| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:26:20 -0400 (Thu, 12 Apr 2018).
| Package 1366/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SummarizedExperiment 1.8.1 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: SummarizedExperiment |
| Version: 1.8.1 |
| Command: rm -rf SummarizedExperiment.buildbin-libdir SummarizedExperiment.Rcheck && mkdir SummarizedExperiment.buildbin-libdir SummarizedExperiment.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SummarizedExperiment.buildbin-libdir SummarizedExperiment_1.8.1.tar.gz >SummarizedExperiment.Rcheck\00install.out 2>&1 && cp SummarizedExperiment.Rcheck\00install.out SummarizedExperiment-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SummarizedExperiment.buildbin-libdir --install="check:SummarizedExperiment-install.out" --force-multiarch --no-vignettes --timings SummarizedExperiment_1.8.1.tar.gz |
| StartedAt: 2018-04-12 03:29:35 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 03:33:58 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 263.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SummarizedExperiment.Rcheck |
| Warnings: 1 |
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### Running command:
###
### rm -rf SummarizedExperiment.buildbin-libdir SummarizedExperiment.Rcheck && mkdir SummarizedExperiment.buildbin-libdir SummarizedExperiment.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SummarizedExperiment.buildbin-libdir SummarizedExperiment_1.8.1.tar.gz >SummarizedExperiment.Rcheck\00install.out 2>&1 && cp SummarizedExperiment.Rcheck\00install.out SummarizedExperiment-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=SummarizedExperiment.buildbin-libdir --install="check:SummarizedExperiment-install.out" --force-multiarch --no-vignettes --timings SummarizedExperiment_1.8.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/SummarizedExperiment.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.8.1'
* 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-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/Assays-class.Rd:117: missing file link 'SimpleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:116: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:119: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:122: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:123: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:126: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:126: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:151: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:152: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:216: missing file link 'shift'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:217: missing file link 'isDisjoint'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:218: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:219: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:220: missing file link 'nearest'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:264: missing file link 'shift'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:265: missing file link 'isDisjoint'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:266: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:267: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:268: missing file link 'nearest'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:271: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/SummarizedExperiment-class.Rd:133: missing file link 'mcols'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/SummarizedExperiment-class.Rd:206: missing file link 'mcols'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/SummarizedExperiment-class.Rd:393: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/SummarizedExperiment-class.Rd:393: missing file link 'SimpleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/SummarizedExperiment-class.Rd:394: missing file link 'Annotated'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/SummarizedExperiment-class.Rd:396: missing file link 'metadata'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/SummarizedExperiment-class.Rd:397: missing file link 'mcols'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/coverage-methods.Rd:26: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/coverage-methods.Rd:34: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/coverage-methods.Rd:34: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/coverage-methods.Rd:40: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/coverage-methods.Rd:42: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/coverage-methods.Rd:42: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/coverage-methods.Rd:47: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/coverage-methods.Rd:55: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/coverage-methods.Rd:57: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/coverage-methods.Rd:58: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/findOverlaps-methods.Rd:43: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/findOverlaps-methods.Rd:47: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/findOverlaps-methods.Rd:55: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/findOverlaps-methods.Rd:55: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/findOverlaps-methods.Rd:63: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/findOverlaps-methods.Rd:65: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/findOverlaps-methods.Rd:65: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/findOverlaps-methods.Rd:70: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/findOverlaps-methods.Rd:78: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/findOverlaps-methods.Rd:80: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/findOverlaps-methods.Rd:81: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/inter-range-methods.Rd:30: missing file link 'isDisjoint'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/inter-range-methods.Rd:38: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/inter-range-methods.Rd:38: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/inter-range-methods.Rd:48: missing file link 'isDisjoint'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/inter-range-methods.Rd:50: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/inter-range-methods.Rd:50: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/inter-range-methods.Rd:55: missing file link 'isDisjoint'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/inter-range-methods.Rd:63: missing file link 'isDisjoint'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/inter-range-methods.Rd:65: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/inter-range-methods.Rd:66: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:57: missing file link 'shift'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:61: missing file link 'shift'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:65: missing file link 'shift'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:69: missing file link 'shift'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:73: missing file link 'shift'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:81: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:81: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:91: missing file link 'shift'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:93: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:93: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:101: missing file link 'shift'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:103: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:104: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/makeSummarizedExperimentFromDataFrame.Rd:31: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:18: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:20: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:39: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:42: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:45: missing file link 'rownames'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:45: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:47: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:64: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:70: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:79: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:81: missing file link 'TxDb'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/nearest-methods.Rd:66: missing file link 'nearest'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/nearest-methods.Rd:79: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/nearest-methods.Rd:79: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/nearest-methods.Rd:88: missing file link 'nearest'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/nearest-methods.Rd:90: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/nearest-methods.Rd:90: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/nearest-methods.Rd:95: missing file link 'nearest'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/nearest-methods.Rd:103: missing file link 'nearest'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/nearest-methods.Rd:105: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/nearest-methods.Rd:106: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/saveHDF5SummarizedExperiment.Rd:74: missing file link 'HDF5Array'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/saveHDF5SummarizedExperiment.Rd:75: missing file link 'HDF5Array'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/saveHDF5SummarizedExperiment.Rd:82: missing file link 'HDF5Array'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/saveHDF5SummarizedExperiment.Rd:95: missing file link 'HDF5Array'
See 'C:/Users/biocbuild/bbs-3.6-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 ... NOTE
'library' or 'require' calls in package code:
'HDF5Array' 'rhdf5'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 installed files from 'inst/doc' ... 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 6.05 0.17 13.53
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
makeSummarizedExperimentFromExpressionSet 6.44 0.23 6.68
* 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/biocbuild/bbs-3.6-bioc/meat/SummarizedExperiment.Rcheck/00check.log'
for details.
