Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:43 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
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
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the RgnTX package: - 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RgnTX.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RgnTX_1.6.0.tar.gz |
StartedAt: 2024-05-07 00:19:49 -0400 (Tue, 07 May 2024) |
EndedAt: 2024-05-07 00:22:57 -0400 (Tue, 07 May 2024) |
EllapsedTime: 187.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RgnTX.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RgnTX.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RgnTX_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/RgnTX.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-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 Ventura 13.6.5 * 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 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 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 12.613 0.421 13.035 permTestTxIA_customPick 7.159 0.201 7.360 permTestTxIA 7.127 0.185 7.314 permTestTx 6.070 0.125 6.196 permTestTx_customPick 5.367 0.081 5.450 permTestTx_customAll 5.081 0.080 5.160 * 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RgnTX ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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: aarch64-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(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': anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, 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': expand.grid, I, 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 18.864 0.446 19.312
RgnTX.Rcheck/RgnTX-Ex.timings
name | user | system | elapsed | |
GRanges2GRangesList | 0.051 | 0.003 | 0.055 | |
GRangesList2GRanges | 1.973 | 0.057 | 2.031 | |
calculateShift | 1.250 | 0.025 | 1.276 | |
distanceTx | 2.646 | 0.047 | 2.694 | |
extractRegions | 0.908 | 0.023 | 0.932 | |
getPermSpaceByFeatures | 1.586 | 0.036 | 1.624 | |
getPermSpaceByTxID | 1.015 | 0.021 | 1.037 | |
getPermSpaceByType | 0.831 | 0.023 | 0.853 | |
getStopCodon | 2.564 | 0.046 | 2.611 | |
getTransInfo | 0.219 | 0.022 | 0.241 | |
overlapCountsTx | 1.299 | 0.028 | 1.327 | |
overlapCountsTxIA | 3.370 | 0.109 | 3.478 | |
overlapWidthTx | 2.427 | 0.055 | 2.482 | |
permTestTx | 6.070 | 0.125 | 6.196 | |
permTestTxIA | 7.127 | 0.185 | 7.314 | |
permTestTxIA_customPick | 7.159 | 0.201 | 7.360 | |
permTestTx_customAll | 5.081 | 0.080 | 5.160 | |
permTestTx_customPick | 5.367 | 0.081 | 5.450 | |
plotPermResults | 0.162 | 0.003 | 0.165 | |
plotShiftedZScoreTx | 0.045 | 0.000 | 0.045 | |
randomizeFeaturesTx | 2.309 | 0.052 | 2.361 | |
randomizeFeaturesTxIA | 1.868 | 0.065 | 1.933 | |
randomizeTransByOrder | 1.422 | 0.027 | 1.449 | |
randomizeTx | 1.545 | 0.033 | 1.579 | |
shiftTx | 0.898 | 0.017 | 0.914 | |
shiftedZScoreTx | 12.613 | 0.421 | 13.035 | |