Bioconductor Package Maintainer
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/IRanges |
| Branch: master |
| Last Commit: f6eb2f0 |
| Last Changed Date: 2019-02-14 20:30:08 -0400 (Thu, 14 Feb 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:53:37 -0400 (Tue, 09 Apr 2019).
| Package 817/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| IRanges 2.17.4 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
| Package: IRanges |
| Version: 2.17.4 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IRanges.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings IRanges_2.17.4.tar.gz |
| StartedAt: 2019-04-09 03:41:40 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 03:48:15 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 394.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: IRanges.Rcheck |
| Warnings: 4 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IRanges.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings IRanges_2.17.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/IRanges.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 'IRanges/DESCRIPTION' ... OK
* this is package 'IRanges' version '2.17.4'
* 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 'IRanges' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/AtomicList-class.Rd:307: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:38: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:39: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:44: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:49: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:50: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:60: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:66: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:81: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-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-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:87: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:89: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:95: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:100: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:105: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:110: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:118: file link 'classNameForDisplay' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:124: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:127: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/Hits-class-leftovers.Rd:31: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/Hits-class-leftovers.Rd:68: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/IPos-class.Rd:96: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/IPos-class.Rd:106: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/IPos-class.Rd:120: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/IPosRanges-class.Rd:200: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/IPosRanges-class.Rd:225: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/IPosRanges-class.Rd:225: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/IPosRanges-class.Rd:226: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/IPosRanges-class.Rd:226: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/IPosRanges-class.Rd:227: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/IPosRanges-comparison.Rd:164: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/IRanges-class.Rd:97: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/List-class-leftovers.Rd:11: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/List-class-leftovers.Rd:35: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/MaskCollection-class.Rd:206: file link 'alphabetFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/NCList-class.Rd:81: file link 'GNCList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/NCList-class.Rd:101: file link 'GNCList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/NCList-class.Rd:102: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/NCList-class.Rd:110: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/NCList-class.Rd:126: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/NCList-class.Rd:128: file link 'GNCList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/NCList-class.Rd:131: file link 'GNCList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/NCList-class.Rd:155: file link 'GNCList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/RangedData-class.Rd:78: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/RangedData-class.Rd:78: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/RangedData-class.Rd:80: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/RangedData-class.Rd:80: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/RangedData-class.Rd:84: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/RangedData-class.Rd:85: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/Rle-class-leftovers.Rd:22: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/Rle-class-leftovers.Rd:71: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/Vector-class-leftovers.Rd:29: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/Vector-class-leftovers.Rd:109: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/Views-class.Rd:48: file link 'XIntegerViews' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/Views-class.Rd:49: file link 'XStringViews' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/Views-class.Rd:158: file link 'XVector' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractList.Rd:24: file link 'split' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractList.Rd:95: file link 'relistToClass' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractList.Rd:149: file link 'relistToClass' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractList.Rd:160: file link 'unsplit' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractList.Rd:163: file link 'split' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractList.Rd:166: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractList.Rd:166: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractList.Rd:167: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractList.Rd:167: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractList.Rd:169: