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BioC 3.6: CHECK report for Basic4Cseq on veracruz1

This page was generated on 2017-08-16 13:45:01 -0400 (Wed, 16 Aug 2017).

Package 87/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Basic4Cseq 1.13.1
Carolin Walter
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Basic4Cseq
Last Changed Rev: 131713 / Revision: 131943
Last Changed Date: 2017-08-02 07:09:27 -0400 (Wed, 02 Aug 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: Basic4Cseq
Version: 1.13.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Basic4Cseq_1.13.1.tar.gz
StartedAt: 2017-08-16 00:10:26 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:14:09 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 222.7 seconds
RetCode: 0
Status:  OK 
CheckDir: Basic4Cseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Basic4Cseq_1.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/Basic4Cseq.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Basic4Cseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Basic4Cseq’ version ‘1.13.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... NOTE
Found the following apparent object files/libraries:
  inst/extdata/veryShortReference.fasta.sa
Object files/libraries should not be included in a source package.
* 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 ‘Basic4Cseq’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... 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
readsToFragments 3.435  1.803   5.353
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/Basic4Cseq.Rcheck/00check.log’
for details.


Basic4Cseq.Rcheck/00install.out:

* installing *source* package ‘Basic4Cseq’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Basic4Cseq)

Basic4Cseq.Rcheck/Basic4Cseq-Ex.timings:

nameusersystemelapsed
Data4Cseq-class0.0020.0000.001
Data4Cseq0.2660.0090.276
checkRestrictionEnzymeSequence0.0010.0000.001
chooseNearCisFragments0.0120.0020.014
createVirtualFragmentLibrary0.0010.0010.000
drawDigestionFragmentHistogram0.0070.0000.008
drawHeatmap0.0010.0000.001
exportVisualizationFragmentData0.0000.0000.001
getReadDistribution0.0990.0020.101
giveEnzymeSequence0.0030.0000.003
importVisualizationFragmentData0.0140.0030.022
liverData0.0040.0020.007
liverDataRaw0.0040.0020.005
normalizeFragmentData0.4000.0030.420
plotTransInteractions0.0010.0000.001
prepare4CseqData0.0010.0000.001
printBEDFragmentLibrary0.0010.0010.001
printWigFile0.0010.0000.001
readPointsOfInterestFile0.0030.0000.004
readsToFragments3.4351.8035.353
simulateDigestion0.0020.0000.003
visualizeViewpoint0.1970.0030.205