Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:49 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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 RgnTX package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1654/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RgnTX 1.1.0 (landing page) Yue Wang
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: RgnTX |
Version: 1.1.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:RgnTX.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings RgnTX_1.1.0.tar.gz |
StartedAt: 2023-02-28 12:59:03 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 13:12:00 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 777.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RgnTX.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:RgnTX.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings RgnTX_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/RgnTX.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘RgnTX/DESCRIPTION’ ... OK * this is package ‘RgnTX’ version ‘1.1.0’ * 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 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed shiftedZScoreTx 53.471 0.380 53.852 permTestTxIA_customPick 31.267 0.515 31.783 permTestTxIA 28.729 0.604 29.333 permTestTx 25.364 0.635 26.000 permTestTx_customPick 21.690 0.172 21.862 permTestTx_customAll 20.600 0.264 20.864 overlapCountsTxIA 11.257 0.203 11.461 overlapWidthTx 10.071 0.165 10.236 getStopCodon 9.868 0.276 10.144 distanceTx 9.564 0.215 9.780 randomizeFeaturesTx 8.732 0.052 8.784 GRangesList2GRanges 6.520 0.412 6.932 overlapCountsTx 5.883 0.200 6.084 randomizeFeaturesTxIA 5.914 0.076 5.990 randomizeTransByOrder 5.871 0.048 5.919 randomizeTx 5.515 0.048 5.564 * 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 ... ‘RgnTX.Rmd’ using ‘UTF-8’... OK NONE * 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-3.17-bioc/R/bin/R CMD INSTALL RgnTX ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (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(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, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' 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 67.035 1.733 68.755
RgnTX.Rcheck/RgnTX-Ex.timings
name | user | system | elapsed | |
GRanges2GRangesList | 0.225 | 0.001 | 0.226 | |
GRangesList2GRanges | 6.520 | 0.412 | 6.932 | |
calculateShift | 4.106 | 0.176 | 4.282 | |
distanceTx | 9.564 | 0.215 | 9.780 | |
extractRegions | 3.230 | 0.109 | 3.337 | |
getPermSpaceByFeatures | 4.564 | 0.124 | 4.689 | |
getPermSpaceByTxID | 3.725 | 0.072 | 3.797 | |
getPermSpaceByType | 3.002 | 0.044 | 3.046 | |
getStopCodon | 9.868 | 0.276 | 10.144 | |
getTransInfo | 0.939 | 0.040 | 0.978 | |
overlapCountsTx | 5.883 | 0.200 | 6.084 | |
overlapCountsTxIA | 11.257 | 0.203 | 11.461 | |
overlapWidthTx | 10.071 | 0.165 | 10.236 | |
permTestTx | 25.364 | 0.635 | 26.000 | |
permTestTxIA | 28.729 | 0.604 | 29.333 | |
permTestTxIA_customPick | 31.267 | 0.515 | 31.783 | |
permTestTx_customAll | 20.600 | 0.264 | 20.864 | |
permTestTx_customPick | 21.690 | 0.172 | 21.862 | |
plotPermResults | 0.673 | 0.020 | 0.696 | |
plotShiftedZScoreTx | 0.273 | 0.000 | 0.273 | |
randomizeFeaturesTx | 8.732 | 0.052 | 8.784 | |
randomizeFeaturesTxIA | 5.914 | 0.076 | 5.990 | |
randomizeTransByOrder | 5.871 | 0.048 | 5.919 | |
randomizeTx | 5.515 | 0.048 | 5.564 | |
shiftTx | 3.301 | 0.020 | 3.320 | |
shiftedZScoreTx | 53.471 | 0.380 | 53.852 | |