SummarizedExperiment.Rcheck/00install.out
install for i386
* installing *source* package 'SummarizedExperiment' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'SummarizedExperiment'
finding HTML links ... done
Assays-class html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/Assays-class.Rd:117: missing file link 'SimpleList'
RangedSummarizedExperiment-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:116: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:119: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:122: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:123: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:126: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:126: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:151: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:152: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:216: missing file link 'shift'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:217: missing file link 'isDisjoint'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:218: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:219: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:220: missing file link 'nearest'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:264: missing file link 'shift'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:265: missing file link 'isDisjoint'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:266: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:267: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:268: missing file link 'nearest'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:271: missing file link 'GRanges'
SummarizedExperiment-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/SummarizedExperiment-class.Rd:133: missing file link 'mcols'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/SummarizedExperiment-class.Rd:206: missing file link 'mcols'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/SummarizedExperiment-class.Rd:393: missing file link 'DataFrame'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/SummarizedExperiment-class.Rd:393: missing file link 'SimpleList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/SummarizedExperiment-class.Rd:394: missing file link 'Annotated'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/SummarizedExperiment-class.Rd:396: missing file link 'metadata'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/SummarizedExperiment-class.Rd:397: missing file link 'mcols'
coverage-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/coverage-methods.Rd:26: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/coverage-methods.Rd:34: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/coverage-methods.Rd:34: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/coverage-methods.Rd:40: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/coverage-methods.Rd:42: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/coverage-methods.Rd:42: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/coverage-methods.Rd:47: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/coverage-methods.Rd:55: missing file link 'coverage'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/coverage-methods.Rd:57: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/coverage-methods.Rd:58: missing file link 'GRangesList'
findOverlaps-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/findOverlaps-methods.Rd:43: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/findOverlaps-methods.Rd:47: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/findOverlaps-methods.Rd:55: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/findOverlaps-methods.Rd:55: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/findOverlaps-methods.Rd:63: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/findOverlaps-methods.Rd:65: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/findOverlaps-methods.Rd:65: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/findOverlaps-methods.Rd:70: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/findOverlaps-methods.Rd:78: missing file link 'findOverlaps'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/findOverlaps-methods.Rd:80: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/findOverlaps-methods.Rd:81: missing file link 'GRangesList'
inter-range-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/inter-range-methods.Rd:30: missing file link 'isDisjoint'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/inter-range-methods.Rd:38: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/inter-range-methods.Rd:38: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/inter-range-methods.Rd:48: missing file link 'isDisjoint'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/inter-range-methods.Rd:50: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/inter-range-methods.Rd:50: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/inter-range-methods.Rd:55: missing file link 'isDisjoint'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/inter-range-methods.Rd:63: missing file link 'isDisjoint'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/inter-range-methods.Rd:65: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/inter-range-methods.Rd:66: missing file link 'GRangesList'
intra-range-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:57: missing file link 'shift'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:61: missing file link 'shift'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:65: missing file link 'shift'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:69: missing file link 'shift'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:73: missing file link 'shift'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:81: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:81: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:91: missing file link 'shift'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:93: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:93: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:101: missing file link 'shift'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:103: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/intra-range-methods.Rd:104: missing file link 'GRangesList'
