Ruizhu Huang
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/TreeSummarizedExperiment |
| Branch: RELEASE_3_9 |
| Last Commit: 49a49bd |
| Last Changed Date: 2019-06-03 11:19:21 -0400 (Mon, 03 Jun 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:18:30 -0400 (Wed, 16 Oct 2019).
| Package 1672/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TreeSummarizedExperiment 1.0.3 Ruizhu Huang
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: TreeSummarizedExperiment |
| Version: 1.0.3 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:TreeSummarizedExperiment.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings TreeSummarizedExperiment_1.0.3.tar.gz |
| StartedAt: 2019-10-16 05:32:23 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:35:30 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 186.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: TreeSummarizedExperiment.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:TreeSummarizedExperiment.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings TreeSummarizedExperiment_1.0.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/TreeSummarizedExperiment.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-pc-linux-gnu (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 ‘1.0.3’ * 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: .travis.yml 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 ... WARNING '::' or ':::' import not declared from: ‘BiocGenerics’ Unexported object imported by a ':::' call: ‘BiocGenerics:::replaceSlots’ 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 ... NOTE toTree: no visible binding for global variable ‘dnn’ Undefined global functions or variables: dnn * 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 data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.9-bioc/meat/TreeSummarizedExperiment.Rcheck/00check.log’ for details.
TreeSummarizedExperiment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL TreeSummarizedExperiment ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘TreeSummarizedExperiment’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(TreeSummarizedExperiment)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
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, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
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")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
>
> test_check("TreeSummarizedExperiment")
t11 can't be matched to any node label of the tree.
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 38 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
9.351 0.484 9.820
TreeSummarizedExperiment.Rcheck/TreeSummarizedExperiment-Ex.timings
| name | user | system | elapsed | |
| LinkDataFrame-constructor | 0.055 | 0.000 | 0.055 | |
| TreeSummarizedExperiment-accessor | 0.355 | 0.016 | 0.371 | |
| TreeSummarizedExperiment-constructor | 0.114 | 0.011 | 0.126 | |
| aggValue | 0.797 | 0.036 | 0.832 | |
| countLeaf | 0.157 | 0.000 | 0.157 | |
| countNode | 0.154 | 0.000 | 0.153 | |
| distNode | 0.195 | 0.000 | 0.195 | |
| findAncestor | 0.160 | 0.000 | 0.159 | |
| findOS | 0.17 | 0.00 | 0.17 | |
| findSibling | 0.163 | 0.000 | 0.163 | |
| isLeaf | 0.151 | 0.000 | 0.152 | |
| matTree | 0.133 | 0.000 | 0.133 | |
| printNode | 0.152 | 0.000 | 0.153 | |
| pruneTree | 0.614 | 0.000 | 0.614 | |
| shareNode | 0.168 | 0.000 | 0.168 | |
| signalNode | 0.168 | 0.004 | 0.172 | |
| toTree | 0.015 | 0.000 | 0.015 | |
| trackNode | 0.29 | 0.00 | 0.29 | |
| transNode | 0.173 | 0.000 | 0.173 | |