Bioconductor Package Maintainer
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/S4Vectors |
| Branch: RELEASE_3_8 |
| Last Commit: 1878b29 |
| Last Changed Date: 2018-11-08 19:08:23 -0400 (Thu, 08 Nov 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:23:53 -0400 (Sat, 13 Apr 2019).
| Package 1376/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| S4Vectors 0.20.1 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: S4Vectors |
| Version: 0.20.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:S4Vectors.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings S4Vectors_0.20.1.tar.gz |
| StartedAt: 2019-04-13 05:17:30 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 05:20:38 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 187.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: S4Vectors.Rcheck |
| Warnings: 3 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:S4Vectors.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings S4Vectors_0.20.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/S4Vectors.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'S4Vectors/DESCRIPTION' ... OK
* this is package 'S4Vectors' version '0.20.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'S4Vectors' can be installed ... WARNING
Found the following significant warnings:
LLint_class.c:358:3: warning: too many arguments for format [-Wformat-extra-args]
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/DataTable-class.Rd:56: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-class.Rd:80: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-class.Rd:176: file link '[' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-class.Rd:187: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-class.Rd:282: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-class.Rd:285: file link 'Hits-examples' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-setops.Rd:47: file link 'union' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-setops.Rd:48: file link 'intersect' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-setops.Rd:49: file link 'setdiff' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/HitsList-class.Rd:37: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/HitsList-class.Rd:38: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/HitsList-class.Rd:47: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/HitsList-class.Rd:70: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/HitsList-class.Rd:101: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/HitsList-class.Rd:103: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:59: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:73: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:73: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:74: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:75: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.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-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:83: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:84: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:85: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:95: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:144: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:152: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:205: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:206: file link 'LogicalList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:206: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:207: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:208: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:208: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:258: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:261: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:261: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:262: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:94: file link 'sapply' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:105: file link 'Reduce' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:115: file link 'rbind' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:127: file link 'sapply' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:156: file link 'Reduce' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:189: file link 'Reduce' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:192: file link 'within' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:207: file link 'Reduce' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:210: file link 'within' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:214: file link 'rbind' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Pairs-class.Rd:46: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Pairs-class.Rd:47: file link 'findOverlapPairs' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Pairs-class.Rd:105: file link 'findOverlapPairs' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Rle-class.Rd:202: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Rle-class.Rd:221: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Rle-class.Rd:363: file link 'aggregate' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Rle-runstat.Rd:95: file link 'RleList-class' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/SimpleList-class.Rd:85: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/SimpleList-class.Rd:89: file link 'SimpleIntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-class.Rd:215: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-class.Rd:223: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-class.Rd:358: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-class.Rd:373: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-class.Rd:374: file link 'XRaw' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-comparison.Rd:292: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-comparison.Rd:325: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-comparison.Rd:341: missing file link 'IntegerRanges-comparison'
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-merge.Rd:22: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-merge.Rd:22: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-setops.Rd:90: file link 'union' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-setops.Rd:91: file link 'intersect' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-setops.Rd:92: file link 'setdiff' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/aggregate-methods.Rd:38: file link 'end' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/aggregate-methods.Rd:38: file link 'width' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/aggregate-methods.Rd:42: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/aggregate-methods.Rd:44: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/aggregate-methods.Rd:45: file link 'SimpleAtomicList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/aggregate-methods.Rd:96: file link 'end' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/aggregate-methods.Rd:97: file link 'width' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/integer-utils.Rd:70: file link 'seq_len' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/shiftApply-methods.Rd:44: file link 'window' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/shiftApply-methods.Rd:45: file link 'aggregate' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/split-methods.Rd:47: file link 'splitAsList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/split-methods.Rd:64: file link 'splitAsList' in package 'IRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/S4Vectors.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
'data.table:::as.data.frame.data.table'
'stats:::na.exclude.data.frame' 'stats:::na.omit.data.frame'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
evalSeparately,FilterRules : <anonymous>: no visible global function
definition for '.'
