BioC 3.1: CHECK report for geneplotter on petty

Package: geneplotter

Version: 1.46.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings geneplotter_1.46.0.tar.gz

StartedAt: 2015-10-08 23:12:37 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:15:30 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 172.7 seconds

RetCode: 0

Status:  OK

CheckDir: geneplotter.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 geneplotter_1.46.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/geneplotter.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geneplotter/DESCRIPTION’ ... OK
* this is package ‘geneplotter’ version ‘1.46.0’
* 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 ‘geneplotter’ can be installed ... [14s/14s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘annotate’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘Rgraphviz’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘lattice’
  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 ... 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 ... [32s/32s] 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/geneplotter.Rcheck/00check.log’
for details.

* installing *source* package ‘geneplotter’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (geneplotter)

name	user	system	elapsed
GetColor	0.003	0.000	0.004
Makesense	3.686	0.112	4.143
alongChrom	3.682	0.060	3.801
amplicon.plot	0.001	0.001	0.001
cColor	3.599	0.015	3.618
cPlot	3.446	0.013	3.467
cScale	3.240	0.007	3.248
eset133a	0.201	0.010	0.212
groupedHeatmap	0.986	0.020	1.007
histStack	0.025	0.002	0.037
imageMap	0.118	0.012	0.151
make.chromOrd	0.251	0.029	0.299
multiecdf	0.082	0.007	0.090
openHtmlPage	0.004	0.001	0.005
plotChr	2.882	0.072	2.959
plotExpressionGraph	2.071	0.044	2.165
plotMA	0.019	0.001	0.021
savepng	0.306	0.081	0.427