| Back to "Blame Jeroen" build/check report for BioC 3.11 |
This page was generated on 2020-04-15 03:20:10 -0400 (Wed, 15 Apr 2020).
| These builds are using Rtools40 and R-testing by Jeroen Ooms (available at https://cran.r-project.org/bin/windows/testing/rtools40.html) |
| TO THE DEVELOPERS/MAINTAINERS OF THE SummarizedExperiment PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 81/89 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| SummarizedExperiment 1.17.5 Bioconductor Package Maintainer
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK |
| Package: SummarizedExperiment |
| Version: 1.17.5 |
| Command: C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD check --force-multiarch --install=check:SummarizedExperiment.install-out.txt --library=C:\Users\bioctesting\bbs-3.11-bioc-testing\R\library --no-vignettes --timings SummarizedExperiment_1.17.5.tar.gz |
| StartedAt: 2020-04-14 21:39:05 -0400 (Tue, 14 Apr 2020) |
| EndedAt: 2020-04-14 21:44:03 -0400 (Tue, 14 Apr 2020) |
| EllapsedTime: 297.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SummarizedExperiment.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD check --force-multiarch --install=check:SummarizedExperiment.install-out.txt --library=C:\Users\bioctesting\bbs-3.11-bioc-testing\R\library --no-vignettes --timings SummarizedExperiment_1.17.5.tar.gz
###
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* using log directory 'C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/SummarizedExperiment.Rcheck'
* using R version 4.0.0 alpha (Rtools40) (2020-03-31 r78116)
* 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 '1.17.5'
* 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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/SummarizedExperiment/man/SummarizedExperiment-class.Rd:184: file link 'mcols' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/SummarizedExperiment/man/SummarizedExperiment-class.Rd:186: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/SummarizedExperiment/man/SummarizedExperiment-class.Rd:189: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/SummarizedExperiment/man/SummarizedExperiment-class.Rd:193: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/SummarizedExperiment/man/SummarizedExperiment-class.Rd:243: file link 'mcols' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/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 ... NOTE
Unexported object imported by a ':::' call: 'DelayedArray:::simplify_NULL_dimnames'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
makeSummarizedExperimentFromExpressionSet 11.39 0.67 18.18
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
makeSummarizedExperimentFromExpressionSet 11.61 0.39 12.06
* 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, 1 NOTE
See
'C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/SummarizedExperiment.Rcheck/00check.log'
for details.
SummarizedExperiment.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc-testing/src/contrib/SummarizedExperiment_1.17.5.tar.gz && rm -rf SummarizedExperiment.buildbin-libdir && mkdir SummarizedExperiment.buildbin-libdir && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SummarizedExperiment.buildbin-libdir SummarizedExperiment_1.17.5.tar.gz && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL SummarizedExperiment_1.17.5.zip && rm SummarizedExperiment_1.17.5.tar.gz SummarizedExperiment_1.17.5.zip
###
##############################################################################
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 925k 100 925k 0 0 13.0M 0 --:--:-- --:--:-- --:--:-- 14.3M
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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/SummarizedExperiment/man/SummarizedExperiment-class.Rd:184: file link 'mcols' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/SummarizedExperiment/man/SummarizedExperiment-class.Rd:186: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/SummarizedExperiment/man/SummarizedExperiment-class.Rd:189: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/SummarizedExperiment/man/SummarizedExperiment-class.Rd:193: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/SummarizedExperiment/man/SummarizedExperiment-class.Rd:243: file link 'mcols' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/SummarizedExperiment/man/coverage-methods.Rd:42: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
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Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/SummarizedExperiment/man/coverage-methods.Rd:58: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
findOverlaps-methods html
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpiSoA7m/R.INSTALLf086a5d6732/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_1.17.5.zip
* DONE (SummarizedExperiment)
* installing to library 'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library'
package 'SummarizedExperiment' successfully unpacked and MD5 sums checked
|
SummarizedExperiment.Rcheck/tests_i386/run_unitTests.Rout
R version 4.0.0 alpha (Rtools40) (2020-03-31 r78116) -- "Blame Jeroen"
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
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
[1] TRUE
> SummarizedExperiment:::.test()
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
403 genes were dropped because they have exons located on both strands
of the same reference sequence or on more than one reference sequence,
so cannot be represented by a single genomic range.
Use 'single.strand.genes.only=FALSE' to get all the genes in a
GRangesList object, or use suppressMessages() to suppress this message.
RUNIT TEST PROTOCOL -- Tue Apr 14 21:43:37 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
22.57 1.23 24.07
|
SummarizedExperiment.Rcheck/tests_x64/run_unitTests.Rout
R version 4.0.0 alpha (Rtools40) (2020-03-31 r78116) -- "Blame Jeroen"
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
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
[1] TRUE
> SummarizedExperiment:::.test()
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
403 genes were dropped because they have exons located on both strands
of the same reference sequence or on more than one reference sequence,
so cannot be represented by a single genomic range.
Use 'single.strand.genes.only=FALSE' to get all the genes in a
GRangesList object, or use suppressMessages() to suppress this message.
RUNIT TEST PROTOCOL -- Tue Apr 14 21:43:59 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
20.75 0.79 21.54
|
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SummarizedExperiment.Rcheck/examples_i386/SummarizedExperiment-Ex.timings
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SummarizedExperiment.Rcheck/examples_x64/SummarizedExperiment-Ex.timings
|