Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:24:06 -0400 (Tue, 09 Apr 2019).
Package 1574/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
SummarizedExperiment 1.13.0 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: SummarizedExperiment |
Version: 1.13.0 |
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SummarizedExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SummarizedExperiment_1.13.0.tar.gz |
StartedAt: 2019-04-09 06:14:18 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 06:18:32 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 254.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: SummarizedExperiment.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SummarizedExperiment.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SummarizedExperiment_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SummarizedExperiment.Rcheck' * using R Under development (unstable) (2019-03-09 r76216) * 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 '1.13.0' * 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-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/Assays-class.Rd:118: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:120: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:123: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:126: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:127: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:130: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:130: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:155: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:156: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:220: file link 'shift' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:221: file link 'isDisjoint' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:222: file link 'coverage' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:223: file link 'findOverlaps' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:224: file link 'nearest' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:268: file link 'shift' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:269: file link 'isDisjoint' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:270: file link 'coverage' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:271: file link 'findOverlaps' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:272: file link 'nearest' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:275: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/SummarizedExperiment-class.Rd:173: file link 'mcols' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/SummarizedExperiment-class.Rd:175: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/SummarizedExperiment-class.Rd:178: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/SummarizedExperiment-class.Rd:182: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/SummarizedExperiment-class.Rd:232: file link 'mcols' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/SummarizedExperiment-class.Rd:422: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/SummarizedExperiment-class.Rd:422: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/SummarizedExperiment-class.Rd:423: file link 'Annotated' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/SummarizedExperiment-class.Rd:425: file link 'metadata' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/SummarizedExperiment-class.Rd:426: file link 'mcols' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/SummarizedExperiment-class.Rd:430: file link 'loadHDF5SummarizedExperiment' in package 'HDF5Array' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/coverage-methods.Rd:26: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/coverage-methods.Rd:34: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/coverage-methods.Rd:34: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/coverage-methods.Rd:40: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/coverage-methods.Rd:42: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/coverage-methods.Rd:42: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/coverage-methods.Rd:47: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/coverage-methods.Rd:55: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/coverage-methods.Rd:57: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/coverage-methods.Rd:58: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/findOverlaps-methods.Rd:43: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/findOverlaps-methods.Rd:47: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/findOverlaps-methods.Rd:55: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/findOverlaps-methods.Rd:55: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/findOverlaps-methods.Rd:63: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/findOverlaps-methods.Rd:65: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/findOverlaps-methods.Rd:65: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/findOverlaps-methods.Rd:70: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/findOverlaps-methods.Rd:78: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/findOverlaps-methods.Rd:80: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/findOverlaps-methods.Rd:81: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/inter-range-methods.Rd:30: file link 'isDisjoint' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/inter-range-methods.Rd:38: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/inter-range-methods.Rd:38: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/inter-range-methods.Rd:48: file link 'isDisjoint' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/inter-range-methods.Rd:50: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/inter-range-methods.Rd:50: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/inter-range-methods.Rd:55: file link 'isDisjoint' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/inter-range-methods.Rd:63: file link 'isDisjoint' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/inter-range-methods.Rd:65: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/inter-range-methods.Rd:66: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/intra-range-methods.Rd:77: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/intra-range-methods.Rd:77: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/intra-range-methods.Rd:89: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/intra-range-methods.Rd:89: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/intra-range-methods.Rd:99: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/intra-range-methods.Rd:100: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/makeSummarizedExperimentFromDataFrame.Rd:31: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:18: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:20: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:39: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:42: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:45: file link 'rownames' in package 'base' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:45: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:47: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:64: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:70: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:79: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:81: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/nearest-methods.Rd:66: file link 'nearest' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/nearest-methods.Rd:79: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/nearest-methods.Rd:79: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/nearest-methods.Rd:88: file link 'nearest' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/nearest-methods.Rd:90: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/nearest-methods.Rd:90: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/nearest-methods.Rd:95: file link 'nearest' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/nearest-methods.Rd:103: file link 'nearest' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/nearest-methods.Rd:105: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/nearest-methods.Rd:106: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SummarizedExperiment.Rcheck/00install.out' for details. * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * loading checks for arch 'x64' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed makeSummarizedExperimentFromExpressionSet 8.87 0.35 9.38 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed makeSummarizedExperimentFromExpressionSet 9.75 0.2 9.95 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'run_unitTests.R' OK ** running tests for arch 'x64' ... Running 'run_unitTests.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SummarizedExperiment.Rcheck/00check.log' for details.
