Package: SummarizedExperiment

Version: 1.16.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SummarizedExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SummarizedExperiment_1.16.1.tar.gz

StartedAt: 2020-04-15 06:02:29 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:05:56 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 207.5 seconds

RetCode: 0

Status:  OK

CheckDir: SummarizedExperiment.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SummarizedExperiment.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SummarizedExperiment_1.16.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/SummarizedExperiment.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SummarizedExperiment/DESCRIPTION’ ... OK
* this is package ‘SummarizedExperiment’ version ‘1.16.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SummarizedExperiment’ 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                           user system elapsed
makeSummarizedExperimentFromExpressionSet 9.413  0.252   9.842
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.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: OK

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SummarizedExperiment
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘SummarizedExperiment’ ...
** using staged installation
** R
** 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 (SummarizedExperiment)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> require("SummarizedExperiment") || stop("unable to load SummarizedExperiment package")
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

[1] TRUE
> SummarizedExperiment:::.test()


'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns


RUNIT TEST PROTOCOL -- Wed Apr 15 06:05:48 2020 
*********************************************** 
Number of test functions: 35 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
SummarizedExperiment RUnit Tests - 35 test functions, 0 errors, 0 failures
Number of test functions: 35 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In normarg_mcols(value, class(x), length(x)) :
  You supplied a metadata column of length 2 to set on an object of
  length 5. However please note that the latter is not a multiple of the
  former.
2: In normarg_mcols(value, class(x), length(x)) :
  You supplied metadata columns of length 2 to set on an object of length
  3. However please note that the latter is not a multiple of the former.
3: In S4Vectors:::V_recycle(arg, x, argname, "x") :
  'length(x)' is not a multiple of 'NROW(weight)'
4: In S4Vectors:::V_recycle(arg, x, argname, "x") :
  'length(x)' is not a multiple of 'NROW(weight)'
5: In .deprecatedColsMessage() :
  Accessing gene location information via 'CHR','CHRLOC','CHRLOCEND' is
  deprecated. Please use a range based accessor like genes(), or select()
  with columns values like TXCHROM and TXSTART on a TxDb or OrganismDb
  object instead.
6: 144 probes could not be mapped. 
7: 169 probes could not be mapped. 
> 
> proc.time()
   user  system elapsed 
 26.900   0.826  27.892 

name	user	system	elapsed
Assays-class	0.139	0.005	0.145
RangedSummarizedExperiment-class	0.728	0.034	0.867
SummarizedExperiment-class	1.208	0.043	1.272
coverage-methods	0.130	0.001	0.131
findOverlaps-methods	0.233	0.004	0.238
inter-range-methods	0.251	0.032	0.285
intra-range-methods	0.474	0.062	0.693
makeSummarizedExperimentFromDataFrame	0.101	0.014	0.117
makeSummarizedExperimentFromExpressionSet	9.413	0.252	9.842
makeSummarizedExperimentFromLoom	0.142	0.005	0.149
nearest-methods	0.577	0.010	0.591
readKallisto	0.500	0.070	0.602