BioC 3.1: CHECK report for RIPSeeker on petty
This page was generated on 2015-10-09 09:35:21 -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 |
Version: 1.8.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RIPSeeker_1.8.0.tar.gz |
StartedAt: 2015-10-09 01:38:01 -0700 (Fri, 09 Oct 2015) |
EndedAt: 2015-10-09 01:43:06 -0700 (Fri, 09 Oct 2015) |
EllapsedTime: 304.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RIPSeeker.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RIPSeeker_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/RIPSeeker.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘RIPSeeker’ can be installed ... [21s/21s] 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
* 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:
‘biomaRt’ ‘ChIPpeakAnno’ ‘GenomicFeatures’ ‘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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following files look like leftovers/mistakes:
‘nar.aux’, ‘SD.aux’
Please remove them from your package.
* checking examples ... [79s/94s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
mainSeek 13.467 0.052 13.518
disambiguateMultihits 12.767 0.036 12.819
nbh 5.491 0.022 5.519
selectBinSize 5.119 0.363 5.482
combineRIP 3.444 0.112 18.697
* 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
‘/Users/biocbuild/bbs-3.1-bioc/meat/RIPSeeker.Rcheck/00check.log’
for details.
RIPSeeker.Rcheck/00install.out:
* 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’
* DONE (RIPSeeker)
RIPSeeker.Rcheck/RIPSeeker-Ex.timings:
name | user | system | elapsed
|
RIPSeeker-package | 0.002 | 0.001 | 0.003 |
|
addDummyProb | 1.819 | 0.020 | 1.841 |
|
addPseudoAlignment | 1.214 | 0.016 | 1.232 |
|
annotateRIP | 0.039 | 0.001 | 0.040 |
|
binCount | 2.110 | 0.034 | 2.147 |
|
combineAlignGals | 1.130 | 0.024 | 1.155 |
|
combineRIP | 3.444 | 0.112 | 18.697 |
|
computeLogOdd | 3.215 | 0.038 | 3.259 |
|
computeRPKM | 0.004 | 0.001 | 0.005 |
|
disambiguateMultihits | 12.767 | 0.036 | 12.819 |
|
empiricalFDR | 0.003 | 0.000 | 0.003 |
|
evalBinSize | 1.400 | 0.032 | 1.431 |
|
exportGRanges | 0.003 | 0.000 | 0.003 |
|
galp2gal | 0.618 | 0.014 | 0.665 |
|
getAlignGal | 0.660 | 0.012 | 0.672 |
|
logScoreWithControl | 0.018 | 0.000 | 0.018 |
|
logScoreWithoutControl | 0.011 | 0.000 | 0.011 |
|
mainSeek | 13.467 | 0.052 | 13.518 |
|
mainSeekSingleChrom | 3.000 | 0.023 | 3.026 |
|
nbh.GRanges | 0.001 | 0.000 | 0.002 |
|
nbh | 5.491 | 0.022 | 5.519 |
|
nbh.integer | 0.002 | 0.000 | 0.001 |
|
nbh_chk | 0.002 | 0.001 | 0.002 |
|
nbh_em | 0.577 | 0.004 | 0.582 |
|
nbh_gen | 0.007 | 0.001 | 0.007 |
|
nbh_init | 3.715 | 0.008 | 3.728 |
|
nbh_vit | 0.539 | 0.004 | 0.544 |
|
nbm_chk | 0.002 | 0.000 | 0.002 |
|
nbm_em | 0.586 | 0.003 | 0.591 |
|
plotCoverage | 1.990 | 0.079 | 2.070 |
|
plotStrandedCoverage | 2.868 | 0.146 | 3.132 |
|
randindx | 0.311 | 0.025 | 0.361 |
|
ripSeek | 0.020 | 0.000 | 0.021 |
|
rulebaseRIPSeek | 0.005 | 0.000 | 0.005 |
|
scoreMergedBins | 0.032 | 0.001 | 0.034 |
|
seekRIP | 0.021 | 0.001 | 0.023 |
|
selectBinSize | 5.119 | 0.363 | 5.482 |
|
statdis | 0.564 | 0.005 | 0.570 |
|
viewRIP | 0.013 | 0.001 | 0.014 |
|