BioC 3.1: CHECK report for RIPSeeker on moscato2
This page was generated on 2015-10-09 09:30:01 -0700 (Fri, 09 Oct 2015).
RIPSeeker 1.8.0 Yue Li
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/RIPSeeker | Last Changed Rev: 102591 / Revision: 109384 | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK |  |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |  |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |  |
Summary
Package: RIPSeeker
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Version: 1.8.0
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Command: rm -rf RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && mkdir RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RIPSeeker.buildbin-libdir RIPSeeker_1.8.0.tar.gz >RIPSeeker.Rcheck\00install.out 2>&1 && cp RIPSeeker.Rcheck\00install.out RIPSeeker-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=RIPSeeker.buildbin-libdir --install="check:RIPSeeker-install.out" --force-multiarch --no-vignettes --timings RIPSeeker_1.8.0.tar.gz
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StartedAt: 2015-10-09 05:37:29 -0700 (Fri, 09 Oct 2015)
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EndedAt: 2015-10-09 05:42:54 -0700 (Fri, 09 Oct 2015)
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EllapsedTime: 324.8 seconds
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RetCode: 0
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Status: OK
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CheckDir: RIPSeeker.Rcheck
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Warnings: 0
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Command output
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### Running command:
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### rm -rf RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && mkdir RIPSeeker.buildbin-libdir RIPSeeker.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RIPSeeker.buildbin-libdir RIPSeeker_1.8.0.tar.gz >RIPSeeker.Rcheck\00install.out 2>&1 && cp RIPSeeker.Rcheck\00install.out RIPSeeker-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=RIPSeeker.buildbin-libdir --install="check:RIPSeeker-install.out" --force-multiarch --no-vignettes --timings RIPSeeker_1.8.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/RIPSeeker.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.8.0'
* 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 'RIPSeeker' can be installed ... OK
* 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addDummyProb: no visible global function definition for 'metadata<-'
addPseudoAlignment: no visible global function definition for 'Rle'
annotateRIP: no visible global function definition for 'getAnnotation'
annotateRIP: no visible global function definition for 'getBM'
binCount: no visible global function definition for 'runValue'
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 'SimpleList'
computeRPKM: no visible global function definition for 'getBM'
galp2gal: no visible global function definition for 'seqlengths'
getAlignGal: no visible global function definition for 'seqlengths<-'
getAlignGal: no visible global function definition for 'seqlengths'
getAlignGal: no visible global function definition for 'runValue'
getAlignGal: no visible global function definition for 'metadata<-'
getAlignGal: no visible global function definition for 'Rle'
mainSeek: no visible global function definition for 'mclapply'
mainSeekSingleChrom: no visible global function definition for
'runValue'
mainSeekSingleChrom: no visible global function definition for
'seqlengths'
nbh.GRanges: no visible global function definition for 'metadata<-'
plotCoverage: no visible global function definition for 'runValue'
plotCoverage: no visible global function definition for 'seqlengths'
rulebaseRIPSeek: no visible global function definition for 'getBM'
seekRIP: no visible global function definition for 'runValue'
selectBinSize: no visible global function definition for 'seqlengths'
viewRIP: no visible global function definition for 'runValue'
viewRIP: no visible global function definition for
'GRangesForUCSCGenome'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... NOTE
The following files look like leftovers/mistakes:
'SD.aux', 'nar.aux'
Please remove them from your package.
* checking examples ...
** running examples for arch 'i386' ... [60s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
mainSeek 7.36 0.00 7.36
disambiguateMultihits 7.25 0.00 7.30
combineRIP 2.58 0.03 17.33
** running examples for arch 'x64' ... [71s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
mainSeek 10.25 0.03 10.28
disambiguateMultihits 10.10 0.00 10.09
combineRIP 3.15 0.05 19.59
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
'E:/biocbld/bbs-3.1-bioc/meat/RIPSeeker.Rcheck/00check.log'
for details.
