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This page was generated on 2021-10-15 15:06:56 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the TreeSummarizedExperiment package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TreeSummarizedExperiment.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1958/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TreeSummarizedExperiment 2.0.3 (landing page) Ruizhu Huang
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: TreeSummarizedExperiment |
Version: 2.0.3 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TreeSummarizedExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TreeSummarizedExperiment_2.0.3.tar.gz |
StartedAt: 2021-10-15 00:55:09 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 01:03:08 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 478.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TreeSummarizedExperiment.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TreeSummarizedExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TreeSummarizedExperiment_2.0.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/TreeSummarizedExperiment.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TreeSummarizedExperiment/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TreeSummarizedExperiment’ version ‘2.0.3’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘TreeSummarizedExperiment’ 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 ... NOTE Unexported objects imported by ':::' calls: ‘BiocGenerics:::replaceSlots’ ‘S4Vectors:::disableValidity’ See the note in ?`:::` about the use of this operator. * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed TreeSummarizedExperiment-accessor 7.565 0.161 7.728 TreeSummarizedExperiment-combine 5.447 0.018 5.469 * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/TreeSummarizedExperiment.Rcheck/00check.log’ for details.
TreeSummarizedExperiment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TreeSummarizedExperiment ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘TreeSummarizedExperiment’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (TreeSummarizedExperiment)
TreeSummarizedExperiment.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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(TreeSummarizedExperiment) Loading required package: SingleCellExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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, 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 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: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit > > test_check("TreeSummarizedExperiment") | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% [ FAIL 0 | WARN 6 | SKIP 0 | PASS 383 ] > > proc.time() user system elapsed 207.614 7.302 190.738
TreeSummarizedExperiment.Rcheck/TreeSummarizedExperiment-Ex.timings
name | user | system | elapsed | |
LinkDataFrame-constructor | 0.069 | 0.002 | 0.070 | |
TreeSummarizedExperiment-accessor | 7.565 | 0.161 | 7.728 | |
TreeSummarizedExperiment-combine | 5.447 | 0.018 | 5.469 | |
TreeSummarizedExperiment-constructor | 0.705 | 0.004 | 0.710 | |
addLabel | 0.816 | 0.029 | 0.846 | |
aggTSE | 2.655 | 0.012 | 2.671 | |
asLeaf | 0.605 | 0.005 | 0.612 | |
asPhylo | 0.903 | 0.009 | 0.948 | |
changeTree | 2.209 | 0.007 | 2.217 | |
convertNode | 0.167 | 0.004 | 0.171 | |
countLeaf | 0.183 | 0.004 | 0.188 | |
countNode | 0.176 | 0.004 | 0.181 | |
detectLoop | 0.059 | 0.001 | 0.061 | |
distNode | 0.178 | 0.004 | 0.183 | |
dot-all_equal_in_list | 0.000 | 0.000 | 0.001 | |
dot-name_y_with_x | 0.000 | 0.000 | 0.001 | |
dot-update_whichTree | 0 | 0 | 0 | |
findAncestor | 0.187 | 0.006 | 0.193 | |
findChild | 0.203 | 0.005 | 0.209 | |
findDescendant | 0.174 | 0.004 | 0.179 | |
findSibling | 0.145 | 0.003 | 0.148 | |
isLeaf | 0.168 | 0.005 | 0.173 | |
joinNode | 0.177 | 0.004 | 0.182 | |
makeTSE | 1.421 | 0.005 | 1.427 | |
matTree | 0.184 | 0.004 | 0.189 | |
printNode | 0.165 | 0.004 | 0.171 | |
resolveLoop | 0.371 | 0.003 | 0.375 | |
shareNode | 0.210 | 0.004 | 0.214 | |
showNode | 0.200 | 0.006 | 0.207 | |
toTree | 0.653 | 0.005 | 0.659 | |
trackNode | 0.352 | 0.005 | 0.358 | |
unionLeaf | 0.210 | 0.005 | 0.215 | |