BioC 3.3: CHECK report for motifStack on linux2.bioconductor.org

Package: motifStack

Version: 1.15.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings motifStack_1.15.0.tar.gz

StartedAt: 2015-10-27 06:03:33 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:07:07 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 214.0 seconds

RetCode: 0

Status:  OK

CheckDir: motifStack.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings motifStack_1.15.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/motifStack.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifStack/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifStack’ version ‘1.15.0’
* 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 ‘motifStack’ can be installed ... [13s/13s] 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘motifStack’ for: ‘plot’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17s/17s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [9s/9s]
 [9s/9s] 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
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/motifStack.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
DNAmotifAlignment	0.274	0.000	0.274
colorset	0.001	0.000	0.001
getRankedUniqueMotifs	0.003	0.000	0.002
highlightCol	0.002	0.000	0.002
mergeMotifs	0.566	0.000	0.576
motifCircos	0.006	0.000	0.006
motifCloud	0.004	0.000	0.004
motifPiles	0.008	0.000	0.007
motifSignature	0.004	0.000	0.004
motifStack	0.002	0.000	0.002
ouNode-class	0.003	0.000	0.003
pcm-class	0.720	0.162	0.907
pcm-methods	0.009	0.000	0.010
pfm-class	0.738	0.175	0.919
pfm-methods	0.010	0.000	0.011
pfm2pwm	0.950	0.032	0.997
plotMotifLogo	0.516	0.131	0.648
plotMotifLogoA	0.907	0.173	1.108
plotMotifLogoStack	0.728	0.225	0.982
plotMotifLogoStackWithTree	2.089	0.454	2.699
plotMotifOverMotif	0.861	0.200	1.082
plotMotifStackWithPhylog	0.004	0.000	0.005
plotMotifStackWithRadialPhylog	0.005	0.000	0.006
readPCM	0.018	0.000	0.018
reorderUPGMAtree	0.000	0.000	0.003