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This page was generated on 2022-04-13 12:07:28 -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 tidySummarizedExperiment on tokay2


To the developers/maintainers of the tidySummarizedExperiment package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tidySummarizedExperiment.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 1952/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tidySummarizedExperiment 1.4.1  (landing page)
Stefano Mangiola
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/tidySummarizedExperiment
git_branch: RELEASE_3_14
git_last_commit: d6496b2
git_last_commit_date: 2021-10-27 09:29:01 -0400 (Wed, 27 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: tidySummarizedExperiment
Version: 1.4.1
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tidySummarizedExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings tidySummarizedExperiment_1.4.1.tar.gz
StartedAt: 2022-04-13 04:01:58 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 04:08:02 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 364.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: tidySummarizedExperiment.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tidySummarizedExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings tidySummarizedExperiment_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/tidySummarizedExperiment.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 'tidySummarizedExperiment/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'tidySummarizedExperiment' version '1.4.1'
* 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 'tidySummarizedExperiment' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking S3 generic/method consistency ... WARNING
pivot_wider:
  function(data, id_cols, id_expand, names_from, names_prefix,
           names_sep, names_glue, names_sort, names_vary, names_expand,
           names_repair, values_from, values_fill, values_fn,
           unused_fn, ...)
pivot_wider.SummarizedExperiment:
  function(data, id_cols, names_from, names_prefix, names_sep,
           names_glue, names_sort, names_repair, values_from,
           values_fill, values_fn, ...)

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.as_tibble_optimised: no visible global function definition for
  'setNames'
change_reserved_column_names: no visible global function definition for
  'setNames'
change_reserved_column_names: no visible binding for global variable
  '.'
extract.SummarizedExperiment: no visible binding for global variable
  'se'
extract.SummarizedExperiment: no visible binding for global variable
  '.'
nest.SummarizedExperiment: no visible binding for global variable '.'
print.SummarizedExperiment: no visible binding for global variable '.'
pull.SummarizedExperiment: no visible binding for global variable '.'
select.SummarizedExperiment: no visible binding for global variable '.'
separate.SummarizedExperiment: no visible binding for global variable
  'se'
separate.SummarizedExperiment: no visible binding for global variable
  '.'
simulate_feature_sample_from_tibble: no visible binding for global
  variable '.'
slice_optimised: no visible binding for global variable '.'
subset_tibble_output: no visible binding for global variable '.'
unite.SummarizedExperiment: no visible binding for global variable 'se'
unite.SummarizedExperiment: no visible binding for global variable '.'
update_SE_from_tibble: no visible global function definition for 'head'
update_SE_from_tibble: no visible binding for global variable 'value'
update_SE_from_tibble: no visible binding for global variable 'data___'
update_SE_from_tibble: no visible binding for global variable 'name'
show,SummarizedExperiment: no visible global function definition for
  'getMethod'
Undefined global functions or variables:
  . data___ getMethod head name se setNames value
Consider adding
  importFrom("methods", "getMethod")
  importFrom("stats", "setNames")
  importFrom("utils", "head")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
tidyr-methods 10.24   0.26    10.5
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
tidyr-methods   11   0.15   11.14
* 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 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/tidySummarizedExperiment.Rcheck/00check.log'
for details.



Installation output

tidySummarizedExperiment.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/tidySummarizedExperiment_1.4.1.tar.gz && rm -rf tidySummarizedExperiment.buildbin-libdir && mkdir tidySummarizedExperiment.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=tidySummarizedExperiment.buildbin-libdir tidySummarizedExperiment_1.4.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL tidySummarizedExperiment_1.4.1.zip && rm tidySummarizedExperiment_1.4.1.tar.gz tidySummarizedExperiment_1.4.1.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  244k  100  244k    0     0   912k      0 --:--:-- --:--:-- --:--:--  916k

install for i386

* installing *source* package 'tidySummarizedExperiment' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to '>' 
** help
*** installing help indices
  converting help for package 'tidySummarizedExperiment'
    finding HTML links ... done
    bind                                    html  
    finding level-2 HTML links ... done

    count                                   html  
    dplyr-methods                           html  
    formatting                              html  
    ggplot2-methods                         html  
    pasilla                                 html  
    pipe                                    html  
    plot_ly                                 html  
    se                                      html  
    tibble-methods                          html  
    tidy                                    html  
    tidyr-methods                           html  
*** copying figures
** 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 'tidySummarizedExperiment' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'tidySummarizedExperiment' as tidySummarizedExperiment_1.4.1.zip
* DONE (tidySummarizedExperiment)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'tidySummarizedExperiment' successfully unpacked and MD5 sums checked

Tests output

tidySummarizedExperiment.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(tidySummarizedExperiment)
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


Attaching package: 'tidySummarizedExperiment'

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

    slice

The following object is masked from 'package:S4Vectors':

    rename

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

    count

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

    filter

> 
> test_check("tidySummarizedExperiment")
[ FAIL 0 | WARN 3 | SKIP 2 | PASS 47 ]

== Skipped tests ===============================================================
* empty test (2)

[ FAIL 0 | WARN 3 | SKIP 2 | PASS 47 ]
> 
> proc.time()
   user  system elapsed 
  47.73    1.42   49.14 

tidySummarizedExperiment.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(tidySummarizedExperiment)
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


Attaching package: 'tidySummarizedExperiment'

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

    slice

The following object is masked from 'package:S4Vectors':

    rename

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

    count

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

    filter

> 
> test_check("tidySummarizedExperiment")
[ FAIL 0 | WARN 3 | SKIP 2 | PASS 47 ]

== Skipped tests ===============================================================
* empty test (2)

[ FAIL 0 | WARN 3 | SKIP 2 | PASS 47 ]
> 
> proc.time()
   user  system elapsed 
  57.67    0.98   58.64 

Example timings

tidySummarizedExperiment.Rcheck/examples_i386/tidySummarizedExperiment-Ex.timings

nameusersystemelapsed
bind3.470.323.78
count0.130.000.13
dplyr-methods3.560.373.93
formatting0.110.020.13
ggplot2-methods0.670.120.80
pipe0.020.000.01
plot_ly000
tibble-methods0.180.030.22
tidy0.110.020.13
tidyr-methods10.24 0.2610.50

tidySummarizedExperiment.Rcheck/examples_x64/tidySummarizedExperiment-Ex.timings

nameusersystemelapsed
bind3.350.153.50
count0.110.000.11
dplyr-methods3.780.163.94
formatting0.220.000.22
ggplot2-methods1.40.01.4
pipe0.020.000.02
plot_ly000
tibble-methods0.280.010.29
tidy0.160.000.16
tidyr-methods11.00 0.1511.14