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CHECK report for SummarizedExperiment on tokay2

This page was generated on 2018-10-17 08:40:37 -0400 (Wed, 17 Oct 2018).

Package 1446/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SummarizedExperiment 1.10.1
Bioconductor Package Maintainer
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/SummarizedExperiment
Branch: RELEASE_3_7
Last Commit: 7ad2e99
Last Changed Date: 2018-05-09 21:23:02 -0400 (Wed, 09 May 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: SummarizedExperiment
Version: 1.10.1
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SummarizedExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings SummarizedExperiment_1.10.1.tar.gz
StartedAt: 2018-10-17 05:06:15 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 05:10:11 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 236.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: SummarizedExperiment.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SummarizedExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings SummarizedExperiment_1.10.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/SummarizedExperiment.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SummarizedExperiment/DESCRIPTION' ... OK
* this is package 'SummarizedExperiment' version '1.10.1'
* 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 'SummarizedExperiment' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/Assays-class.Rd:118: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:120: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:123: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:126: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:127: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:130: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:130: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:155: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:156: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:220: file link 'shift' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:221: file link 'isDisjoint' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:222: file link 'coverage' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:223: file link 'findOverlaps' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:224: file link 'nearest' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:268: file link 'shift' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:269: file link 'isDisjoint' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:270: file link 'coverage' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:271: file link 'findOverlaps' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:272: file link 'nearest' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:275: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/SummarizedExperiment-class.Rd:138: file link 'mcols' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/SummarizedExperiment-class.Rd:224: file link 'mcols' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/SummarizedExperiment-class.Rd:416: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/SummarizedExperiment-class.Rd:416: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/SummarizedExperiment-class.Rd:417: file link 'Annotated' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/SummarizedExperiment-class.Rd:419: file link 'metadata' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/SummarizedExperiment-class.Rd:420: file link 'mcols' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/SummarizedExperiment-class.Rd:424: file link 'loadHDF5SummarizedExperiment' in package 'HDF5Array' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/coverage-methods.Rd:26: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/coverage-methods.Rd:34: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/coverage-methods.Rd:34: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/coverage-methods.Rd:40: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/coverage-methods.Rd:42: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/coverage-methods.Rd:42: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/coverage-methods.Rd:47: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/coverage-methods.Rd:55: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/coverage-methods.Rd:57: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/coverage-methods.Rd:58: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/findOverlaps-methods.Rd:43: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/findOverlaps-methods.Rd:47: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/findOverlaps-methods.Rd:55: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/findOverlaps-methods.Rd:55: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/findOverlaps-methods.Rd:63: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/findOverlaps-methods.Rd:65: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/findOverlaps-methods.Rd:65: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/findOverlaps-methods.Rd:70: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/findOverlaps-methods.Rd:78: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/findOverlaps-methods.Rd:80: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/findOverlaps-methods.Rd:81: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/inter-range-methods.Rd:30: file link 'isDisjoint' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/inter-range-methods.Rd:38: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/inter-range-methods.Rd:38: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/inter-range-methods.Rd:48: file link 'isDisjoint' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/inter-range-methods.Rd:50: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/inter-range-methods.Rd:50: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/inter-range-methods.Rd:55: file link 'isDisjoint' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/inter-range-methods.Rd:63: file link 'isDisjoint' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/inter-range-methods.Rd:65: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/inter-range-methods.Rd:66: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:57: missing file link 'shift'
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:61: missing file link 'shift'
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:65: missing file link 'shift'
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:69: missing file link 'shift'
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:73: missing file link 'shift'
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:81: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:81: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:91: missing file link 'shift'
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:93: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:93: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:101: missing file link 'shift'
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:103: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:104: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/makeSummarizedExperimentFromDataFrame.Rd:31: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:18: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:20: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:39: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:42: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:45: file link 'rownames' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:45: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:47: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:64: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:70: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:79: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:81: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/nearest-methods.Rd:66: file link 'nearest' in package 'GenomicRanges' does not exist and so has been treated as a topic
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  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/nearest-methods.Rd:103: file link 'nearest' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/nearest-methods.Rd:105: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/nearest-methods.Rd:106: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/SummarizedExperiment.Rcheck/00install.out' for details.
* 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 ... 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 ... WARNING
Missing link or links in documentation object 'intra-range-methods.Rd':
  '[GenomicRanges]{shift}'

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                                          user system elapsed
makeSummarizedExperimentFromExpressionSet 7.55    0.2    7.84
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                                          user system elapsed
makeSummarizedExperimentFromExpressionSet 7.02   0.08     7.1
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'run_unitTests.R'
 OK
** running tests for arch 'x64' ...
  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: 2 WARNINGs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/SummarizedExperiment.Rcheck/00check.log'
for details.



