BioC 3.4: CHECK report for motifbreakR on malbec1

Package: motifbreakR

Version: 1.4.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings motifbreakR_1.4.0.tar.gz

StartedAt: 2017-04-14 23:58:21 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-15 00:03:52 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 331.0 seconds

RetCode: 0

Status:  OK

CheckDir: motifbreakR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings motifbreakR_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/motifbreakR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifbreakR/DESCRIPTION’ ... OK
* this is package ‘motifbreakR’ version ‘1.4.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘motifbreakR’ 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 ... NOTE
Packages in Depends field not imported from:
  'MotifDb' 'grid'
  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 ... NOTE
plotMotifLogoStack.2: no visible global function definition for 'par'
snps.from.file: no visible global function definition for 'info'
snps.from.file: no visible global function definition for 'rowRanges'
snps.from.rsid: no visible global function definition for 'snpsById'
Undefined global functions or variables:
  info par rowRanges snpsById
Consider adding
  importFrom("graphics", "par")
to your NAMESPACE file.
* 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
snps.from.rsid 39.092  0.868  40.096
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/motifbreakR.Rcheck/00check.log’
for details.

* installing *source* package ‘motifbreakR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
See system.file("LICENSE", package="MotifDb") for use restrictions.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
See system.file("LICENSE", package="MotifDb") for use restrictions.
* DONE (motifbreakR)

name	user	system	elapsed
calculatePvalue	0.740	0.000	0.743
encodemotif	0.024	0.004	0.028
example.results	0.080	0.008	0.088
factorbook	0.000	0.004	0.006
hocomoco	0.008	0.000	0.009
homer	0.008	0.000	0.007
motifbreakR	4.480	0.068	4.552
motifbreakR_motif	0.040	0.000	0.042
plotMB	0.052	0.004	0.059
snps.from.file	0.508	0.004	0.734
snps.from.rsid	39.092	0.868	40.096