file link 'relistToClass' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractList.Rd:170: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractListFragments.Rd:78: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractListFragments.Rd:79: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractListFragments.Rd:80: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractListFragments.Rd:87: file link 'relistToClass' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractListFragments.Rd:104: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractListFragments.Rd:104: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractListFragments.Rd:107: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:62: file link 'findOverlaps,GenomicRanges,GenomicRanges-method' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:64: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:64: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:175: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:183: file link 'HitsList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:195: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:195: file link 'HitsList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:253: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:253: file link 'HitsList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:261: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:262: file link 'HitsList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:293: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:293: file link 'HitsList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:297: file link 'findOverlaps,GenomicRanges,GenomicRanges-method' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:299: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:299: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/inter-range-methods.Rd:266: file link 'endoapply' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/intra-range-methods.Rd:94: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/intra-range-methods.Rd:102: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/intra-range-methods.Rd:123: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/intra-range-methods.Rd:136: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/intra-range-methods.Rd:146: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/intra-range-methods.Rd:160: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/intra-range-methods.Rd:188: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/intra-range-methods.Rd:251: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/intra-range-methods.Rd:252: file link 'promoters,GenomicRanges-method' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/intra-range-methods.Rd:297: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/intra-range-methods.Rd:307: file link 'endoapply' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/nearest-methods.Rd:148: file link 'breakTies' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/nearest-methods.Rd:174: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/nearest-methods.Rd:175: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/nearest-methods.Rd:188: file link 'precede,GenomicRanges,GenomicRanges-method' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:15: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:16: file link 'grglist' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:18: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:19: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:20: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:21: file link 'grglist' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:32: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:33: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:34: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:35: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:36: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:37: file link 'Pairs' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:63: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:64: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:77: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:93: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:96: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:97: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:98: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/setops-methods.Rd:91: file link 'Pairs' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/setops-methods.Rd:116: file link 'Pairs' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/setops-methods.Rd:166: file link 'mendoapply' in package 'S4Vectors' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/IRanges.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
':::' call which should be '::': 'S4Vectors:::transform.DataTable'
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
setCompressedListSummaryMethod : <anonymous>: no visible binding for
global variable 'C_fun'
setCompressedListWhichSummaryMethod : def: no visible binding for
global variable 'C_fun'
Undefined global functions or variables:
C_fun
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'intra-range-methods.Rd':
'RangesList'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'%poutside%' '%pover%' '%pwithin%' 'RangesList' 'cvg' 'heads'
'slidingIRanges' 'slidingViews' 'tails' 'windows'
Undocumented S4 classes:
'SimpleRangesList' 'IPosList' 'SimpleIPosList'
'CompressedDataFrameList' 'Pos' 'CompressedIPosList' 'RangesList'
'BaseManyToManyGrouping' 'Ranges' 'CompressedRangesList'
'CompressedIntegerRangesList' 'SimplePosList' 'PosList'
'CompressedPosList'
Undocumented S4 methods:
generic 'anyDuplicated' and siglist 'RangesNSBS'
generic 'as.factor' and siglist 'ManyToOneGrouping'
generic 'as.integer' and siglist 'NormalIRanges'
generic 'as.integer' and siglist 'Pos'
generic 'as.integer' and siglist 'RangesNSBS'
generic 'cbind' and siglist 'Rle'
