Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-28 17:42 -0400 (Fri, 28 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" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4362 |
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 | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | 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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RgnTX.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings RgnTX_1.6.0.tar.gz |
StartedAt: 2024-06-27 05:21:23 -0400 (Thu, 27 Jun 2024) |
EndedAt: 2024-06-27 05:29:26 -0400 (Thu, 27 Jun 2024) |
EllapsedTime: 482.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RgnTX.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RgnTX.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings RgnTX_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/RgnTX.Rcheck' * using R version 4.4.0 (2024-04-24 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * 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 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 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 31.84 1.17 32.96 permTestTxIA_customPick 17.39 0.56 17.93 permTestTxIA 17.27 0.36 17.62 permTestTx 15.93 0.23 16.18 permTestTx_customPick 13.01 0.20 13.22 permTestTx_customAll 11.89 0.19 12.07 overlapCountsTxIA 7.11 0.27 7.37 overlapWidthTx 5.19 0.16 5.36 randomizeFeaturesTx 5.23 0.09 5.33 distanceTx 5.12 0.09 5.22 * 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: OK
RgnTX.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL RgnTX ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows 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 46.68 1.73 48.68
RgnTX.Rcheck/RgnTX-Ex.timings
name | user | system | elapsed | |
GRanges2GRangesList | 0.22 | 0.03 | 0.25 | |
GRangesList2GRanges | 4.65 | 0.33 | 4.98 | |
calculateShift | 2.67 | 0.16 | 2.84 | |
distanceTx | 5.12 | 0.09 | 5.22 | |
extractRegions | 2.86 | 0.06 | 2.93 | |
getPermSpaceByFeatures | 2.73 | 0.18 | 2.91 | |
getPermSpaceByTxID | 2.93 | 0.07 | 3.06 | |
getPermSpaceByType | 1.62 | 0.08 | 1.70 | |
getStopCodon | 4.31 | 0.17 | 4.49 | |
getTransInfo | 0.71 | 0.07 | 0.78 | |
overlapCountsTx | 3.06 | 0.07 | 3.14 | |
overlapCountsTxIA | 7.11 | 0.27 | 7.37 | |
overlapWidthTx | 5.19 | 0.16 | 5.36 | |
permTestTx | 15.93 | 0.23 | 16.18 | |
permTestTxIA | 17.27 | 0.36 | 17.62 | |
permTestTxIA_customPick | 17.39 | 0.56 | 17.93 | |
permTestTx_customAll | 11.89 | 0.19 | 12.07 | |
permTestTx_customPick | 13.01 | 0.20 | 13.22 | |
plotPermResults | 0.49 | 0.06 | 0.56 | |
plotShiftedZScoreTx | 0.18 | 0.00 | 0.19 | |
randomizeFeaturesTx | 5.23 | 0.09 | 5.33 | |
randomizeFeaturesTxIA | 4.39 | 0.19 | 4.58 | |
randomizeTransByOrder | 4.25 | 0.08 | 4.32 | |
randomizeTx | 2.55 | 0.06 | 2.61 | |
shiftTx | 2 | 0 | 2 | |
shiftedZScoreTx | 31.84 | 1.17 | 32.96 | |