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CHECK report for REDseq on malbec1

This page was generated on 2018-04-12 13:09:37 -0400 (Thu, 12 Apr 2018).

Package 1152/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
REDseq 1.24.0
Lihua Julie Zhu
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/REDseq
Branch: RELEASE_3_6
Last Commit: 49dc861
Last Changed Date: 2017-10-30 12:39:34 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: REDseq
Version: 1.24.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings REDseq_1.24.0.tar.gz
StartedAt: 2018-04-12 02:16:58 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:20:58 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 240.2 seconds
RetCode: 0
Status:  OK 
CheckDir: REDseq.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings REDseq_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/REDseq.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘REDseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘REDseq’ version ‘1.24.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘BSgenome.Celegans.UCSC.ce2’ ‘multtest’ ‘Biostrings’
  ‘BSgenome’ ‘ChIPpeakAnno’
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 ‘REDseq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BiocGenerics’ ‘Biostrings’ ‘ChIPpeakAnno’ ‘multtest’
A package should be listed in only one of these fields.
* 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
Package in Depends field not imported from: 'BSgenome.Celegans.UCSC.ce2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
buildREmap 5.596  0.064   5.707
* 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-3.6-bioc/meat/REDseq.Rcheck/00check.log’
for details.



Installation output

REDseq.Rcheck/00install.out

* installing *source* package ‘REDseq’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in package 'IRanges' for requests: '%in%', 'rep.int' when loading 'REDseq'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package 'IRanges' for requests: '%in%', 'rep.int' when loading 'REDseq'
* DONE (REDseq)

Tests output


Example timings

REDseq.Rcheck/REDseq-Ex.timings

nameusersystemelapsed
REDseq-package0.0040.0000.005
assignSeq2REsite1.0920.0081.101
binom.test.REDseq0.0240.0000.025
buildREmap5.5960.0645.707
compareREDseq0.1440.0000.145
distanceHistSeq2RE0.0160.0080.024
example.REDseq0.0040.0000.002
example.assignedREDseq0.0040.0000.003
example.map0.0000.0000.002
plotCutDistribution0.0160.0080.024
searchPattern2.6280.0442.675
summarizeByRE0.0280.0000.029
summarizeBySeq0.0040.0040.007
writeHits0.0080.0000.007