Yue Li
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/RIPSeeker |
| Branch: RELEASE_3_7 |
| Last Commit: 52de3ea |
| Last Changed Date: 2018-04-30 10:35:27 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:36:41 -0400 (Wed, 17 Oct 2018).
| Package 1245/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| RIPSeeker 1.20.0 Yue Li
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | [ OK ] | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: RIPSeeker |
| Version: 1.20.0 |
| Command: rm -rf RIPSeeker.buildbin-libdir && mkdir RIPSeeker.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RIPSeeker.buildbin-libdir RIPSeeker_1.20.0.tar.gz |
| StartedAt: 2018-10-17 06:54:14 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 06:54:48 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 33.8 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: RIPSeeker_1.20.0.zip |
| PackageFileSize: 2.003 MiB |
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###
### Running command:
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### rm -rf RIPSeeker.buildbin-libdir && mkdir RIPSeeker.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RIPSeeker.buildbin-libdir RIPSeeker_1.20.0.tar.gz
###
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install for i386
* installing *source* package 'RIPSeeker' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'RIPSeeker'
finding HTML links ... done
RIPSeeker-package html
addDummyProb html
addPseudoAlignment html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/addPseudoAlignment.Rd:52: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/addPseudoAlignment.Rd:52: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
annotateRIP html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/annotateRIP.Rd:21: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
binCount html
combineAlignGals html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/combineAlignGals.Rd:54: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/combineAlignGals.Rd:54: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
combineRIP html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/combineRIP.Rd:58: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/combineRIP.Rd:70: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/combineRIP.Rd:95: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/combineRIP.Rd:95: file link 'reduce' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/combineRIP.Rd:95: file link 'countOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
computeLogOdd html
computeRPKM html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/computeRPKM.Rd:47: file link 'exonsBy' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/computeRPKM.Rd:47: file link 'cdsBy' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/computeRPKM.Rd:47: file link 'intronsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/computeRPKM.Rd:47: file link 'fiveUTRsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/computeRPKM.Rd:47: file link 'threeUTRsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/computeRPKM.Rd:67: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/computeRPKM.Rd:76: file link 'summarizeOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/computeRPKM.Rd:84: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/computeRPKM.Rd:113: file link 'exonsBy' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/computeRPKM.Rd:113: file link 'cdsBy' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/computeRPKM.Rd:113: file link 'intronsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/computeRPKM.Rd:113: file link 'fiveUTRsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/computeRPKM.Rd:113: file link 'threeUTRsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/computeRPKM.Rd:113: file link 'summarizeOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/computeRPKM.Rd:113: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/computeRPKM.Rd:113: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
disambiguateMultihits html
empiricalFDR html
evalBinSize html
exportGRanges html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/exportGRanges.Rd:19: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
galp2gal html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/galp2gal.Rd:50: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/galp2gal.Rd:50: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
getAlignGal html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/getAlignGal.Rd:42: file link 'scanBamFlag' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/getAlignGal.Rd:63: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/getAlignGal.Rd:63: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/getAlignGal.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-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/getAlignGal.Rd:96: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/getAlignGal.Rd:96: file link 'import' in package 'rtracklayer' does not exist and so has been treated as a topic
logScoreWithControl html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/logScoreWithControl.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-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/logScoreWithControl.Rd:23: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/logScoreWithControl.Rd:36: file link 'pnorm' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/logScoreWithControl.Rd:44: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
logScoreWithoutControl html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/logScoreWithoutControl.Rd:28: file link 'pnorm' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/logScoreWithoutControl.Rd:36: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
mainSeek html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/mainSeek.Rd:60: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/mainSeek.Rd:100: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
mainSeekSingleChrom html
nbh.GRanges html
nbh html
nbh.integer html
nbh_chk html
nbh_em html
nbh_gen html
nbh_init html
nbh_vit html
nbm_chk html
nbm_em html
plotCoverage html
plotStrandedCoverage html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/plotStrandedCoverage.Rd:19: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
randindx html
ripSeek html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/ripSeek.Rd:106: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/ripSeek.Rd:108: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/ripSeek.Rd:113: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
rulebaseRIPSeek html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/rulebaseRIPSeek.Rd:76: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/rulebaseRIPSeek.Rd:106: file link 'exonsBy' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/rulebaseRIPSeek.Rd:106: file link 'cdsBy' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/rulebaseRIPSeek.Rd:106: file link 'intronsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/rulebaseRIPSeek.Rd:106: file link 'fiveUTRsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/rulebaseRIPSeek.Rd:106: file link 'threeUTRsByTranscript' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/rulebaseRIPSeek.Rd:106: file link 'summarizeOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/rulebaseRIPSeek.Rd:106: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/rulebaseRIPSeek.Rd:106: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
scoreMergedBins html
seekRIP html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/seekRIP.Rd:21: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/seekRIP.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/seekRIP.Rd:50: file link 'pnorm' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/seekRIP.Rd:61: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
selectBinSize html
statdis html
viewRIP html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/viewRIP.Rd:21: file link 'GRangesList' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/viewRIP.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/viewRIP.Rd:29: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/viewRIP.Rd:33: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/viewRIP.Rd:54: file link 'browserSession' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/viewRIP.Rd:54: file link 'track' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/viewRIP.Rd:54: file link 'browserView' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/viewRIP.Rd:80: file link 'browserSession' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/viewRIP.Rd:80: file link 'track' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpQhSM0I/R.INSTALL161c4e9f5109/RIPSeeker/man/viewRIP.Rd:80: file link 'browserView' in package 'rtracklayer' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'RIPSeeker' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RIPSeeker' as RIPSeeker_1.20.0.zip
* DONE (RIPSeeker)
In R CMD INSTALL
In R CMD INSTALL