Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-07 20:24 -0400 (Fri, 07 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4755 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4489 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4520 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 1753/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RgnTX 1.6.0 (landing page) Yue Wang
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | 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 | |||||||||
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: 1.6.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:RgnTX.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings RgnTX_1.6.0.tar.gz |
StartedAt: 2024-06-06 02:43:53 -0400 (Thu, 06 Jun 2024) |
EndedAt: 2024-06-06 02:53:31 -0400 (Thu, 06 Jun 2024) |
EllapsedTime: 578.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RgnTX.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:RgnTX.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings RgnTX_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/RgnTX.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘RgnTX/DESCRIPTION’ ... OK * this is package ‘RgnTX’ version ‘1.6.0’ * 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 34.321 0.224 34.545 permTestTxIA_customPick 19.181 0.176 19.358 permTestTxIA 18.517 0.184 18.701 permTestTx 16.964 0.132 17.096 permTestTx_customPick 14.124 0.092 14.216 permTestTx_customAll 13.320 0.124 13.445 overlapCountsTxIA 7.903 0.191 8.095 distanceTx 6.598 0.187 6.787 overlapWidthTx 6.229 0.100 6.329 randomizeFeaturesTx 5.883 0.004 5.888 getStopCodon 5.268 0.096 5.364 GRangesList2GRanges 4.739 0.368 5.107 * 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-3.19-bioc/R/bin/R CMD INSTALL RgnTX ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24) -- "Puppy Cup" 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, 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 48.720 1.472 50.201
RgnTX.Rcheck/RgnTX-Ex.timings
name | user | system | elapsed | |
GRanges2GRangesList | 0.144 | 0.012 | 0.155 | |
GRangesList2GRanges | 4.739 | 0.368 | 5.107 | |
calculateShift | 2.244 | 0.072 | 2.316 | |
distanceTx | 6.598 | 0.187 | 6.787 | |
extractRegions | 2.199 | 0.052 | 2.253 | |
getPermSpaceByFeatures | 3.085 | 0.020 | 3.105 | |
getPermSpaceByTxID | 2.498 | 0.031 | 2.530 | |
getPermSpaceByType | 2.746 | 0.092 | 2.837 | |
getStopCodon | 5.268 | 0.096 | 5.364 | |
getTransInfo | 0.554 | 0.023 | 0.578 | |
overlapCountsTx | 3.242 | 0.041 | 3.282 | |
overlapCountsTxIA | 7.903 | 0.191 | 8.095 | |
overlapWidthTx | 6.229 | 0.100 | 6.329 | |
permTestTx | 16.964 | 0.132 | 17.096 | |
permTestTxIA | 18.517 | 0.184 | 18.701 | |
permTestTxIA_customPick | 19.181 | 0.176 | 19.358 | |
permTestTx_customAll | 13.320 | 0.124 | 13.445 | |
permTestTx_customPick | 14.124 | 0.092 | 14.216 | |
plotPermResults | 0.487 | 0.004 | 0.492 | |
plotShiftedZScoreTx | 0.175 | 0.003 | 0.178 | |
randomizeFeaturesTx | 5.883 | 0.004 | 5.888 | |
randomizeFeaturesTxIA | 3.905 | 0.056 | 3.960 | |
randomizeTransByOrder | 3.792 | 0.004 | 3.796 | |
randomizeTx | 3.103 | 0.044 | 3.146 | |
shiftTx | 2.220 | 0.012 | 2.232 | |
shiftedZScoreTx | 34.321 | 0.224 | 34.545 | |