Installation output

SummarizedExperiment.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/SummarizedExperiment_1.10.1.tar.gz && rm -rf SummarizedExperiment.buildbin-libdir && mkdir SummarizedExperiment.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SummarizedExperiment.buildbin-libdir SummarizedExperiment_1.10.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL SummarizedExperiment_1.10.1.zip && rm SummarizedExperiment_1.10.1.tar.gz SummarizedExperiment_1.10.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100  896k  100  896k    0     0  14.0M      0 --:--:-- --:--:-- --:--:-- 15.9M

install for i386

* installing *source* package 'SummarizedExperiment' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SummarizedExperiment'
    finding HTML links ... done
    Assays-class                            html  
    finding level-2 HTML links ... done

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    RangedSummarizedExperiment-class        html  
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Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:221: file link 'isDisjoint' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:223: file link 'findOverlaps' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:224: file link 'nearest' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
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    SummarizedExperiment-class              html  
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    coverage-methods                        html  
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    findOverlaps-methods                    html  
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    inter-range-methods                     html  
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Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/inter-range-methods.Rd:50: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/inter-range-methods.Rd:50: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/inter-range-methods.Rd:55: file link 'isDisjoint' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/inter-range-methods.Rd:63: file link 'isDisjoint' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/inter-range-methods.Rd:65: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/inter-range-methods.Rd:66: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
    intra-range-methods                     html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:57: missing file link 'shift'
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:61: missing file link 'shift'
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:65: missing file link 'shift'
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:69: missing file link 'shift'
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:73: missing file link 'shift'
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:81: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:81: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:91: missing file link 'shift'
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:93: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:93: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:101: missing file link 'shift'
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:103: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/intra-range-methods.Rd:104: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
    makeSummarizedExperimentFromDataFrame   html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/makeSummarizedExperimentFromDataFrame.Rd:31: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
    makeSummarizedExperimentFromExpressionSet
                                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:18: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:20: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:39: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:42: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:45: file link 'rownames' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:45: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:47: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:64: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:70: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:79: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:81: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
    makeSummarizedExperimentFromLoom        html  
    nearest-methods                         html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/nearest-methods.Rd:66: file link 'nearest' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/nearest-methods.Rd:79: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/nearest-methods.Rd:79: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/nearest-methods.Rd:88: file link 'nearest' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/nearest-methods.Rd:90: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/nearest-methods.Rd:90: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/nearest-methods.Rd:95: file link 'nearest' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/nearest-methods.Rd:103: file link 'nearest' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/nearest-methods.Rd:105: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpczHhh9/R.INSTALL1c2c6e12922/SummarizedExperiment/man/nearest-methods.Rd:106: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
    readKallisto                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'SummarizedExperiment' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SummarizedExperiment' as SummarizedExperiment_1.10.1.zip
* DONE (SummarizedExperiment)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'SummarizedExperiment' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

SummarizedExperiment.Rcheck/tests_i386/run_unitTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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.

> 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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

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")'.

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

[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 Oct 17 05:09:44 2018 
*********************************************** 
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 V_recycle(value, x, x_what = "value", skeleton_what = "x") :
  'length(x)' is not a multiple of 'NROW(value)'
2: In V_recycle(value, x, x_what = "value", skeleton_what = "x") :
  'length(x)' is not a multiple of 'NROW(value)'
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: 145 probes could not be mapped. 
7: 169 probes could not be mapped. 
> 
> proc.time()
   user  system elapsed 
  17.31    1.12   20.09 

SummarizedExperiment.Rcheck/tests_x64/run_unitTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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.

> 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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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

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")'.

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

[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 Oct 17 05:10:06 2018 
*********************************************** 
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 V_recycle(value, x, x_what = "value", skeleton_what = "x") :
  'length(x)' is not a multiple of 'NROW(value)'
2: In V_recycle(value, x, x_what = "value", skeleton_what = "x") :
  'length(x)' is not a multiple of 'NROW(value)'
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: 145 probes could not be mapped. 
7: 169 probes could not be mapped. 
> 
> proc.time()
   user  system elapsed 
  21.18    0.46   21.64 

Example timings

SummarizedExperiment.Rcheck/examples_i386/SummarizedExperiment-Ex.timings

nameusersystemelapsed
Assays-class0.460.000.45
RangedSummarizedExperiment-class0.530.010.55
SummarizedExperiment-class0.750.210.95
coverage-methods0.100.040.14
findOverlaps-methods0.180.040.22
inter-range-methods0.140.000.14
intra-range-methods0.270.000.26
makeSummarizedExperimentFromDataFrame0.070.000.08
makeSummarizedExperimentFromExpressionSet7.550.207.84
makeSummarizedExperimentFromLoom0.220.030.28
nearest-methods1.270.091.36
readKallisto0.760.021.13

SummarizedExperiment.Rcheck/examples_x64/SummarizedExperiment-Ex.timings

nameusersystemelapsed
Assays-class0.450.000.46
RangedSummarizedExperiment-class0.320.010.33
SummarizedExperiment-class0.470.050.51
coverage-methods0.060.000.06
findOverlaps-methods0.110.000.11
inter-range-methods0.10.00.1
intra-range-methods0.180.000.18
makeSummarizedExperimentFromDataFrame0.050.000.05
makeSummarizedExperimentFromExpressionSet7.020.087.10
makeSummarizedExperimentFromLoom0.170.000.17
nearest-methods0.310.050.36
readKallisto0.550.070.62