Yue Li
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/RIPSeeker |
| Branch: RELEASE_3_9 |
| Last Commit: 50db7d9 |
| Last Changed Date: 2019-05-02 11:53:39 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
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: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RIPSeeker.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RIPSeeker_1.24.0.tar.gz |
| StartedAt: 2019-10-16 06:39:09 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:46:02 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 412.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: RIPSeeker.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RIPSeeker.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RIPSeeker_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/RIPSeeker.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RIPSeeker/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RIPSeeker' version '1.24.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'S4Vectors', 'IRanges', 'GenomicRanges', 'SummarizedExperiment',
'Rsamtools', 'GenomicAlignments', 'rtracklayer'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'RIPSeeker' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/RIPSeeker/man/addPseudoAlignment.Rd:52: 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/RtmpiAZ5m9/R.INSTALL16f829416cd5/RIPSeeker/man/annotateRIP.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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/RIPSeeker/man/combineAlignGals.Rd:54: 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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/RIPSeeker/man/combineRIP.Rd:95: file link 'countOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/RIPSeeker/man/computeRPKM.Rd:113: 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/RtmpiAZ5m9/R.INSTALL16f829416cd5/RIPSeeker/man/exportGRanges.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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/RIPSeeker/man/galp2gal.Rd:50: 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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/RIPSeeker/man/getAlignGal.Rd:96: 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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/RIPSeeker/man/logScoreWithControl.Rd:44: 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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/RIPSeeker/man/logScoreWithoutControl.Rd:36: 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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/RIPSeeker/man/mainSeek.Rd:100: 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/RtmpiAZ5m9/R.INSTALL16f829416cd5/RIPSeeker/man/plotStrandedCoverage.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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/RIPSeeker/man/ripSeek.Rd:113: 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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/RIPSeeker/man/rulebaseRIPSeek.Rd:106: 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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/RIPSeeker/man/seekRIP.Rd:61: 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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/RIPSeeker/man/viewRIP.Rd:80: file link 'browserView' in package 'rtracklayer' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/RIPSeeker.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
'library' or 'require' call to 'Rsamtools' which was already attached by Depends.
Please remove these calls from your code.
'library' or 'require' calls in package code:
'ChIPpeakAnno' 'GenomicFeatures' 'biomaRt' 'parallel'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
nbh.GRanges nbh.integer
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annotateRIP: no visible global function definition for 'getAnnotation'
annotateRIP: no visible global function definition for 'getBM'
annotateRIP: no visible global function definition for 'write.table'
binCount: no visible global function definition for 'seqlengths'
combineRIP: no visible global function definition for 'seqlengths<-'
combineRIP: no visible global function definition for 'seqlengths'
computeRPKM: no visible global function definition for 'exonsBy'
computeRPKM: no visible global function definition for 'cdsBy'
computeRPKM: no visible global function definition for
'intronsByTranscript'
computeRPKM: no visible global function definition for
'fiveUTRsByTranscript'
computeRPKM: no visible global function definition for
'threeUTRsByTranscript'
computeRPKM: no visible global function definition for 'seqlevels<-'
computeRPKM: no visible global function definition for 'seqlevels'
computeRPKM: no visible global function definition for 'read.delim'
computeRPKM: no visible global function definition for 'getBM'
exportGRanges: no visible global function definition for 'write.table'
galp2gal: no visible global function definition for 'seqlengths'
getAlignGal: no visible global function definition for 'seqlengths<-'
getAlignGal: no visible global function definition for 'seqlengths'
mainSeek: no visible global function definition for 'mclapply'
mainSeekSingleChrom: no visible global function definition for
'seqlengths'
plotCoverage: no visible global function definition for 'seqlengths'
ripSeek: no visible global function definition for 'as.roman'
ripSeek: no visible global function definition for 'write.table'
rulebaseRIPSeek: no visible global function definition for 'getBM'
rulebaseRIPSeek: no visible global function definition for
'write.table'
selectBinSize: no visible global function definition for 'seqlengths'
viewRIP: no visible global function definition for
'GRangesForUCSCGenome'
Undefined global functions or variables:
GRangesForUCSCGenome as.roman cdsBy exonsBy fiveUTRsByTranscript
getAnnotation getBM intronsByTranscript mclapply read.delim
seqlengths seqlengths<- seqlevels seqlevels<- threeUTRsByTranscript
write.table
Consider adding
importFrom("utils", "as.roman", "read.delim", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
mainSeek 13.80 0.14 14.00
disambiguateMultihits 13.20 0.01 13.22
combineRIP 1.44 0.18 13.62
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
mainSeek 20.99 0.00 20.99
disambiguateMultihits 16.12 0.03 16.16
combineRIP 1.42 0.05 13.55
* 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: 1 WARNING, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/RIPSeeker.Rcheck/00check.log'
for details.
RIPSeeker.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/RIPSeeker_1.24.0.tar.gz && 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 && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL RIPSeeker_1.24.0.zip && rm RIPSeeker_1.24.0.tar.gz RIPSeeker_1.24.0.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 1578k 100 1578k 0 0 21.6M 0 --:--:-- --:--:-- --:--:-- 24.0M
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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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/RtmpiAZ5m9/R.INSTALL16f829416cd5/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)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'RIPSeeker' successfully unpacked and MD5 sums checked
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RIPSeeker.Rcheck/examples_i386/RIPSeeker-Ex.timings
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RIPSeeker.Rcheck/examples_x64/RIPSeeker-Ex.timings
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