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CHECK report for SummarizedExperiment on malbec2

This page was generated on 2020-10-17 11:55:52 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE SummarizedExperiment PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1758/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SummarizedExperiment 1.18.2
Bioconductor Package Maintainer
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/SummarizedExperiment
Branch: RELEASE_3_11
Last Commit: e22fafe
Last Changed Date: 2020-07-09 13:43:22 -0400 (Thu, 09 Jul 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SummarizedExperiment
Version: 1.18.2
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:SummarizedExperiment.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings SummarizedExperiment_1.18.2.tar.gz
StartedAt: 2020-10-17 05:54:18 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:57:37 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 199.2 seconds
RetCode: 0
Status:  OK 
CheckDir: SummarizedExperiment.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:SummarizedExperiment.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings SummarizedExperiment_1.18.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/SummarizedExperiment.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SummarizedExperiment/DESCRIPTION’ ... OK
* this is package ‘SummarizedExperiment’ version ‘1.18.2’
* 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 ... NOTE
Unexported object imported by a ':::' call: ‘DelayedArray:::simplify_NULL_dimnames’
  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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                           user system elapsed
makeSummarizedExperimentFromExpressionSet 9.103  0.093  12.085
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/SummarizedExperiment.Rcheck/00check.log’
for details.



Installation output

SummarizedExperiment.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL SummarizedExperiment
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/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)

Tests output

SummarizedExperiment.Rcheck/tests/run_unitTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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


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
  403 genes were dropped because they have exons located on both strands
  of the same reference sequence or on more than one reference sequence,
  so cannot be represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a
  GRangesList object, or use suppressMessages() to suppress this message.


RUNIT TEST PROTOCOL -- Sat Oct 17 05:57:32 2020 
*********************************************** 
Number of test functions: 36 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
SummarizedExperiment RUnit Tests - 36 test functions, 0 errors, 0 failures
Number of test functions: 36 
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 
 28.505   0.444  31.725 

Example timings

SummarizedExperiment.Rcheck/SummarizedExperiment-Ex.timings

nameusersystemelapsed
Assays-class0.6190.0040.624
RangedSummarizedExperiment-class0.7750.0480.823
SummarizedExperiment-class0.7870.0360.824
coverage-methods0.1460.0000.146
findOverlaps-methods0.290.000.29
inter-range-methods0.2590.0040.263
intra-range-methods0.3020.0080.310
makeSummarizedExperimentFromDataFrame0.0680.0000.069
makeSummarizedExperimentFromExpressionSet 9.103 0.09312.085
makeSummarizedExperimentFromLoom0.1780.0120.201
nearest-methods0.5160.0440.560
readKallisto0.5800.0520.656