generic 'cbind' and siglist 'RleList'
generic 'coerce' and siglist 'ANY,IPosRanges'
generic 'coerce' and siglist 'AtomicList,RleViews'
generic 'coerce' and siglist 'IPosRanges,CompressedIntegerList'
generic 'coerce' and siglist 'IPosRanges,IntegerList'
generic 'coerce' and siglist 'IRanges,IPosList'
generic 'coerce' and siglist 'IntegerRanges,CompressedIPosList'
generic 'coerce' and siglist 'IntegerRanges,IPosList'
generic 'coerce' and siglist 'PartitioningByEnd,PartitioningMap'
generic 'coerce' and siglist 'factor,ManyToOneGrouping'
generic 'colnames' and siglist 'SDFLWrapperForTransform'
generic 'colnames' and siglist 'SplitDataFrameList'
generic 'cvg' and siglist 'IntegerRanges'
generic 'cvg' and siglist 'IntegerRangesList'
generic 'extractROWS' and siglist 'CompressedList,ANY'
generic 'extractROWS' and siglist 'IPos,ANY'
generic 'extractROWS' and siglist 'MaskCollection,ANY'
generic 'extractROWS' and siglist 'NormalIRanges,ANY'
generic 'extractROWS' and siglist 'Partitioning,ANY'
generic 'extractROWS' and siglist 'Rle,RangesNSBS'
generic 'extractROWS' and siglist 'vector_OR_factor,RangesNSBS'
generic 'getListElement' and siglist 'CompressedList'
generic 'getListElement' and siglist 'CompressedNormalIRangesList'
generic 'getListElement' and siglist 'H2LGrouping'
generic 'getListElement' and siglist 'MaskCollection'
generic 'getListElement' and siglist 'NCLists'
generic 'getListElement' and siglist 'Partitioning'
generic 'getListElement' and siglist 'Views'
generic 'ifelse2' and siglist 'ANY,List,List'
generic 'is.unsorted' and siglist 'CompressedIntegerList'
generic 'is.unsorted' and siglist 'CompressedLogicalList'
generic 'is.unsorted' and siglist 'CompressedNumericList'
generic 'isNormal' and siglist 'IntegerRanges'
generic 'length' and siglist 'RangesNSBS'
generic 'pcompareRecursively' and siglist 'IPosRanges'
generic 'range' and siglist 'CompressedRleList'
generic 'relist' and siglist 'grouping,missing'
generic 'replaceROWS' and siglist 'IRanges'
generic 'replaceROWS' and siglist 'NormalIRanges'
generic 'showAsCell' and siglist 'Views'
generic 'slidingWindows' and siglist 'IntegerRanges'
generic 'splitAsList' and siglist 'ANY'
generic 'stack' and siglist 'matrix'
generic 'tile' and siglist 'IntegerRanges'
generic 'updateObject' and siglist 'CompressedList'
generic 'updateObject' and siglist 'IPosRanges'
generic 'whichFirstNotNormal' and siglist 'IntegerRanges'
generic 'windows' and siglist 'list_OR_List'
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 ... WARNING
Documented arguments not in \usage in documentation object 'nearest-methods':
'hits'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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-3.9-bioc/R/library/IRanges/libs/i386/IRanges.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/IRanges/libs/x64/IRanges.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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
IPos-class 6.5 0.61 9.87
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
IPos-class 6.91 0.48 7.39
* 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: 4 WARNINGs, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/IRanges.Rcheck/00check.log'
for details.
IRanges.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/IRanges_2.17.4.tar.gz && rm -rf IRanges.buildbin-libdir && mkdir IRanges.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IRanges.buildbin-libdir IRanges_2.17.4.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL IRanges_2.17.4.zip && rm IRanges_2.17.4.tar.gz IRanges_2.17.4.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 259k 100 259k 0 0 1196k 0 --:--:-- --:--:-- --:--:-- 1236k
install for i386
* installing *source* package 'IRanges' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c CompressedList_class.c -o CompressedList_class.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c Grouping_class.c -o Grouping_class.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c IPosRanges_comparison.c -o IPosRanges_comparison.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c IRanges_class.c -o IRanges_class.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c IRanges_constructor.c -o IRanges_constructor.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c NCList.c -o NCList.o
NCList.c:202:22: warning: 'next_top_down' defined but not used [-Wunused-function]
static const NCList *next_top_down(const NCList *nclist)
^
NCList.c:1173:13: warning: 'NCList_get_y_overlaps_rec' defined but not used [-Wunused-function]
static void NCList_get_y_overlaps_rec(const NCList *x_nclist,
^
NCList.c: In function 'NCList_find_overlaps':
NCList.c:1465:7: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
SEXP ans;
^
NCList.c: In function 'NCList_find_overlaps_in_groups':
NCList.c:1546:7: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
SEXP ans;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c R_init_IRanges.c -o R_init_IRanges.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c Ranges_class.c -o Ranges_class.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c RleViews_utils.c -o RleViews_utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c coverage_methods.c -o coverage_methods.o
coverage_methods.c: In function 'compute_coverage_from_IRanges_holder':
coverage_methods.c:503:28: warning: 'x_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (*out_ranges_are_tiles && x_end != cvg_len)
^
coverage_methods.c:419:21: note: 'x_end' was declared here
i, j, x_start, x_end, shift_elt, tmp;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c extractListFragments.c -o extractListFragments.o
extractListFragments.c: In function 'find_partition_overlaps':
extractListFragments.c:85:4: warning: 'split_partitions_buf' may be used uninitialized in this function [-Wmaybe-uninitialized]
IntAE_insert_at(split_partitions_buf,
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c inter_range_methods.c -o inter_range_methods.o
inter_range_methods.c: In function 'IntegerRanges_reduce':
inter_range_methods.c:154:11: warning: 'gapwidth' may be used uninitialized in this function [-Wmaybe-uninitialized]
delta += gapwidth;
^
