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CHECK report for REDseq on malbec2

This page was generated on 2019-04-09 11:30:42 -0400 (Tue, 09 Apr 2019).

Package 1322/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
REDseq 1.29.0
Lihua Julie Zhu
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/REDseq
Branch: master
Last Commit: b5e415a
Last Changed Date: 2018-10-30 11:54:29 -0400 (Tue, 30 Oct 2018)
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  OK  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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: REDseq
Version: 1.29.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:REDseq.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings REDseq_1.29.0.tar.gz
StartedAt: 2019-04-09 03:07:39 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:12:28 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 288.4 seconds
RetCode: 0
Status:  OK 
CheckDir: REDseq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:REDseq.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings REDseq_1.29.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/REDseq.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.29.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
buildREmap 9.12  0.128   9.727
* 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-3.9-bioc/meat/REDseq.Rcheck/00check.log’
for details.



Installation output

REDseq.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL REDseq
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘REDseq’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare 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 from temporary location
No methods found in package 'IRanges' for requests: '%in%', 'rep.int' when loading 'REDseq'
** testing if installed package can be loaded from final location
No methods found in package 'IRanges' for requests: '%in%', 'rep.int' when loading 'REDseq'
** testing if installed package keeps a record of temporary installation path
* DONE (REDseq)

Tests output


Example timings

REDseq.Rcheck/REDseq-Ex.timings

nameusersystemelapsed
REDseq-package0.0070.0000.007
assignSeq2REsite0.9790.0681.048
binom.test.REDseq0.0140.0000.014
buildREmap9.1200.1289.727
compareREDseq0.0220.0000.022
distanceHistSeq2RE0.0350.0000.035
example.REDseq0.0000.0020.003
example.assignedREDseq0.0000.0030.002
example.map0.0020.0010.003
plotCutDistribution0.0360.0040.040
searchPattern3.0460.0443.092
summarizeByRE0.0060.0000.006
summarizeBySeq0.0030.0040.008
writeHits0.0080.0000.007