BioC 3.2: CHECK report for Basic4Cseq on perceval

Package: Basic4Cseq

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Basic4Cseq_1.6.0.tar.gz

StartedAt: 2015-11-10 02:22:14 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 02:26:01 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 226.8 seconds

RetCode: 0

Status:  OK

CheckDir: Basic4Cseq.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Basic4Cseq_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/Basic4Cseq.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘1.6.0’
* 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 ... [20s/20s] 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 ... [16s/17s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
readsToFragments  3.4   2.38   5.781
* 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-3.2-bioc/meat/Basic4Cseq.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
Data4Cseq-class	0.003	0.001	0.003
Data4Cseq	0.098	0.004	0.102
checkRestrictionEnzymeSequence	0.001	0.001	0.001
chooseNearCisFragments	0.015	0.001	0.016
createVirtualFragmentLibrary	0.001	0.000	0.001
drawDigestionFragmentHistogram	0.008	0.000	0.008
drawHeatmap	0.001	0.001	0.001
exportVisualizationFragmentData	0.001	0.000	0.001
getReadDistribution	0.105	0.007	0.112
giveEnzymeSequence	0.002	0.001	0.003
importVisualizationFragmentData	0.017	0.005	0.021
liverData	0.004	0.001	0.005
liverDataRaw	0.003	0.000	0.004
normalizeFragmentData	0.009	0.001	0.010
plotTransInteractions	0.002	0.000	0.001
prepare4CseqData	0.001	0.000	0.001
printBEDFragmentLibrary	0.001	0.000	0.001
printWigFile	0.001	0.000	0.001
readPointsOfInterestFile	0.005	0.001	0.004
readsToFragments	3.400	2.380	5.781
simulateDigestion	0.003	0.001	0.004
visualizeViewpoint	0.031	0.002	0.048