SummarizedExperiment.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/SummarizedExperiment_1.13.0.tar.gz && rm -rf SummarizedExperiment.buildbin-libdir && mkdir SummarizedExperiment.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SummarizedExperiment.buildbin-libdir SummarizedExperiment_1.13.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL SummarizedExperiment_1.13.0.zip && rm SummarizedExperiment_1.13.0.tar.gz SummarizedExperiment_1.13.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 905k 100 905k 0 0 13.0M 0 --:--:-- --:--:-- --:--:-- 14.7M install for i386 * installing *source* package 'SummarizedExperiment' ... ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'SummarizedExperiment' finding HTML links ... done Assays-class html finding level-2 HTML links ... done Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/Assays-class.Rd:118: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic RangedSummarizedExperiment-class html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:120: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:123: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:126: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:127: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:130: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:130: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:155: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:156: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:220: file link 'shift' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:221: file link 'isDisjoint' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:222: file link 'coverage' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:223: file link 'findOverlaps' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:224: file link 'nearest' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:268: file link 'shift' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:269: file link 'isDisjoint' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:270: file link 'coverage' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:271: file link 'findOverlaps' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:272: file link 'nearest' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:275: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic SummarizedExperiment-class html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/SummarizedExperiment-class.Rd:173: file link 'mcols' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/SummarizedExperiment-class.Rd:175: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/SummarizedExperiment-class.Rd:178: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/SummarizedExperiment-class.Rd:182: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/SummarizedExperiment-class.Rd:232: file link 'mcols' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/SummarizedExperiment-class.Rd:422: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/SummarizedExperiment-class.Rd:422: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/SummarizedExperiment-class.Rd:423: file link 'Annotated' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/SummarizedExperiment-class.Rd:425: file link 'metadata' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/SummarizedExperiment-class.Rd:426: file link 'mcols' in package 'S4Vectors' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/SummarizedExperiment-class.Rd:430: file link 'loadHDF5SummarizedExperiment' in package 'HDF5Array' does not exist and so has been treated as a topic coverage-methods html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/coverage-methods.Rd:26: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/coverage-methods.Rd:34: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/coverage-methods.Rd:34: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/coverage-methods.Rd:40: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/coverage-methods.Rd:42: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/coverage-methods.Rd:42: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/coverage-methods.Rd:47: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/coverage-methods.Rd:55: file link 'coverage' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/coverage-methods.Rd:57: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/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/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/findOverlaps-methods.Rd:43: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/findOverlaps-methods.Rd:47: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/findOverlaps-methods.Rd:55: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/findOverlaps-methods.Rd:55: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/findOverlaps-methods.Rd:63: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/findOverlaps-methods.Rd:65: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/findOverlaps-methods.Rd:65: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/findOverlaps-methods.Rd:70: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/findOverlaps-methods.Rd:78: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/findOverlaps-methods.Rd:80: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/findOverlaps-methods.Rd:81: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic inter-range-methods html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/inter-range-methods.Rd:30: file link 'isDisjoint' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/inter-range-methods.Rd:38: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/inter-range-methods.Rd:38: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/inter-range-methods.Rd:48: file link 'isDisjoint' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/inter-range-methods.Rd:50: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/inter-range-methods.Rd:50: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/inter-range-methods.Rd:55: file link 'isDisjoint' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/inter-range-methods.Rd:63: file link 'isDisjoint' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/inter-range-methods.Rd:65: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/inter-range-methods.Rd:66: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic intra-range-methods