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CHECK report for RIPSeeker on malbec2

This page was generated on 2019-10-16 12:01:56 -0400 (Wed, 16 Oct 2019).

Package 1381/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RIPSeeker 1.24.0
Yue Li
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/RIPSeeker
Branch: RELEASE_3_9
Last Commit: 50db7d9
Last Changed Date: 2019-05-02 11:53:39 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RIPSeeker
Version: 1.24.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:RIPSeeker.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings RIPSeeker_1.24.0.tar.gz
StartedAt: 2019-10-16 04:34:40 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:38:14 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 214.7 seconds
RetCode: 0
Status:  OK 
CheckDir: RIPSeeker.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:RIPSeeker.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings RIPSeeker_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/RIPSeeker.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.24.0’
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  nbh.GRanges nbh.integer
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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
disambiguateMultihits 14.127  0.016  14.143
mainSeek              13.392  0.000  13.392
combineRIP             1.120  0.056  16.929
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/RIPSeeker.Rcheck/00check.log’
for details.



Installation output

RIPSeeker.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL RIPSeeker
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘RIPSeeker’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RIPSeeker)

Tests output


Example timings

RIPSeeker.Rcheck/RIPSeeker-Ex.timings

nameusersystemelapsed
RIPSeeker-package0.0000.0000.001
addDummyProb0.5820.0121.634
addPseudoAlignment0.2740.0040.278
annotateRIP0.0060.0000.006
binCount0.7500.0040.754
combineAlignGals0.2490.0000.403
combineRIP 1.120 0.05616.929
computeLogOdd1.6810.0121.694
computeRPKM0.0020.0000.001
disambiguateMultihits14.127 0.01614.143
empiricalFDR0.0000.0000.001
evalBinSize0.2910.0080.300
exportGRanges0.0020.0000.001
galp2gal0.1670.0080.192
getAlignGal0.1360.0000.137
logScoreWithControl0.0030.0000.003
logScoreWithoutControl0.0020.0000.001
mainSeek13.392 0.00013.392
mainSeekSingleChrom1.1610.0041.166
nbh.GRanges0.0010.0000.000
nbh1.0570.0001.057
nbh.integer0.0010.0000.000
nbh_chk000
nbh_em0.1400.0000.141
nbh_gen0.0020.0000.001
nbh_init0.9050.0000.905
nbh_vit0.1120.0040.116
nbm_chk000
nbm_em0.1910.0000.192
plotCoverage0.5780.0160.594
plotStrandedCoverage1.1360.0121.148
randindx0.1420.0080.149
ripSeek0.0040.0000.003
rulebaseRIPSeek0.0010.0000.001
scoreMergedBins0.0060.0000.006
seekRIP0.0030.0000.003
selectBinSize1.8030.0081.812
statdis0.1220.0040.138
viewRIP0.0030.0000.002