Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:27:09 -0400 (Wed, 16 Oct 2019).
Package 1381/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
RIPSeeker 1.24.0 Yue Li
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | [ OK ] | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: RIPSeeker |
Version: 1.24.0 |
Command: rm -rf RIPSeeker.buildbin-libdir && mkdir RIPSeeker.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RIPSeeker.buildbin-libdir RIPSeeker_1.24.0.tar.gz |
StartedAt: 2019-10-16 10:04:54 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 10:06:01 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 67.1 seconds |
RetCode: 0 |
Status: OK |
PackageFile: RIPSeeker_1.24.0.zip |
PackageFileSize: 2.005 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf RIPSeeker.buildbin-libdir && mkdir RIPSeeker.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RIPSeeker.buildbin-libdir RIPSeeker_1.24.0.tar.gz ### ############################################################################## ############################################################################## install for i386 * installing *source* package 'RIPSeeker' ... ** using staged installation ** 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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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-3.9-bioc/tmpdir/RtmpKY7E18/R.INSTALL8cc2c4b4fcd/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 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 'RIPSeeker' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'RIPSeeker' as RIPSeeker_1.24.0.zip * DONE (RIPSeeker)