BioC 3.1: CHECK report for RIPSeeker on zin2
This page was generated on 2015-10-09 09:25:13 -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: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings RIPSeeker_1.8.0.tar.gz |
StartedAt: 2015-10-09 04:59:56 -0700 (Fri, 09 Oct 2015) |
EndedAt: 2015-10-09 05:02:42 -0700 (Fri, 09 Oct 2015) |
EllapsedTime: 166.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RIPSeeker.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings RIPSeeker_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/RIPSeeker.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ... [11s/11s] 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:
‘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 ... [39s/56s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
mainSeek 8.010 0.004 8.040
disambiguateMultihits 7.180 0.004 7.184
combineRIP 1.834 0.032 18.589
* 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
‘/home/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 | 0.001 | 0.000 | 0.001 |
|
addDummyProb | 0.666 | 0.004 | 0.669 |
|
addPseudoAlignment | 0.273 | 0.004 | 0.280 |
|
annotateRIP | 0.010 | 0.000 | 0.009 |
|
binCount | 0.573 | 0.000 | 0.576 |
|
combineAlignGals | 0.197 | 0.004 | 0.200 |
|
combineRIP | 1.834 | 0.032 | 18.589 |
|
computeLogOdd | 1.249 | 0.004 | 1.262 |
|
computeRPKM | 0.002 | 0.000 | 0.002 |
|
disambiguateMultihits | 7.180 | 0.004 | 7.184 |
|
empiricalFDR | 0.002 | 0.000 | 0.002 |
|
evalBinSize | 0.611 | 0.004 | 0.614 |
|
exportGRanges | 0.001 | 0.000 | 0.001 |
|
galp2gal | 0.319 | 0.000 | 0.319 |
|
getAlignGal | 0.122 | 0.004 | 0.126 |
|
logScoreWithControl | 0.004 | 0.000 | 0.004 |
|
logScoreWithoutControl | 0.000 | 0.000 | 0.003 |
|
mainSeek | 8.010 | 0.004 | 8.040 |
|
mainSeekSingleChrom | 1.258 | 0.000 | 1.262 |
|
nbh.GRanges | 0.000 | 0.000 | 0.001 |
|
nbh | 2.087 | 0.000 | 2.091 |
|
nbh.integer | 0.000 | 0.000 | 0.001 |
|
nbh_chk | 0.000 | 0.004 | 0.000 |
|
nbh_em | 0.256 | 0.000 | 0.258 |
|
nbh_gen | 0.004 | 0.000 | 0.004 |
|
nbh_init | 1.820 | 0.000 | 1.821 |
|
nbh_vit | 0.245 | 0.004 | 0.250 |
|
nbm_chk | 0.000 | 0.000 | 0.001 |
|
nbm_em | 0.353 | 0.000 | 0.353 |
|
plotCoverage | 1.215 | 0.008 | 1.223 |
|
plotStrandedCoverage | 1.858 | 0.020 | 1.880 |
|
randindx | 0.155 | 0.003 | 0.160 |
|
ripSeek | 0.006 | 0.001 | 0.005 |
|
rulebaseRIPSeek | 0.002 | 0.000 | 0.002 |
|
scoreMergedBins | 0.008 | 0.000 | 0.009 |
|
seekRIP | 0.004 | 0.000 | 0.004 |
|
selectBinSize | 3.093 | 0.007 | 3.125 |
|
statdis | 0.275 | 0.000 | 0.276 |
|
viewRIP | 0.001 | 0.000 | 0.004 |
|