| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-10-28 11:49 -0400 (Mon, 28 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4501 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4761 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4504 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4535 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4483 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4491 |
| 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 2192/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TreeSummarizedExperiment 2.13.0 (landing page) Ruizhu Huang
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| 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: 2024-10-28 04:33:08 -0400 (Mon, 28 Oct 2024) |
| EndedAt: 2024-10-28 04:38:44 -0400 (Mon, 28 Oct 2024) |
| EllapsedTime: 336.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TreeSummarizedExperiment.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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 4.4.1 (2024-06-14)
* 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 13.6.7
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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.
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)
TreeSummarizedExperiment.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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, saveRDS, 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
31.781 29.940 41.227
TreeSummarizedExperiment.Rcheck/TreeSummarizedExperiment-Ex.timings
| name | user | system | elapsed | |
| LinkDataFrame-constructor | 0.016 | 0.000 | 0.017 | |
| TreeSummarizedExperiment-accessor | 1.159 | 0.015 | 1.174 | |
| TreeSummarizedExperiment-combine | 0.536 | 0.004 | 0.540 | |
| TreeSummarizedExperiment-constructor | 0.072 | 0.002 | 0.073 | |
| addLabel | 0.192 | 0.008 | 0.200 | |
| aggTSE | 0.271 | 0.003 | 0.274 | |
| asLeaf | 0.138 | 0.003 | 0.140 | |
| asPhylo | 0.206 | 0.002 | 0.208 | |
| changeTree | 0.259 | 0.002 | 0.260 | |
| convertNode | 0.043 | 0.001 | 0.044 | |
| countLeaf | 0.044 | 0.001 | 0.045 | |
| countNode | 0.040 | 0.002 | 0.041 | |
| detectLoop | 0.009 | 0.000 | 0.009 | |
| distNode | 0.046 | 0.002 | 0.048 | |
| dot-all_equal_in_list | 0 | 0 | 0 | |
| dot-name_y_with_x | 0 | 0 | 0 | |
| dot-update_whichTree | 0 | 0 | 0 | |
| findAncestor | 0.044 | 0.002 | 0.046 | |
| findChild | 0.052 | 0.002 | 0.054 | |
| findDescendant | 0.045 | 0.001 | 0.047 | |
| findSibling | 0.041 | 0.002 | 0.043 | |
| isLeaf | 0.042 | 0.001 | 0.043 | |
| joinNode | 0.045 | 0.002 | 0.046 | |
| makeTSE | 0.147 | 0.001 | 0.148 | |
| matTree | 0.040 | 0.001 | 0.041 | |
| printNode | 0.046 | 0.001 | 0.048 | |
| resolveLoop | 0.043 | 0.001 | 0.044 | |
| shareNode | 0.043 | 0.001 | 0.044 | |
| showNode | 0.043 | 0.001 | 0.045 | |
| toTree | 0.152 | 0.002 | 0.154 | |
| trackNode | 0.078 | 0.002 | 0.080 | |
| unionLeaf | 0.075 | 0.001 | 0.077 | |