inter_range_methods.c:102:31: note: 'gapwidth' was declared here
append_or_drop, max_end, gapwidth, delta, width_inc;
^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o IRanges.dll tmp.def CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_utils.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/IRanges.buildbin-libdir/00LOCK-IRanges/00new/IRanges/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'drop' from package 'base' in package 'IRanges'
Creating a generic function for 'runmed' from package 'stats' in package 'IRanges'
Creating a generic function for 'smoothEnds' from package 'stats' in package 'IRanges'
Creating a generic function for 'chartr' from package 'base' in package 'IRanges'
Creating a generic function for 'tolower' from package 'base' in package 'IRanges'
Creating a generic function for 'toupper' from package 'base' in package 'IRanges'
Creating a generic function for 'sub' from package 'base' in package 'IRanges'
Creating a generic function for 'gsub' from package 'base' in package 'IRanges'
Creating a new generic function for 'windows' in package 'IRanges'
** help
*** installing help indices
converting help for package 'IRanges'
finding HTML links ... done
AtomicList-class html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/AtomicList-class.Rd:307: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
AtomicList-utils html
CompressedHitsList-class html
CompressedList-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:38: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:39: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:44: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:49: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:50: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:60: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:66: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:81: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-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-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:87: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:89: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:95: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:100: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:105: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:110: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:118: file link 'classNameForDisplay' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:124: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/CompressedList-class.Rd:127: file link 'SimpleList' in package 'S4Vectors' does not exist and so has been treated as a topic
DataFrame-utils html
DataFrameList-class html
Grouping-class html
Hits-class-leftovers html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/Hits-class-leftovers.Rd:31: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/Hits-class-leftovers.Rd:68: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
IPos-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/IPos-class.Rd:96: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/IPos-class.Rd:106: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/IPos-class.Rd:120: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
IPosRanges-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/IPosRanges-class.Rd:200: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/IPosRanges-class.Rd:225: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/IPosRanges-class.Rd:225: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/IPosRanges-class.Rd:226: file link 'GPos' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/IPosRanges-class.Rd:226: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/IPosRanges-class.Rd:227: file link 'XStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
IPosRanges-comparison html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/IPosRanges-comparison.Rd:164: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
IRanges-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/IRanges-class.Rd:97: file link 'c' in package 'S4Vectors' does not exist and so has been treated as a topic
IRanges-constructor html
IRanges-internals html
IRanges-utils html
IRangesList-class html
IntegerRanges-class html
IntegerRangesList-class html
List-class-leftovers html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/List-class-leftovers.Rd:11: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/List-class-leftovers.Rd:35: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
MaskCollection-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/MaskCollection-class.Rd:206: file link 'alphabetFrequency' in package 'Biostrings' does not exist and so has been treated as a topic
NCList-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/NCList-class.Rd:81: file link 'GNCList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/NCList-class.Rd:101: file link 'GNCList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/NCList-class.Rd:102: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/NCList-class.Rd:110: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/NCList-class.Rd:126: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/NCList-class.Rd:128: file link 'GNCList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/NCList-class.Rd:131: file link 'GNCList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/NCList-class.Rd:155: file link 'GNCList' in package 'GenomicRanges' does not exist and so has been treated as a topic
RangedData-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/RangedData-class.Rd:78: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/RangedData-class.Rd:78: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/RangedData-class.Rd:80: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/RangedData-class.Rd:80: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/RangedData-class.Rd:84: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/RangedData-class.Rd:85: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
RangedSelection-class html