RIPSeeker.Rcheck/00install.out:
install for i386
* installing *source* package 'RIPSeeker' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
install for x64
* installing *source* package 'RIPSeeker' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'RIPSeeker' as RIPSeeker_1.8.0.zip
* DONE (RIPSeeker)
RIPSeeker.Rcheck/examples_i386/RIPSeeker-Ex.timings:
name | user | system | elapsed
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RIPSeeker-package | 0 | 0 | 0 |
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addDummyProb | 0.60 | 0.00 | 0.61 |
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addPseudoAlignment | 0.86 | 0.00 | 0.85 |
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annotateRIP | 0.02 | 0.00 | 0.02 |
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binCount | 0.92 | 0.00 | 0.92 |
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combineAlignGals | 0.65 | 0.00 | 0.66 |
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combineRIP | 2.58 | 0.03 | 17.33 |
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computeLogOdd | 1.35 | 0.00 | 1.34 |
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computeRPKM | 0 | 0 | 0 |
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disambiguateMultihits | 7.25 | 0.00 | 7.30 |
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empiricalFDR | 0 | 0 | 0 |
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evalBinSize | 0.59 | 0.00 | 0.59 |
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exportGRanges | 0 | 0 | 0 |
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galp2gal | 0.33 | 0.03 | 0.64 |
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getAlignGal | 0.17 | 0.00 | 0.17 |
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logScoreWithControl | 0 | 0 | 0 |
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logScoreWithoutControl | 0.02 | 0.00 | 0.02 |
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mainSeek | 7.36 | 0.00 | 7.36 |
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mainSeekSingleChrom | 1.39 | 0.00 | 1.39 |
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nbh.GRanges | 0 | 0 | 0 |
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nbh | 2.40 | 0.02 | 2.42 |
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nbh.integer | 0 | 0 | 0 |
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nbh_chk | 0.02 | 0.00 | 0.02 |
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nbh_em | 0.26 | 0.01 | 0.28 |
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nbh_gen | 0 | 0 | 0 |
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nbh_init | 2.43 | 0.00 | 2.44 |
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nbh_vit | 0.28 | 0.00 | 0.28 |
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nbm_chk | 0 | 0 | 0 |
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nbm_em | 0.39 | 0.00 | 0.39 |
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plotCoverage | 1.20 | 0.02 | 1.22 |
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plotStrandedCoverage | 2.29 | 0.04 | 2.34 |
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randindx | 0.22 | 0.02 | 0.23 |
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ripSeek | 0 | 0 | 0 |
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rulebaseRIPSeek | 0 | 0 | 0 |
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scoreMergedBins | 0.01 | 0.00 | 0.01 |
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seekRIP | 0 | 0 | 0 |
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selectBinSize | 3.03 | 0.11 | 3.14 |
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statdis | 0.28 | 0.00 | 0.28 |
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viewRIP | 0 | 0 | 0 |
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RIPSeeker.Rcheck/examples_x64/RIPSeeker-Ex.timings:
name | user | system | elapsed
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RIPSeeker-package | 0 | 0 | 0 |
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addDummyProb | 0.88 | 0.00 | 0.88 |
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addPseudoAlignment | 0.32 | 0.00 | 0.32 |
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annotateRIP | 0.02 | 0.00 | 0.02 |
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binCount | 0.93 | 0.00 | 0.93 |
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combineAlignGals | 0.32 | 0.00 | 0.32 |
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combineRIP | 3.15 | 0.05 | 19.59 |
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computeLogOdd | 2.73 | 0.00 | 2.73 |
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computeRPKM | 0.01 | 0.00 | 0.02 |
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disambiguateMultihits | 10.10 | 0.00 | 10.09 |
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empiricalFDR | 0 | 0 | 0 |
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evalBinSize | 0.45 | 0.00 | 0.45 |
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exportGRanges | 0 | 0 | 0 |
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galp2gal | 0.42 | 0.00 | 0.42 |
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getAlignGal | 0.17 | 0.00 | 0.17 |
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logScoreWithControl | 0 | 0 | 0 |
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logScoreWithoutControl | 0 | 0 | 0 |
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mainSeek | 10.25 | 0.03 | 10.28 |
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mainSeekSingleChrom | 1.73 | 0.01 | 1.75 |
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nbh.GRanges | 0 | 0 | 0 |
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nbh | 3.44 | 0.00 | 3.45 |
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nbh.integer | 0 | 0 | 0 |
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nbh_chk | 0 | 0 | 0 |
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nbh_em | 0.34 | 0.00 | 0.34 |
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nbh_gen | 0 | 0 | 0 |
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nbh_init | 2.29 | 0.00 | 2.30 |
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nbh_vit | 0.33 | 0.00 | 0.32 |
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nbm_chk | 0 | 0 | 0 |
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nbm_em | 0.40 | 0.00 | 0.41 |
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plotCoverage | 1.28 | 0.03 | 1.31 |
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plotStrandedCoverage | 2.7 | 0.0 | 2.7 |
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randindx | 0.22 | 0.02 | 0.24 |
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ripSeek | 0.01 | 0.00 | 0.02 |
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rulebaseRIPSeek | 0 | 0 | 0 |
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scoreMergedBins | 0.02 | 0.00 | 0.02 |
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seekRIP | 0 | 0 | 0 |
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selectBinSize | 4.21 | 0.25 | 4.46 |
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statdis | 0.64 | 0.00 | 0.64 |
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viewRIP | 0 | 0 | 0 |
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