Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:07:31 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for TreeSummarizedExperiment on tokay2


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? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1997/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TreeSummarizedExperiment 2.2.0  (landing page)
Ruizhu Huang
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/TreeSummarizedExperiment
git_branch: RELEASE_3_14
git_last_commit: 3fc3f90
git_last_commit_date: 2021-10-26 12:52:17 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TreeSummarizedExperiment
Version: 2.2.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TreeSummarizedExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings TreeSummarizedExperiment_2.2.0.tar.gz
StartedAt: 2022-04-13 04:22:55 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 04:32:38 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 582.7 seconds
RetCode: 0
Status:   OK  
CheckDir: TreeSummarizedExperiment.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TreeSummarizedExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings TreeSummarizedExperiment_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/TreeSummarizedExperiment.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TreeSummarizedExperiment/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TreeSummarizedExperiment' version '2.2.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
TreeSummarizedExperiment-accessor 5.86   0.14       6
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/TreeSummarizedExperiment.Rcheck/00check.log'
for details.



Installation output

TreeSummarizedExperiment.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/TreeSummarizedExperiment_2.2.0.tar.gz && rm -rf TreeSummarizedExperiment.buildbin-libdir && mkdir TreeSummarizedExperiment.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TreeSummarizedExperiment.buildbin-libdir TreeSummarizedExperiment_2.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL TreeSummarizedExperiment_2.2.0.zip && rm TreeSummarizedExperiment_2.2.0.tar.gz TreeSummarizedExperiment_2.2.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  369k  100  369k    0     0   532k      0 --:--:-- --:--:-- --:--:--  533k

install for i386

* 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
  converting help for package 'TreeSummarizedExperiment'
    finding HTML links ... done
    LinkDataFrame-class                     html  
    LinkDataFrame-constructor               html  
    TreeSummarizedExperiment-accessor       html  
    TreeSummarizedExperiment-class          html  
    TreeSummarizedExperiment-combine        html  
    TreeSummarizedExperiment-constructor    html  
    finding level-2 HTML links ... done

    TreeSummarizedExperiment-internal       html  
    TreeeSummarizedExperiment-package       html  
    addLabel                                html  
    aggTSE                                  html  
    aggValue                                html  
    asLeaf                                  html  
    asPhylo                                 html  
    changeTree                              html  
    convertNode                             html  
    countLeaf                               html  
    countNode                               html  
    detectLoop                              html  
    distNode                                html  
    dot-all_equal_in_list                   html  
    dot-all_have_DNAStringSet               html  
    dot-all_have_DNAStringSetList           html  
    dot-all_nonnull_in_list                 html  
    dot-all_null_in_list                    html  
    dot-any_null_in_list                    html  
    dot-auto_rename_list                    html  
    dot-bind_link_tree                      html  
    dot-is_equal_link                       html  
    dot-match_phylo                         html  
    dot-match_phylo_list                    html  
    dot-match_x_dupY                        html  
    dot-name_y_with_x                       html  
    dot-numeric_ij                          html  
    dot-rbind_refSeq                        html  
    dot-replace_link_tree_1d                html  
    dot-subset_leaf                         html  
    dot-update_whichTree                    html  
    findAncestor                            html  
    findChild                               html  
    findDescendant                          html  
    findSibling                             html  
    isLeaf                                  html  
    joinNode                                html  
    makeTSE                                 html  
    matTree                                 html  
    phylo                                   html  
    printNode                               html  
    resolveLoop                             html  
    shareNode                               html  
    showNode                                html  
    tinyTree                                html  
    toTree                                  html  
    trackNode                               html  
    unionLeaf                               html  
    updateObject-TreeSummarizedExperiment-method
                                            html  
** 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

install for x64

* installing *source* package 'TreeSummarizedExperiment' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TreeSummarizedExperiment' as TreeSummarizedExperiment_2.2.0.zip
* DONE (TreeSummarizedExperiment)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'TreeSummarizedExperiment' successfully unpacked and MD5 sums checked

Tests output

TreeSummarizedExperiment.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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

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, 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

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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 7 | SKIP 0 | PASS 383 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 383 ]
> 
> proc.time()
   user  system elapsed 
 141.14    1.40  142.54 

TreeSummarizedExperiment.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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

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, 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

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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 7 | SKIP 0 | PASS 383 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 383 ]
> 
> proc.time()
   user  system elapsed 
 154.64    0.93  155.73 

Example timings

TreeSummarizedExperiment.Rcheck/examples_i386/TreeSummarizedExperiment-Ex.timings

nameusersystemelapsed
LinkDataFrame-constructor0.10.00.1
TreeSummarizedExperiment-accessor4.640.034.67
TreeSummarizedExperiment-combine3.490.003.49
TreeSummarizedExperiment-constructor0.470.020.48
addLabel0.640.040.69
aggTSE2.640.002.64
asLeaf0.490.020.50
asPhylo0.650.000.66
changeTree1.660.041.69
convertNode0.160.000.15
countLeaf0.140.000.14
countNode0.140.010.15
detectLoop0.070.000.07
distNode0.140.020.15
dot-all_equal_in_list000
dot-name_y_with_x000
dot-update_whichTree000
findAncestor0.120.000.12
findChild0.140.020.16
findDescendant0.160.010.17
findSibling0.170.000.17
isLeaf0.160.000.16
joinNode0.150.020.17
makeTSE1.110.001.11
matTree0.130.000.13
printNode0.120.020.14
resolveLoop0.310.010.32
shareNode0.150.000.15
showNode0.140.000.14
toTree0.640.000.64
trackNode0.390.020.41
unionLeaf0.170.000.17

TreeSummarizedExperiment.Rcheck/examples_x64/TreeSummarizedExperiment-Ex.timings

nameusersystemelapsed
LinkDataFrame-constructor0.060.000.07
TreeSummarizedExperiment-accessor5.860.146.00
TreeSummarizedExperiment-combine4.450.034.49
TreeSummarizedExperiment-constructor0.600.000.59
addLabel0.650.020.67
aggTSE2.020.012.03
asLeaf0.480.000.49
asPhylo0.740.000.73
changeTree2.070.002.08
convertNode0.150.020.16
countLeaf0.140.020.15
countNode0.120.010.14
detectLoop0.060.000.06
distNode0.190.000.19
dot-all_equal_in_list000
dot-name_y_with_x000
dot-update_whichTree000
findAncestor0.140.000.14
findChild0.160.000.16
findDescendant0.170.020.19
findSibling0.140.000.14
isLeaf0.130.010.14
joinNode0.140.020.15
makeTSE1.140.011.16
matTree0.120.000.13
printNode0.140.020.15
resolveLoop0.390.000.39
shareNode0.190.020.21
showNode0.230.000.23
toTree0.930.000.92
trackNode0.420.010.44
unionLeaf0.240.000.24