| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:25:00 -0400 (Wed, 15 Apr 2020).
| Package 1685/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SummarizedExperiment 1.16.1 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: SummarizedExperiment |
| Version: 1.16.1 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SummarizedExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings SummarizedExperiment_1.16.1.tar.gz |
| StartedAt: 2020-04-15 06:58:28 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 07:02:58 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 270.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SummarizedExperiment.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SummarizedExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings SummarizedExperiment_1.16.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/SummarizedExperiment.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.16.1'
* 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 whether package 'SummarizedExperiment' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/Assays-class.Rd:71: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/Assays-class.Rd:72: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/Assays-class.Rd:84: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/Assays-class.Rd:119: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/Assays-class.Rd:131: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:110: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:112: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:118: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:121: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:124: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:125: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:128: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:128: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:147: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:148: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:212: file link 'shift' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:213: file link 'isDisjoint' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:214: file link 'coverage' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:215: file link 'findOverlaps' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:216: file link 'nearest' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:260: file link 'shift' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:261: file link 'isDisjoint' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:262: file link 'coverage' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:263: file link 'findOverlaps' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:264: file link 'nearest' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:267: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/SummarizedExperiment-class.Rd:174: file link 'mcols' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/SummarizedExperiment-class.Rd:176: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/SummarizedExperiment-class.Rd:179: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/SummarizedExperiment-class.Rd:183: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/SummarizedExperiment-class.Rd:233: file link 'mcols' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/SummarizedExperiment-class.Rd:423: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/SummarizedExperiment-class.Rd:423: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/SummarizedExperiment-class.Rd:424: file link 'Annotated' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/SummarizedExperiment-class.Rd:426: file link 'metadata' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/SummarizedExperiment-class.Rd:427: file link 'mcols' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/SummarizedExperiment-class.Rd:431: file link 'loadHDF5SummarizedExperiment' in package 'HDF5Array' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/intra-range-methods.Rd:77: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/intra-range-methods.Rd:77: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/intra-range-methods.Rd:89: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/intra-range-methods.Rd:89: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/intra-range-methods.Rd:99: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/intra-range-methods.Rd:100: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:39: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
makeSummarizedExperimentFromExpressionSet 9.47 0.38 10.02
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
makeSummarizedExperimentFromExpressionSet 8.77 0.33 9.1
* 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: 1 WARNING
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/SummarizedExperiment.Rcheck/00check.log'
for details.
SummarizedExperiment.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/SummarizedExperiment_1.16.1.tar.gz && rm -rf SummarizedExperiment.buildbin-libdir && mkdir SummarizedExperiment.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SummarizedExperiment.buildbin-libdir SummarizedExperiment_1.16.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL SummarizedExperiment_1.16.1.zip && rm SummarizedExperiment_1.16.1.tar.gz SummarizedExperiment_1.16.1.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
12 922k 12 112k 0 0 672k 0 0:00:01 --:--:-- 0:00:01 682k
100 922k 100 922k 0 0 4628k 0 --:--:-- --:--:-- --:--:-- 4704k
install for i386
* installing *source* package 'SummarizedExperiment' ...
** using staged installation
** 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
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Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/Assays-class.Rd:84: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/Assays-class.Rd:119: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/Assays-class.Rd:131: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
RangedSummarizedExperiment-class html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:110: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:112: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:118: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:121: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:124: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:125: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:128: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:128: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:147: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:148: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:212: file link 'shift' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:213: file link 'isDisjoint' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:214: file link 'coverage' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:215: file link 'findOverlaps' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:216: file link 'nearest' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:260: file link 'shift' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:261: file link 'isDisjoint' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:262: file link 'coverage' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:263: file link 'findOverlaps' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:264: file link 'nearest' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:267: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
SummarizedExperiment-class html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/SummarizedExperiment-class.Rd:174: file link 'mcols' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/SummarizedExperiment-class.Rd:176: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/SummarizedExperiment-class.Rd:179: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/SummarizedExperiment-class.Rd:183: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/SummarizedExperiment-class.Rd:233: file link 'mcols' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/SummarizedExperiment-class.Rd:423: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/SummarizedExperiment-class.Rd:423: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/SummarizedExperiment-class.Rd:424: file link 'Annotated' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/SummarizedExperiment-class.Rd:426: file link 'metadata' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/SummarizedExperiment-class.Rd:427: file link 'mcols' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/SummarizedExperiment-class.Rd:431: file link 'loadHDF5SummarizedExperiment' in package 'HDF5Array' does not exist and so has been treated as a topic
coverage-methods html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/coverage-methods.Rd:34: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
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findOverlaps-methods html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/findOverlaps-methods.Rd:43: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/findOverlaps-methods.Rd:81: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
inter-range-methods html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/intra-range-methods.Rd:77: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/intra-range-methods.Rd:77: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/intra-range-methods.Rd:89: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/intra-range-methods.Rd:89: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/intra-range-methods.Rd:99: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/SummarizedExperiment/man/intra-range-methods.Rd:100: 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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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-3.10-bioc/tmpdir/Rtmpw9B3yD/R.INSTALL1ab0ffa11ad/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 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 'SummarizedExperiment' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SummarizedExperiment' as SummarizedExperiment_1.16.1.zip
* DONE (SummarizedExperiment)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'SummarizedExperiment' successfully unpacked and MD5 sums checked
|
SummarizedExperiment.Rcheck/tests_i386/run_unitTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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, 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
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, 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 07:02:30 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
17.93 1.03 19.34
|
SummarizedExperiment.Rcheck/tests_x64/run_unitTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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, 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
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, 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 07:02:52 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
21.03 0.62 21.64
|
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SummarizedExperiment.Rcheck/examples_i386/SummarizedExperiment-Ex.timings
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SummarizedExperiment.Rcheck/examples_x64/SummarizedExperiment-Ex.timings
|