Undefined global functions or variables:
.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'Vector-comparison.Rd':
'[IRanges]{IntegerRanges-comparison}'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'cbind.DataFrame' 'head.LLint' 'pcompareRecursively' 'phead' 'ptail'
'rbind.DataFrame' 'selectHits' 't.Hits' 't.HitsList' 'tail.LLint'
'window.LLint'
Undocumented S4 classes:
'integer_OR_LLint' 'list_OR_List'
Undocumented S4 methods:
generic '!' and siglist 'List'
generic '<=' and siglist 'List,List'
generic '<=' and siglist 'List,list'
generic '<=' and siglist 'list,List'
generic '==' and siglist 'List,List'
generic '==' and siglist 'List,list'
generic '==' and siglist 'list,List'
generic 'NSBS' and siglist 'Rle'
generic '[' and siglist 'LLint'
generic 'anyDuplicated' and siglist 'Rle'
generic 'anyDuplicated' and siglist 'RleNSBS'
generic 'anyNA' and siglist 'List'
generic 'anyNA' and siglist 'Rle'
generic 'as.integer' and siglist 'RleNSBS'
generic 'by' and siglist 'Vector'
generic 'coerce' and siglist 'ANY,DataTable_OR_NULL'
generic 'countMatches' and siglist 'ANY'
generic 'do.call' and siglist 'ANY,List'
generic 'droplevels' and siglist 'DataFrame'
generic 'duplicated' and siglist 'List'
generic 'eval' and siglist 'expression,Vector'
generic 'eval' and siglist 'language,Vector'
generic 'extractROWS' and siglist 'DataFrame,ANY'
generic 'extractROWS' and siglist 'LLint,ANY'
generic 'extractROWS' and siglist 'LLint,NSBS'
generic 'extractROWS' and siglist 'LLint,RangeNSBS'
generic 'extractROWS' and siglist 'Rle,NSBS'
generic 'extractROWS' and siglist 'Rle,RleNSBS'
generic 'extractROWS' and siglist 'Vector,ANY'
generic 'filterRules' and siglist 'FilterResults'
generic 'from' and siglist 'HitsList'
generic 'getListElement' and siglist 'SimpleList'
generic 'grep' and siglist 'ANY,Rle'
generic 'grepl' and siglist 'ANY,Rle'
generic 'head' and siglist 'LLint'
generic 'is.na' and siglist 'List'
generic 'is.unsorted' and siglist 'List'
generic 'isStrictlySorted' and siglist 'Rle'
generic 'isStrictlySorted' and siglist 'RleNSBS'
generic 'length' and siglist 'RleNSBS'
generic 'match' and siglist 'ANY,Rle'
generic 'match' and siglist 'List,List'
generic 'match' and siglist 'List,Vector'
generic 'match' and siglist 'List,list'
generic 'match' and siglist 'List,vector'
generic 'match' and siglist 'Rle,Rle'
generic 'match' and siglist 'list,List'
generic 'order' and siglist 'List'
generic 'order' and siglist 'Rle'
generic 'pcompare' and siglist 'List,List'
generic 'pcompare' and siglist 'List,list'
generic 'pcompare' and siglist 'list,List'
generic 'pcompareRecursively' and siglist 'List'
generic 'pcompareRecursively' and siglist 'list'
generic 'rank' and siglist 'List'
generic 'rank' and siglist 'Rle'
generic 'rep.int' and siglist 'LLint'
generic 'rep' and siglist 'DataFrame'
generic 'replaceROWS' and siglist 'ANY'
generic 'replaceROWS' and siglist 'DataFrame'
generic 'replaceROWS' and siglist 'Rle'
generic 'replaceROWS' and siglist 'Vector'
generic 'sort' and siglist 'DataTable'
generic 'sort' and siglist 'List'
generic 'sort' and siglist 'SortedByQueryHits'
generic 'summary' and siglist 'FilterResults'
generic 't' and siglist 'Pairs'
generic 'tail' and siglist 'LLint'
generic 'to' and siglist 'HitsList'
generic 'transform' and siglist 'Vector'
generic 'unique' and siglist 'List'
generic 'unique' and siglist 'SimpleList'
generic 'updateObject' and siglist 'Vector'
generic 'window' and siglist 'LLint'
generic 'with' and siglist 'Vector'
generic 'xtabs' and siglist 'Vector'
generic 'xtfrm' and siglist 'Rle'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/libs/i386/S4Vectors.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
shiftApply-methods 14.98 2.12 17.11
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
shiftApply-methods 14.28 2.26 16.54
* 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: 3 WARNINGs, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/S4Vectors.Rcheck/00check.log'
for details.
