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BioC 3.5: CHECK report for RIPSeeker on malbec2

This page was generated on 2017-10-18 14:14:55 -0400 (Wed, 18 Oct 2017).

Package 1117/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RIPSeeker 1.16.0
Yue Li
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/RIPSeeker
Branch: RELEASE_3_5
Last Commit: 21b725f
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RIPSeeker
Version: 1.16.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings RIPSeeker_1.16.0.tar.gz
StartedAt: 2017-10-18 02:05:19 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 02:08:55 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 215.9 seconds
RetCode: 0
Status:  OK 
CheckDir: RIPSeeker.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings RIPSeeker_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/RIPSeeker.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.16.0’
* 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 for sufficient/correct file permissions ... 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
* 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
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mainSeek              13.728   0.02  13.762
disambiguateMultihits 12.956   0.00  12.966
combineRIP             2.876   0.02  23.719
* 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-3.5-bioc/meat/RIPSeeker.Rcheck/00check.log’
for details.


RIPSeeker.Rcheck/00install.out:

* installing *source* package ‘RIPSeeker’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RIPSeeker)

RIPSeeker.Rcheck/RIPSeeker-Ex.timings:

nameusersystemelapsed
RIPSeeker-package0.0040.0000.001
addDummyProb1.5600.0041.565
addPseudoAlignment0.6720.0160.684
annotateRIP0.0080.0000.008
binCount0.7680.0000.769
combineAlignGals0.2680.0000.270
combineRIP 2.876 0.02023.719
computeLogOdd1.2000.0001.198
computeRPKM0.0000.0000.003
disambiguateMultihits12.956 0.00012.966
empiricalFDR0.0000.0000.001
evalBinSize0.2760.0280.303
exportGRanges0.0040.0000.002
galp2gal0.5200.0120.534
getAlignGal0.1800.0080.191
logScoreWithControl0.0080.0000.007
logScoreWithoutControl0.0040.0000.004
mainSeek13.728 0.02013.762
mainSeekSingleChrom1.0880.0001.090
nbh.GRanges000
nbh1.3360.0001.337
nbh.integer000
nbh_chk0.0040.0000.001
nbh_em0.2040.0000.204
nbh_gen0.0200.0000.021
nbh_init1.2680.0041.273
nbh_vit0.3040.0000.307
nbm_chk0.0000.0000.001
nbm_em0.4560.0000.458
plotCoverage0.9680.0080.975
plotStrandedCoverage2.2280.0202.250
randindx0.1480.0080.153
ripSeek0.0040.0000.004
rulebaseRIPSeek0.0040.0000.002
scoreMergedBins0.0080.0000.008
seekRIP0.0040.0000.005
selectBinSize2.6480.0082.661
statdis0.1520.0000.151
viewRIP0.0040.0000.003