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

Package: seqplots

Version: 1.9.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings seqplots_1.9.0.tar.gz

StartedAt: 2015-10-27 07:59:21 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:03:33 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 251.1 seconds

RetCode: 0

Status:  OK

CheckDir: seqplots.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 seqplots_1.9.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/seqplots.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 ‘seqplots/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqplots’ version ‘1.9.0’
* 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 ‘seqplots’ can be installed ... [16s/16s] OK
* checking installed package size ... NOTE
  installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc        2.4Mb
    seqplots   4.9Mb
* 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 ... NOTE
Foreign function call to a different package:
  .Call("BWGFile_summary", ..., PACKAGE = "rtracklayer")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
ggHeatmapPlotWrapper: no visible binding for global variable ‘Var2’
ggHeatmapPlotWrapper: no visible binding for global variable ‘Var1’
ggHeatmapPlotWrapper: no visible binding for global variable ‘value’
Undefined global functions or variables:
  Var1 Var2 value
* 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 ... [12s/12s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [17s/17s]
 [17s/17s] 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/seqplots.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
MotifSetup-class	0.009	0.001	0.009
getPlotSetArray	2.946	0.079	3.028
plot	0.607	0.016	0.623
plotAverage	0.570	0.004	0.574
plotHeatmap	0.663	0.007	0.671
run	0.001	0.000	0.000