makeSummarizedExperimentFromDataFrame html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/makeSummarizedExperimentFromDataFrame.Rd:31: missing file link 'DataFrame'
makeSummarizedExperimentFromExpressionSet
html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:18: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:20: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:39: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:42: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:45: missing file link 'rownames'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:45: missing file link 'GRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:47: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:64: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:70: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:79: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:81: missing file link 'TxDb'
nearest-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/nearest-methods.Rd:66: missing file link 'nearest'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/nearest-methods.Rd:79: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/nearest-methods.Rd:79: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/nearest-methods.Rd:88: missing file link 'nearest'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/nearest-methods.Rd:90: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/nearest-methods.Rd:90: missing file link 'GRangesList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/nearest-methods.Rd:95: missing file link 'nearest'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/nearest-methods.Rd:103: missing file link 'nearest'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/nearest-methods.Rd:105: missing file link 'GenomicRanges'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/nearest-methods.Rd:106: missing file link 'GRangesList'
readKallisto html
saveHDF5SummarizedExperiment html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/saveHDF5SummarizedExperiment.Rd:74: missing file link 'HDF5Array'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/saveHDF5SummarizedExperiment.Rd:75: missing file link 'HDF5Array'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/saveHDF5SummarizedExperiment.Rd:82: missing file link 'HDF5Array'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqkxGX0/R.INSTALL1c6827ab3cd7/SummarizedExperiment/man/saveHDF5SummarizedExperiment.Rd:95: missing file link 'HDF5Array'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'SummarizedExperiment' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SummarizedExperiment' as SummarizedExperiment_1.8.1.zip
* DONE (SummarizedExperiment)
In R CMD INSTALL
In R CMD INSTALL
|
SummarizedExperiment.Rcheck/tests_i386/run_unitTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("SummarizedExperiment") || stop("unable to load SummarizedExperiment package")
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
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 object is masked from 'package:base':
apply
[1] TRUE
> SummarizedExperiment:::.test()
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
RUNIT TEST PROTOCOL -- Thu Apr 12 03:33:22 2018
***********************************************
Number of test functions: 34
Number of errors: 0
Number of failures: 0
1 Test Suite :
SummarizedExperiment RUnit Tests - 34 test functions, 0 errors, 0 failures
Number of test functions: 34
Number of errors: 0
Number of failures: 0
Warning messages:
1: In V_recycle(value, x, x_what = "value", skeleton_what = "x") :
'length(x)' is not a multiple of 'NROW(value)'
2: In V_recycle(value, x, x_what = "value", skeleton_what = "x") :
'length(x)' is not a multiple of 'NROW(value)'
3: In .recycle(arg, length(x), arg.label, "x") :
'weight' length is not a divisor of 'x' length
4: In .recycle(arg, length(x), arg.label, "x") :
'weight' length is not a divisor of 'x' length
5: In .deprecatedColsMessage() :
Accessing gene location information via 'CHR','CHRLOC','CHRLOCEND' is
deprecated. Please use a range based accessor like genes(), or select()
with columns values like TXCHROM and TXSTART on a TxDb or OrganismDb
object instead.
6: 145 probes could not be mapped.
7: 169 probes could not be mapped.
>
> proc.time()
user system elapsed
23.03 0.35 23.37
|
SummarizedExperiment.Rcheck/tests_x64/run_unitTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("SummarizedExperiment") || stop("unable to load SummarizedExperiment package")
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
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 object is masked from 'package:base':
apply
[1] TRUE
> SummarizedExperiment:::.test()
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
RUNIT TEST PROTOCOL -- Thu Apr 12 03:33:53 2018
***********************************************
Number of test functions: 34
Number of errors: 0
Number of failures: 0
1 Test Suite :
SummarizedExperiment RUnit Tests - 34 test functions, 0 errors, 0 failures
Number of test functions: 34
Number of errors: 0
Number of failures: 0
Warning messages:
1: In V_recycle(value, x, x_what = "value", skeleton_what = "x") :
'length(x)' is not a multiple of 'NROW(value)'
2: In V_recycle(value, x, x_what = "value", skeleton_what = "x") :
'length(x)' is not a multiple of 'NROW(value)'
3: In .recycle(arg, length(x), arg.label, "x") :
'weight' length is not a divisor of 'x' length
4: In .recycle(arg, length(x), arg.label, "x") :
'weight' length is not a divisor of 'x' length
5: In .deprecatedColsMessage() :
Accessing gene location information via 'CHR','CHRLOC','CHRLOCEND' is
deprecated. Please use a range based accessor like genes(), or select()
with columns values like TXCHROM and TXSTART on a TxDb or OrganismDb
object instead.
6: 145 probes could not be mapped.
7: 169 probes could not be mapped.
>
> proc.time()
user system elapsed
30.43 0.31 30.76
|
|
SummarizedExperiment.Rcheck/examples_i386/SummarizedExperiment-Ex.timings
|
SummarizedExperiment.Rcheck/examples_x64/SummarizedExperiment-Ex.timings
|