S4Vectors.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/S4Vectors_0.20.1.tar.gz && rm -rf S4Vectors.buildbin-libdir && mkdir S4Vectors.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=S4Vectors.buildbin-libdir S4Vectors_0.20.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL S4Vectors_0.20.1.zip && rm S4Vectors_0.20.1.tar.gz S4Vectors_0.20.1.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 224k 100 224k 0 0 5890k 0 --:--:-- --:--:-- --:--:-- 6411k
install for i386
* installing *source* package 'S4Vectors' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c AEbufs.c -o AEbufs.o
AEbufs.c: In function '_increase_buflength':
AEbufs.c:31:2: warning: large integer implicitly truncated to unsigned type [-Woverflow]
return MAX_BUFLENGTH;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c DataFrame_class.c -o DataFrame_class.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c Hits_class.c -o Hits_class.o
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
from ../inst/include/S4Vectors_defines.h:18,
from S4Vectors.h:1,
from Hits_class.c:4:
Hits_class.c: In function 'Hits_new':
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1348:20: warning: 'revmap' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define defineVar Rf_defineVar
^
Hits_class.c:216:12: note: 'revmap' was declared here
SEXP ans, revmap, symbol;
^
Hits_class.c: In function 'select_hits':
Hits_class.c:346:24: warning: 'is_used' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (nodup0 && is_used->elts[ans_elt - 1])
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c LLint_class.c -o LLint_class.o
LLint_class.c: In function 'from_llints_to_STRSXP':
LLint_class.c:358:3: warning: unknown conversion type character 'l' in format [-Wformat=]
if (sprintf(val_buf, "%lld", from_elt) < 0)
^
LLint_class.c:358:3: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c List_class.c -o List_class.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c R_init_S4Vectors.c -o R_init_S4Vectors.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c Rle_class.c -o Rle_class.o
Rle_class.c: In function 'check_integer_runs':
Rle_class.c:218:20: warning: 'len_out' may be used uninitialized in this function [-Wmaybe-uninitialized]
*max_len_out_p = len_out;
^
Rle_class.c: In function '_construct_character_Rle':
Rle_class.c:509:13: warning: 'len_out' may be used uninitialized in this function [-Wmaybe-uninitialized]
len_out += len_in;
^
Rle_class.c:489:30: note: 'len_out' was declared here
unsigned long long int sum, len_out;
^
Rle_class.c: In function '_construct_raw_Rle':
Rle_class.c:606:13: warning: 'len_out' may be used uninitialized in this function [-Wmaybe-uninitialized]
len_out += len_in;
^
Rle_class.c:587:30: note: 'len_out' was declared here
unsigned long long int sum, len_out;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c Rle_utils.c -o Rle_utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c SEXP_utils.c -o SEXP_utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c SimpleList_class.c -o SimpleList_class.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c anyMissing.c -o anyMissing.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c character_utils.c -o character_utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c eval_utils.c -o eval_utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c hash_utils.c -o hash_utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c integer_utils.c -o integer_utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c logical_utils.c -o logical_utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c map_ranges_to_runs.c -o map_ranges_to_runs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c safe_arithm.c -o safe_arithm.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c sort_utils.c -o sort_utils.o
sort_utils.c:263:13: warning: 'sort_uchar_array' defined but not used [-Wunused-function]
static void sort_uchar_array(unsigned char *x, int nelt, int desc)
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c subsetting_utils.c -o subsetting_utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c vector_utils.c -o vector_utils.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o S4Vectors.dll tmp.def AEbufs.o DataFrame_class.o Hits_class.o LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o character_utils.o eval_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/S4Vectors.buildbin-libdir/S4Vectors/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'complete.cases' from package 'stats' in package 'S4Vectors'
Creating a new generic function for 'expand.grid' in package 'S4Vectors'
Creating a generic function for '%in%' from package 'base' in package 'S4Vectors'
Creating a new generic function for 'findMatches' in package 'S4Vectors'
Creating a generic function for 'setequal' from package 'base' in package 'S4Vectors'
Creating a generic function for 'as.factor' from package 'base' in package 'S4Vectors'
Creating a generic function for 'tabulate' from package 'base' in package 'S4Vectors'
Creating a generic function for 'cov' from package 'stats' in package 'S4Vectors'
Creating a generic function for 'cor' from package 'stats' in package 'S4Vectors'
Creating a generic function for 'smoothEnds' from package 'stats' in package 'S4Vectors'
Creating a generic function for 'runmed' from package 'stats' in package 'S4Vectors'
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Creating a generic function for 'substr' from package 'base' in package 'S4Vectors'
Creating a generic function for 'substring' from package 'base' in package 'S4Vectors'
Creating a generic function for 'chartr' from package 'base' in package 'S4Vectors'
Creating a generic function for 'tolower' from package 'base' in package 'S4Vectors'
Creating a generic function for 'toupper' from package 'base' in package 'S4Vectors'
Creating a generic function for 'sub' from package 'base' in package 'S4Vectors'
Creating a generic function for 'gsub' from package 'base' in package 'S4Vectors'
in method for 'coerce' with signature '"data.table","DataFrame"': no definition for class "data.table"
** help
*** installing help indices
converting help for package 'S4Vectors'
finding HTML links ... done
Annotated-class html
DataFrame-class html
DataTable-class html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/DataTable-class.Rd:56: file link 'DelayedMatrix' in package 'DelayedArray' does not exist and so has been treated as a topic
