BioC 3.1: CHECK report for RIPSeeker on morelia
This page was generated on 2015-10-09 09:40:35 -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 05:42:38 -0700 (Fri, 09 Oct 2015) |
EndedAt: 2015-10-09 05:46:02 -0700 (Fri, 09 Oct 2015) |
EllapsedTime: 204.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RIPSeeker.Rcheck |
Warnings: 0 |
Command output
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RIPSeeker_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/RIPSeeker.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ... [14s/14s] 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 loading without being on the library search path ... 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 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:
‘SD.aux’, ‘nar.aux’
Please remove them from your package.
* checking examples ... [43s/59s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
mainSeek 8.010 0.317 8.335
disambiguateMultihits 7.141 0.593 7.737
combineRIP 2.277 0.127 18.314
* 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 | 0.002 |
|
addDummyProb | 0.762 | 0.017 | 0.782 |
|
addPseudoAlignment | 0.337 | 0.010 | 0.348 |
|
annotateRIP | 0.023 | 0.001 | 0.023 |
|
binCount | 0.531 | 0.058 | 0.588 |
|
combineAlignGals | 0.243 | 0.012 | 0.256 |
|
combineRIP | 2.277 | 0.127 | 18.314 |
|
computeLogOdd | 1.270 | 0.064 | 1.333 |
|
computeRPKM | 0.003 | 0.000 | 0.003 |
|
disambiguateMultihits | 7.141 | 0.593 | 7.737 |
|
empiricalFDR | 0.002 | 0.000 | 0.002 |
|
evalBinSize | 0.621 | 0.081 | 0.702 |
|
exportGRanges | 0.003 | 0.000 | 0.002 |
|
galp2gal | 0.437 | 0.012 | 0.449 |
|
getAlignGal | 0.160 | 0.006 | 0.166 |
|
logScoreWithControl | 0.006 | 0.000 | 0.007 |
|
logScoreWithoutControl | 0.004 | 0.001 | 0.004 |
|
mainSeek | 8.010 | 0.317 | 8.335 |
|
mainSeekSingleChrom | 1.356 | 0.058 | 1.415 |
|
nbh.GRanges | 0 | 0 | 0 |
|
nbh | 2.414 | 0.142 | 2.556 |
|
nbh.integer | 0.001 | 0.000 | 0.000 |
|
nbh_chk | 0.001 | 0.000 | 0.001 |
|
nbh_em | 0.198 | 0.001 | 0.199 |
|
nbh_gen | 0.003 | 0.000 | 0.003 |
|
nbh_init | 1.795 | 0.036 | 1.832 |
|
nbh_vit | 0.264 | 0.032 | 0.297 |
|
nbm_chk | 0.001 | 0.000 | 0.001 |
|
nbm_em | 0.349 | 0.004 | 0.353 |
|
plotCoverage | 1.062 | 0.043 | 1.105 |
|
plotStrandedCoverage | 1.497 | 0.150 | 1.671 |
|
randindx | 0.159 | 0.011 | 0.198 |
|
ripSeek | 0.012 | 0.001 | 0.013 |
|
rulebaseRIPSeek | 0.004 | 0.000 | 0.004 |
|
scoreMergedBins | 0.021 | 0.000 | 0.023 |
|
seekRIP | 0.010 | 0.001 | 0.010 |
|
selectBinSize | 3.097 | 0.240 | 3.348 |
|
statdis | 0.271 | 0.028 | 0.298 |
|
viewRIP | 0.007 | 0.000 | 0.007 |
|