Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-06-11 15:43 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 2143/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TreeSummarizedExperiment 2.13.0  (landing page)
Ruizhu Huang
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/TreeSummarizedExperiment
git_branch: devel
git_last_commit: b6da78c
git_last_commit_date: 2024-04-30 11:15:10 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for TreeSummarizedExperiment on kjohnson1

To the developers/maintainers of the TreeSummarizedExperiment package:
- 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 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.

raw results


Summary

Package: TreeSummarizedExperiment
Version: 2.13.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TreeSummarizedExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TreeSummarizedExperiment_2.13.0.tar.gz
StartedAt: 2024-06-11 11:20:18 -0400 (Tue, 11 Jun 2024)
EndedAt: 2024-06-11 11:26:46 -0400 (Tue, 11 Jun 2024)
EllapsedTime: 388.1 seconds
RetCode: 0
Status:   OK  
CheckDir: TreeSummarizedExperiment.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TreeSummarizedExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TreeSummarizedExperiment_2.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/TreeSummarizedExperiment.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TreeSummarizedExperiment/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TreeSummarizedExperiment’ version ‘2.13.0’
* 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 ‘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 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 ... 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 ... NOTE
checkRd: (-1) TreeSummarizedExperiment-constructor.Rd:71: Escaped LaTeX specials: \_
* checking Rd metadata ... NOTE
Invalid package aliases in Rd file 'TreeeSummarizedExperiment-package.Rd':
  ‘TreeeSummarizedExperiment-package’
* 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
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/TreeSummarizedExperiment.Rcheck/00check.log’
for details.


Installation output

TreeSummarizedExperiment.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TreeSummarizedExperiment
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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)

Tests output

TreeSummarizedExperiment.Rcheck/tests/testthat.Rout


R version 4.4.0 Patched (2024-04-24 r86482) -- "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(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

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

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
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")

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[ FAIL 0 | WARN 6 | SKIP 0 | PASS 383 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 383 ]
> 
> proc.time()
   user  system elapsed 
119.224 113.110 156.899 

Example timings

TreeSummarizedExperiment.Rcheck/TreeSummarizedExperiment-Ex.timings

nameusersystemelapsed
LinkDataFrame-constructor0.0780.0020.081
TreeSummarizedExperiment-accessor4.1050.0744.194
TreeSummarizedExperiment-combine2.1040.0212.132
TreeSummarizedExperiment-constructor0.3000.0070.307
addLabel0.7050.0310.739
aggTSE1.1270.0121.146
asLeaf0.3880.0090.400
asPhylo0.6520.0110.669
changeTree1.0410.0101.059
convertNode0.1670.0060.174
countLeaf0.1650.0060.171
countNode0.1550.0050.161
detectLoop0.0390.0010.041
distNode0.1850.0060.193
dot-all_equal_in_list000
dot-name_y_with_x0.0000.0000.001
dot-update_whichTree000
findAncestor0.1650.0060.172
findChild0.1770.0060.183
findDescendant0.1950.0060.201
findSibling0.1640.0050.170
isLeaf0.1620.0060.170
joinNode0.1720.0060.179
makeTSE0.6060.0060.616
matTree0.1600.0050.166
printNode0.1670.0050.173
resolveLoop0.1950.0030.199
shareNode0.1700.0060.176
showNode0.1740.0070.181
toTree0.5600.0070.572
trackNode0.3130.0080.323
unionLeaf0.1900.0060.196