FilterMatrix-class html
FilterRules-class html
Hits-class html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-class.Rd:80: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-class.Rd:176: file link '[' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-class.Rd:187: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-class.Rd:282: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-class.Rd:285: file link 'Hits-examples' in package 'IRanges' does not exist and so has been treated as a topic
Hits-comparison html
Hits-setops html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-setops.Rd:47: file link 'union' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-setops.Rd:48: file link 'intersect' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Hits-setops.Rd:49: file link 'setdiff' in package 'BiocGenerics' does not exist and so has been treated as a topic
HitsList-class html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/HitsList-class.Rd:37: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/HitsList-class.Rd:38: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/HitsList-class.Rd:47: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/HitsList-class.Rd:70: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/HitsList-class.Rd:101: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/HitsList-class.Rd:103: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
LLint-class html
List-class html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:59: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:73: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:73: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:206: file link 'CharacterList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:207: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:208: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:208: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:258: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:261: file link 'IntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:261: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-class.Rd:262: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
List-utils html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:94: file link 'sapply' in package 'base' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:115: file link 'rbind' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:127: file link 'sapply' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:156: file link 'Reduce' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:189: file link 'Reduce' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:192: file link 'within' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:207: file link 'Reduce' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:210: file link 'within' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/List-utils.Rd:214: file link 'rbind' in package 'base' does not exist and so has been treated as a topic
Pairs-class html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Pairs-class.Rd:46: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Pairs-class.Rd:47: file link 'findOverlapPairs' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Pairs-class.Rd:105: file link 'findOverlapPairs' in package 'IRanges' does not exist and so has been treated as a topic
Rle-class html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Rle-class.Rd:202: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Rle-class.Rd:221: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Rle-class.Rd:363: file link 'aggregate' in package 'S4Vectors' does not exist and so has been treated as a topic
Rle-runstat html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Rle-runstat.Rd:95: file link 'RleList-class' in package 'IRanges' does not exist and so has been treated as a topic
Rle-utils html
S4Vectors-internals html
SimpleList-class html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/SimpleList-class.Rd:85: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/SimpleList-class.Rd:89: file link 'SimpleIntegerList' in package 'IRanges' does not exist and so has been treated as a topic
Vector-class html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-class.Rd:215: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-class.Rd:223: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-class.Rd:358: file link 'CompressedList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-class.Rd:373: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-class.Rd:374: file link 'XRaw' in package 'XVector' does not exist and so has been treated as a topic
Vector-comparison html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-comparison.Rd:292: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-comparison.Rd:325: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-comparison.Rd:341: missing file link 'IntegerRanges-comparison'
Vector-merge html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-merge.Rd:22: file link 'IntegerRanges' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-merge.Rd:22: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Vector-setops html
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Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-setops.Rd:91: file link 'intersect' in package 'BiocGenerics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/Vector-setops.Rd:92: file link 'setdiff' in package 'BiocGenerics' does not exist and so has been treated as a topic
aggregate-methods html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/aggregate-methods.Rd:38: file link 'end' in package 'BiocGenerics' does not exist and so has been treated as a topic
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Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/aggregate-methods.Rd:42: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/aggregate-methods.Rd:44: file link 'IntegerRangesList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/aggregate-methods.Rd:45: file link 'SimpleAtomicList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/aggregate-methods.Rd:96: file link 'end' in package 'BiocGenerics' does not exist and so has been treated as a topic
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character-utils html
expand-methods html
integer-utils html
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isSorted html
