Back to Multiple platform build/check report for BioC 3.8
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

CHECK report for RIPSeeker on malbec1

This page was generated on 2019-04-16 11:49:48 -0400 (Tue, 16 Apr 2019).

Package 1314/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RIPSeeker 1.22.0
Yue Li
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/RIPSeeker
Branch: RELEASE_3_8
Last Commit: 3b3bdfa
Last Changed Date: 2018-10-30 11:41:49 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RIPSeeker
Version: 1.22.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:RIPSeeker.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings RIPSeeker_1.22.0.tar.gz
StartedAt: 2019-04-16 02:38:50 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:42:39 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 228.3 seconds
RetCode: 0
Status:  OK 
CheckDir: RIPSeeker.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:RIPSeeker.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings RIPSeeker_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/RIPSeeker.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.22.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mainSeek              16.156  0.004  16.181
disambiguateMultihits 14.844  0.000  14.858
combineRIP             1.456  0.028  16.330
* 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-3.8-bioc/meat/RIPSeeker.Rcheck/00check.log’
for details.



Installation output

RIPSeeker.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL RIPSeeker
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘RIPSeeker’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RIPSeeker)

Tests output


Example timings

RIPSeeker.Rcheck/RIPSeeker-Ex.timings

nameusersystemelapsed
RIPSeeker-package0.0040.0000.000
addDummyProb0.6520.0000.675
addPseudoAlignment0.9440.0000.946
annotateRIP0.0120.0000.010
binCount0.4520.0160.467
combineAlignGals0.2200.0000.268
combineRIP 1.456 0.02816.330
computeLogOdd1.2840.0121.296
computeRPKM0.0000.0000.001
disambiguateMultihits14.844 0.00014.858
empiricalFDR0.0000.0000.001
evalBinSize0.4320.0080.438
exportGRanges0.0000.0000.001
galp2gal0.2720.0000.272
getAlignGal0.1400.0120.155
logScoreWithControl0.0040.0000.006
logScoreWithoutControl0.0040.0000.003
mainSeek16.156 0.00416.181
mainSeekSingleChrom1.6400.0041.661
nbh.GRanges000
nbh2.0920.0122.109
nbh.integer000
nbh_chk000
nbh_em0.3320.0000.331
nbh_gen0.0040.0000.003
nbh_init1.2920.0001.290
nbh_vit0.1920.0040.194
nbm_chk000
nbm_em0.4480.0000.447
plotCoverage0.7760.0360.813
plotStrandedCoverage1.1200.0201.142
randindx0.1440.0080.152
ripSeek0.0040.0000.004
rulebaseRIPSeek0.0040.0000.001
scoreMergedBins0.0040.0000.006
seekRIP0.0040.0000.003
selectBinSize2.4240.0482.474
statdis0.2680.0040.272
viewRIP0.0040.0000.003