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This page was generated on 2020-10-17 11:57:54 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE SummarizedExperiment PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1758/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SummarizedExperiment 1.18.2 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: SummarizedExperiment |
| Version: 1.18.2 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/SummarizedExperiment_1.18.2.tar.gz && rm -rf SummarizedExperiment.buildbin-libdir && mkdir SummarizedExperiment.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SummarizedExperiment.buildbin-libdir SummarizedExperiment_1.18.2.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL SummarizedExperiment_1.18.2.zip && rm SummarizedExperiment_1.18.2.tar.gz SummarizedExperiment_1.18.2.zip |
| StartedAt: 2020-10-16 17:51:54 -0400 (Fri, 16 Oct 2020) |
| EndedAt: 2020-10-16 17:54:05 -0400 (Fri, 16 Oct 2020) |
| EllapsedTime: 131.8 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/SummarizedExperiment_1.18.2.tar.gz && rm -rf SummarizedExperiment.buildbin-libdir && mkdir SummarizedExperiment.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SummarizedExperiment.buildbin-libdir SummarizedExperiment_1.18.2.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL SummarizedExperiment_1.18.2.zip && rm SummarizedExperiment_1.18.2.tar.gz SummarizedExperiment_1.18.2.zip
###
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install for i386
* installing *source* package 'SummarizedExperiment' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'SummarizedExperiment'
finding HTML links ... done
Assays-class html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/SummarizedExperiment/man/Assays-class.Rd:71: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/SummarizedExperiment/man/Assays-class.Rd:72: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/SummarizedExperiment/man/Assays-class.Rd:84: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/SummarizedExperiment/man/Assays-class.Rd:119: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
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RangedSummarizedExperiment-class html
finding level-2 HTML links ... done
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Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:121: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:148: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:212: file link 'shift' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:213: file link 'isDisjoint' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:215: file link 'findOverlaps' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:216: file link 'nearest' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd:260: file link 'shift' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
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SummarizedExperiment-class html
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Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/SummarizedExperiment/man/SummarizedExperiment-class.Rd:186: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/SummarizedExperiment/man/SummarizedExperiment-class.Rd:189: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/SummarizedExperiment/man/SummarizedExperiment-class.Rd:193: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/SummarizedExperiment/man/SummarizedExperiment-class.Rd:243: file link 'mcols' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/SummarizedExperiment/man/SummarizedExperiment-class.Rd:423: file link 'DataFrame' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/SummarizedExperiment/man/SummarizedExperiment-class.Rd:423: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/SummarizedExperiment/man/SummarizedExperiment-class.Rd:424: file link 'Annotated' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/SummarizedExperiment/man/SummarizedExperiment-class.Rd:426: file link 'metadata' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/SummarizedExperiment/man/SummarizedExperiment-class.Rd:427: file link 'mcols' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/SummarizedExperiment/man/SummarizedExperiment-class.Rd:431: file link 'loadHDF5SummarizedExperiment' in package 'HDF5Array' does not exist and so has been treated as a topic
coverage-methods html
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Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/SummarizedExperiment/man/coverage-methods.Rd:34: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/SummarizedExperiment/man/coverage-methods.Rd:57: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
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findOverlaps-methods html
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inter-range-methods html
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intra-range-methods html
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makeSummarizedExperimentFromDataFrame html
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makeSummarizedExperimentFromExpressionSet
html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/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-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/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-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/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-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/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-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/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-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/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-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/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-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/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-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/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-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/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-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/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-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/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-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/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-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/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-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/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-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/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-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/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-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/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-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/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-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/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-3.11-bioc/tmpdir/RtmpqOJAP6/R.INSTALL1acc13bf6f63/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_1.18.2.zip
* DONE (SummarizedExperiment)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'SummarizedExperiment' successfully unpacked and MD5 sums checked