shiftApply-methods html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/shiftApply-methods.Rd:44: file link 'window' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/shiftApply-methods.Rd:45: file link 'aggregate' in package 'S4Vectors' does not exist and so has been treated as a topic
show-utils html
split-methods html
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/split-methods.Rd:47: file link 'splitAsList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp8YRCUB/R.INSTALL3e4353e2d4d/S4Vectors/man/split-methods.Rd:64: file link 'splitAsList' in package 'IRanges' does not exist and so has been treated as a topic
subsetting-utils html
zip-methods html
** building package indices
** installing vignettes
'RleTricks.Rnw' using 'UTF-8'
'S4QuickOverview.Rnw' using 'UTF-8'
'S4VectorsOverview.Rnw' using 'UTF-8'
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'S4Vectors' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c AEbufs.c -o AEbufs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c DataFrame_class.c -o DataFrame_class.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c Hits_class.c -o Hits_class.o
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rdefines.h:40:0,
from ../inst/include/S4Vectors_defines.h:18,
from S4Vectors.h:1,
from Hits_class.c:4:
Hits_class.c: In function 'Hits_new':
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rinternals.h:1348:20: warning: 'revmap' may be used uninitialized in this function [-Wmaybe-uninitialized]
#define defineVar Rf_defineVar
^
Hits_class.c:216:12: note: 'revmap' was declared here
SEXP ans, revmap, symbol;
^
Hits_class.c: In function 'select_hits':
Hits_class.c:346:24: warning: 'is_used' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (nodup0 && is_used->elts[ans_elt - 1])
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c LLint_class.c -o LLint_class.o
LLint_class.c: In function 'from_llints_to_STRSXP':
LLint_class.c:358:3: warning: unknown conversion type character 'l' in format [-Wformat=]
if (sprintf(val_buf, "%lld", from_elt) < 0)
^
LLint_class.c:358:3: warning: too many arguments for format [-Wformat-extra-args]
LLint_class.c: In function 'llints_summary':
LLint_class.c:791:9: warning: 'res' may be used uninitialized in this function [-Wmaybe-uninitialized]
res = _safe_llint_mult(res, in_elt);
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c List_class.c -o List_class.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c R_init_S4Vectors.c -o R_init_S4Vectors.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c Rle_class.c -o Rle_class.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c Rle_utils.c -o Rle_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c SEXP_utils.c -o SEXP_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c SimpleList_class.c -o SimpleList_class.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c anyMissing.c -o anyMissing.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c character_utils.c -o character_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c eval_utils.c -o eval_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c hash_utils.c -o hash_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c integer_utils.c -o integer_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c logical_utils.c -o logical_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c map_ranges_to_runs.c -o map_ranges_to_runs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c safe_arithm.c -o safe_arithm.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c sort_utils.c -o sort_utils.o
sort_utils.c:263:13: warning: 'sort_uchar_array' defined but not used [-Wunused-function]
static void sort_uchar_array(unsigned char *x, int nelt, int desc)
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c subsetting_utils.c -o subsetting_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c vector_utils.c -o vector_utils.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o S4Vectors.dll tmp.def AEbufs.o DataFrame_class.o Hits_class.o LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o character_utils.o eval_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/S4Vectors.buildbin-libdir/S4Vectors/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'S4Vectors' as S4Vectors_0.20.1.zip
* DONE (S4Vectors)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'S4Vectors' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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S4Vectors.Rcheck/tests_i386/run_unitTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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("S4Vectors") || stop("unable to load S4Vectors package")
Loading required package: S4Vectors
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, 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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
[1] TRUE
> S4Vectors:::.test()
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
RUNIT TEST PROTOCOL -- Sat Apr 13 05:20:23 2019
***********************************************
Number of test functions: 60
Number of errors: 0
Number of failures: 0
1 Test Suite :
S4Vectors RUnit Tests - 60 test functions, 0 errors, 0 failures
Number of test functions: 60
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
7.37 0.18 8.28
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S4Vectors.Rcheck/tests_x64/run_unitTests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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("S4Vectors") || stop("unable to load S4Vectors package")
Loading required package: S4Vectors
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, 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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
[1] TRUE
> S4Vectors:::.test()
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
RUNIT TEST PROTOCOL -- Sat Apr 13 05:20:31 2019
***********************************************
Number of test functions: 60
Number of errors: 0
Number of failures: 0
1 Test Suite :
S4Vectors RUnit Tests - 60 test functions, 0 errors, 0 failures
Number of test functions: 60
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
7.65 0.17 7.81
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S4Vectors.Rcheck/examples_i386/S4Vectors-Ex.timings
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S4Vectors.Rcheck/examples_x64/S4Vectors-Ex.timings
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