test_check("RgnTX") Loading required package: GenomicFeatures 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, aperm, 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, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. [ FAIL 0 | WARN 0 | SKIP 0 | PASS 42 ] > > proc.time() user system elapsed 46.425 1.450 47.867
RgnTX.Rcheck/RgnTX-Ex.timings
name | user | system | elapsed | |
GRanges2GRangesList | 0.147 | 0.006 | 0.152 | |
GRangesList2GRanges | 4.679 | 0.316 | 4.996 | |
calculateShift | 1.972 | 0.051 | 2.024 | |
distanceTx | 6.487 | 0.177 | 6.664 | |
extractRegions | 2.912 | 0.048 | 2.960 | |
getPermSpaceByFeatures | 3.788 | 0.047 | 3.837 | |
getPermSpaceByTxID | 2.336 | 0.036 | 2.371 | |
getPermSpaceByType | 2.706 | 0.016 | 2.722 | |
getStopCodon | 6.729 | 0.041 | 6.771 | |
getTransInfo | 0.633 | 0.042 | 0.674 | |
overlapCountsTx | 3.944 | 0.074 | 4.018 | |
overlapCountsTxIA | 8.848 | 0.095 | 8.944 | |
overlapWidthTx | 5.786 | 0.031 | 5.817 | |
permTestTx | 16.503 | 0.088 | 16.593 | |
permTestTxIA | 18.253 | 0.037 | 18.291 | |
permTestTxIA_customPick | 18.62 | 0.04 | 18.66 | |
permTestTx_customAll | 12.649 | 0.008 | 12.657 | |
permTestTx_customPick | 13.848 | 0.043 | 13.892 | |
plotPermResults | 0.506 | 0.003 | 0.520 | |
plotShiftedZScoreTx | 0.133 | 0.000 | 0.134 | |
randomizeFeaturesTx | 5.445 | 0.031 | 5.477 | |
randomizeFeaturesTxIA | 3.621 | 0.021 | 3.643 | |
randomizeTransByOrder | 3.679 | 0.012 | 3.691 | |
randomizeTx | 2.893 | 0.021 | 2.915 | |
shiftTx | 2.141 | 0.012 | 2.152 | |
shiftedZScoreTx | 33.129 | 0.064 | 33.194 | |