Rle-class-leftovers html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/Rle-class-leftovers.Rd:22: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/Rle-class-leftovers.Rd:71: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
RleViews-class html
RleViewsList-class html
Vector-class-leftovers html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/Vector-class-leftovers.Rd:29: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/Vector-class-leftovers.Rd:109: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Views-class html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/Views-class.Rd:48: file link 'XIntegerViews' in package 'XVector' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/Views-class.Rd:49: file link 'XStringViews' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/Views-class.Rd:158: file link 'XVector' in package 'XVector' does not exist and so has been treated as a topic
ViewsList-class html
coverage-methods html
extractList html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractList.Rd:24: file link 'split' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractList.Rd:95: file link 'relistToClass' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractList.Rd:149: file link 'relistToClass' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractList.Rd:160: file link 'unsplit' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractList.Rd:163: file link 'split' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractList.Rd:166: file link 'Vector' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractList.Rd:166: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractList.Rd:167: file link 'Rle' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractList.Rd:167: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractList.Rd:169: file link 'relistToClass' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractList.Rd:170: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
extractListFragments html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractListFragments.Rd:78: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractListFragments.Rd:79: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractListFragments.Rd:80: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractListFragments.Rd:87: file link 'relistToClass' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractListFragments.Rd:104: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractListFragments.Rd:104: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/extractListFragments.Rd:107: file link 'List' in package 'S4Vectors' does not exist and so has been treated as a topic
findOverlaps-methods html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:62: file link 'findOverlaps,GenomicRanges,GenomicRanges-method' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:64: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:64: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:175: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:183: file link 'HitsList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:195: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:195: file link 'HitsList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:253: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:253: file link 'HitsList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:261: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:262: file link 'HitsList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:293: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:293: file link 'HitsList' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:297: file link 'findOverlaps,GenomicRanges,GenomicRanges-method' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:299: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/findOverlaps-methods.Rd:299: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/inter-range-methods.Rd:266: file link 'endoapply' in package 'S4Vectors' 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/intra-range-methods.Rd:94: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/intra-range-methods.Rd:102: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/intra-range-methods.Rd:123: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/intra-range-methods.Rd:136: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/intra-range-methods.Rd:146: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/intra-range-methods.Rd:160: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/intra-range-methods.Rd:188: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/intra-range-methods.Rd:251: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/intra-range-methods.Rd:252: file link 'promoters,GenomicRanges-method' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/intra-range-methods.Rd:297: missing link 'RangesList'
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/intra-range-methods.Rd:307: file link 'endoapply' in package 'S4Vectors' does not exist and so has been treated as a topic
multisplit html
nearest-methods html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/nearest-methods.Rd:148: file link 'breakTies' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/nearest-methods.Rd:174: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/nearest-methods.Rd:175: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/nearest-methods.Rd:188: file link 'precede,GenomicRanges,GenomicRanges-method' in package 'GenomicRanges' does not exist and so has been treated as a topic
range-squeezers html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:15: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:16: file link 'grglist' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:18: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:19: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:20: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:21: file link 'grglist' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:32: 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/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:33: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:34: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:35: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:36: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:37: file link 'Pairs' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:63: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:64: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:77: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:93: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:96: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:97: file link 'GAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/range-squeezers.Rd:98: file link 'GAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