html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/intra-range-methods.Rd:77: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/intra-range-methods.Rd:77: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/intra-range-methods.Rd:89: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/intra-range-methods.Rd:89: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/intra-range-methods.Rd:99: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/intra-range-methods.Rd:100: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic makeSummarizedExperimentFromDataFrame html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/makeSummarizedExperimentFromDataFrame.Rd:31: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic makeSummarizedExperimentFromExpressionSet html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:18: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:20: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:39: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:42: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:45: file link 'rownames' in package 'base' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:45: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:47: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:64: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:70: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:79: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd:81: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic makeSummarizedExperimentFromLoom html nearest-methods html Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/nearest-methods.Rd:66: file link 'nearest' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/nearest-methods.Rd:79: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/nearest-methods.Rd:79: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/nearest-methods.Rd:88: file link 'nearest' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/nearest-methods.Rd:90: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/nearest-methods.Rd:90: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/nearest-methods.Rd:95: file link 'nearest' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/nearest-methods.Rd:103: file link 'nearest' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/SummarizedExperiment/man/nearest-methods.Rd:105: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpuc87EB/R.INSTALL1a285d42488/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_1.13.0.zip * DONE (SummarizedExperiment) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'SummarizedExperiment' successfully unpacked and MD5 sums checked
SummarizedExperiment.Rcheck/tests_i386/run_unitTests.Rout R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > require("SummarizedExperiment") || stop("unable to load SummarizedExperiment package") Loading required package: SummarizedExperiment Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colSums, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: DelayedArray Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Loading required package: BiocParallel Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following objects are masked from 'package:base': aperm, apply, rowsum [1] TRUE > SummarizedExperiment:::.test() 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns RUNIT TEST PROTOCOL -- Tue Apr 09 06:18:07 2019 *********************************************** Number of test functions: 35 Number of errors: 0 Number of failures: 0 1 Test Suite : SummarizedExperiment RUnit Tests - 35 test functions, 0 errors, 0 failures Number of test functions: 35 Number of errors: 0 Number of failures: 0 Warning messages: 1: In V_recycle(value, x, x_what = "value", skeleton_what = "x") : 'length(x)' is not a multiple of 'NROW(value)' 2: In V_recycle(value, x, x_what = "value", skeleton_what = "x") : 'length(x)' is not a multiple of 'NROW(value)' 3: In S4Vectors:::V_recycle(arg, x, argname, "x") : 'length(x)' is not a multiple of 'NROW(weight)' 4: In S4Vectors:::V_recycle(arg, x, argname, "x") : 'length(x)' is not a multiple of 'NROW(weight)' 5: In .deprecatedColsMessage() : Accessing gene location information via 'CHR','CHRLOC','CHRLOCEND' is deprecated. Please use a range based accessor like genes(), or select() with columns values like TXCHROM and TXSTART on a TxDb or OrganismDb object instead. 6: 145 probes could not be mapped. 7: 169 probes could not be mapped. > > proc.time() user system elapsed 16.79 1.28 18.86 |
SummarizedExperiment.Rcheck/tests_x64/run_unitTests.Rout R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > require("SummarizedExperiment") || stop("unable to load SummarizedExperiment package") Loading required package: SummarizedExperiment Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colSums, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: DelayedArray Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Loading required package: BiocParallel Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following objects are masked from 'package:base': aperm, apply, rowsum [1] TRUE > SummarizedExperiment:::.test() 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns RUNIT TEST PROTOCOL -- Tue Apr 09 06:18:26 2019 *********************************************** Number of test functions: 35 Number of errors: 0 Number of failures: 0 1 Test Suite : SummarizedExperiment RUnit Tests - 35 test functions, 0 errors, 0 failures Number of test functions: 35 Number of errors: 0 Number of failures: 0 Warning messages: 1: In V_recycle(value, x, x_what = "value", skeleton_what = "x") : 'length(x)' is not a multiple of 'NROW(value)' 2: In V_recycle(value, x, x_what = "value", skeleton_what = "x") : 'length(x)' is not a multiple of 'NROW(value)' 3: In S4Vectors:::V_recycle(arg, x, argname, "x") : 'length(x)' is not a multiple of 'NROW(weight)' 4: In S4Vectors:::V_recycle(arg, x, argname, "x") : 'length(x)' is not a multiple of 'NROW(weight)' 5: In .deprecatedColsMessage() : Accessing gene location information via 'CHR','CHRLOC','CHRLOCEND' is deprecated. Please use a range based accessor like genes(), or select() with columns values like TXCHROM and TXSTART on a TxDb or OrganismDb object instead. 6: 145 probes could not be mapped. 7: 169 probes could not be mapped. > > proc.time() user system elapsed 18.14 0.48 18.60 |
SummarizedExperiment.Rcheck/examples_i386/SummarizedExperiment-Ex.timings
|
SummarizedExperiment.Rcheck/examples_x64/SummarizedExperiment-Ex.timings
|