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BioC 2.14: CHECK report for Basic4Cseq on petty

This page was generated on 2014-10-08 09:01:42 -0700 (Wed, 08 Oct 2014).

Package 66/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Basic4Cseq 1.0.2
Carolin Walter
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/Basic4Cseq
Last Changed Rev: 92018 / Revision: 95116
Last Changed Date: 2014-06-30 04:40:57 -0700 (Mon, 30 Jun 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: Basic4Cseq
Version: 1.0.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Basic4Cseq_1.0.2.tar.gz
StartedAt: 2014-10-07 20:50:23 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 20:57:19 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 415.3 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 --no-multiarch Basic4Cseq_1.0.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/Basic4Cseq.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.0.2’
* 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 ... [36s/37s] 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 ... [23s/23s] OK
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-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-class0.0040.0010.005
Data4Cseq0.3080.0150.323
checkRestrictionEnzymeSequence0.0010.0000.002
chooseNearCisFragments0.0610.0140.076
createVirtualFragmentLibrary0.0020.0010.003
drawDigestionFragmentHistogram0.0110.0010.012
drawHeatmap0.0010.0000.001
exportVisualizationFragmentData0.0010.0000.002
getReadDistribution0.6820.0170.700
giveEnzymeSequence0.0070.0010.008
importVisualizationFragmentData0.0290.0070.035
liverData0.0240.0120.036
liverDataRaw0.0260.0120.038
normalizeFragmentData0.0330.0120.044
plotTransInteractions0.0030.0000.002
prepare4CseqData0.0020.0000.002
printBEDFragmentLibrary0.0010.0000.002
printWigFile0.0020.0000.002
readPointsOfInterestFile0.0100.0020.011
readsToFragments2.3530.6663.048
simulateDigestion0.0070.0000.007
visualizeViewpoint0.0800.0140.096