read.Mask html
reverse-methods html
seqapply html
setops-methods html
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/setops-methods.Rd:91: file link 'Pairs' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/setops-methods.Rd:116: file link 'Pairs' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpg1eFWI/R.INSTALL12f4edf25a6/IRanges/man/setops-methods.Rd:166: file link 'mendoapply' in package 'S4Vectors' does not exist and so has been treated as a topic
slice-methods html
view-summarization-methods 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 'IRanges' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c CompressedList_class.c -o CompressedList_class.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c Grouping_class.c -o Grouping_class.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c IPosRanges_comparison.c -o IPosRanges_comparison.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c IRanges_class.c -o IRanges_class.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c IRanges_constructor.c -o IRanges_constructor.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c NCList.c -o NCList.o
NCList.c:202:22: warning: 'next_top_down' defined but not used [-Wunused-function]
static const NCList *next_top_down(const NCList *nclist)
^
NCList.c:1173:13: warning: 'NCList_get_y_overlaps_rec' defined but not used [-Wunused-function]
static void NCList_get_y_overlaps_rec(const NCList *x_nclist,
^
NCList.c: In function 'NCList_find_overlaps_in_groups':
NCList.c:1546:7: warning: 'ans' may be used uninitialized in this function [-Wmaybe-uninitialized]
SEXP ans;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c R_init_IRanges.c -o R_init_IRanges.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c Ranges_class.c -o Ranges_class.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c RleViews_utils.c -o RleViews_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c coverage_methods.c -o coverage_methods.o
coverage_methods.c: In function 'compute_coverage_from_IRanges_holder':
coverage_methods.c:503:28: warning: 'x_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (*out_ranges_are_tiles && x_end != cvg_len)
^
coverage_methods.c:419:21: note: 'x_end' was declared here
i, j, x_start, x_end, shift_elt, tmp;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c extractListFragments.c -o extractListFragments.o
extractListFragments.c: In function 'find_partition_overlaps':
extractListFragments.c:85:4: warning: 'split_partitions_buf' may be used uninitialized in this function [-Wmaybe-uninitialized]
IntAE_insert_at(split_partitions_buf,
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/S4Vectors/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c inter_range_methods.c -o inter_range_methods.o
inter_range_methods.c: In function 'reduce_ranges':
inter_range_methods.c:165:5: warning: 'revmap_elt' may be used uninitialized in this function [-Wmaybe-uninitialized]
IntAE_insert_at(revmap_elt,
^
inter_range_methods.c:154:11: warning: 'delta' may be used uninitialized in this function [-Wmaybe-uninitialized]
delta += gapwidth;
^
inter_range_methods.c:154:11: warning: 'gapwidth' may be used uninitialized in this function [-Wmaybe-uninitialized]
inter_range_methods.c:156:14: warning: 'max_end' may be used uninitialized in this function [-Wmaybe-uninitialized]
width_inc = end_j - max_end;
^
inter_range_methods.c:131:6: warning: 'append_or_drop' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (append_or_drop) {
^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o IRanges.dll tmp.def CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_utils.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/IRanges.buildbin-libdir/IRanges/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IRanges' as IRanges_2.17.4.zip
* DONE (IRanges)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'IRanges' successfully unpacked and MD5 sums checked
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IRanges.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("IRanges") || stop("unable to load IRanges package")
Loading required package: IRanges
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
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
[1] TRUE
> IRanges:::.test()
RUNIT TEST PROTOCOL -- Tue Apr 09 03:46:20 2019
***********************************************
Number of test functions: 89
Number of errors: 0
Number of failures: 0
1 Test Suite :
IRanges RUnit Tests - 89 test functions, 0 errors, 0 failures
Number of test functions: 89
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
79.76 0.26 84.09
|
IRanges.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("IRanges") || stop("unable to load IRanges package")
Loading required package: IRanges
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
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
[1] TRUE
> IRanges:::.test()
RUNIT TEST PROTOCOL -- Tue Apr 09 03:47:52 2019
***********************************************
Number of test functions: 89
Number of errors: 0
Number of failures: 0
1 Test Suite :
IRanges RUnit Tests - 89 test functions, 0 errors, 0 failures
Number of test functions: 89
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
92.06 0.10 92.15
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IRanges.Rcheck/examples_i386/IRanges-Ex.timings
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IRanges.Rcheck/examples_x64/IRanges-Ex.timings
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