BioC 3.3: CHECK report for TarSeqQC on oaxaca

Package: TarSeqQC

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TarSeqQC_1.2.0.tar.gz

StartedAt: 2016-10-13 06:47:31 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 06:50:23 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 171.9 seconds

RetCode: 0

Status:  OK

CheckDir: TarSeqQC.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 TarSeqQC_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/TarSeqQC.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TarSeqQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TarSeqQC’ version ‘1.2.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘TarSeqQC’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
buildFeaturePanel,TargetExperiment : <anonymous>: no visible binding
  for global variable ‘sd’
buildFeaturePanel,TargetExperiment : <anonymous>: no visible binding
  for global variable ‘median’
buildFeaturePanel,TargetExperiment : <anonymous>: no visible binding
  for global variable ‘IQR’
buildReport,TargetExperiment: no visible global function definition for
  ‘plot’
ggplotColours,TargetExperiment: no visible global function definition
  for ‘hcl’
initialize,TargetExperiment: no visible global function definition for
  ‘read.delim’
plot,TargetExperiment-ANY: no visible global function definition for
  ‘head’
plot,TargetExperiment-ANY: no visible global function definition for
  ‘tail’
plot,TargetExperiment-ANY: no visible global function definition for
  ‘aggregate’
plotAttrExpl,TargetExperiment: no visible global function definition
  for ‘sd’
plotAttrExpl,TargetExperiment: no visible global function definition
  for ‘median’
plotAttrExpl,TargetExperiment: no visible global function definition
  for ‘IQR’
plotMetaDataExpl,TargetExperiment: no visible global function
  definition for ‘sd’
plotMetaDataExpl,TargetExperiment: no visible global function
  definition for ‘median’
plotMetaDataExpl,TargetExperiment: no visible global function
  definition for ‘IQR’
setBedFile<-,TargetExperiment-character: no visible global function
  definition for ‘read.delim’
summarizePanel,TargetExperiment : <anonymous>: no visible global
  function definition for ‘median’
summarizePanel,TargetExperiment : <anonymous>: no visible global
  function definition for ‘IQR’
summarizePanel,TargetExperiment : <anonymous>: no visible global
  function definition for ‘sd’
Undefined global functions or variables:
  IQR aggregate hcl head median plot read.delim sd tail
Consider adding
  importFrom("grDevices", "hcl")
  importFrom("graphics", "plot")
  importFrom("stats", "IQR", "aggregate", "median", "sd")
  importFrom("utils", "head", "read.delim", "tail")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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-3.3-bioc/meat/TarSeqQC.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
TargetExperiment-biasExploration	0.048	0.012	0.060
TargetExperiment-buildFeaturePanel	0.001	0.000	0.001
TargetExperiment-buildReport	0.470	0.035	0.545
TargetExperiment-constructor	0.002	0.001	0.002
TargetExperiment-getters	0.124	0.011	0.135
TargetExperiment-initialize	0.002	0.000	0.002
TargetExperiment-plot	0.002	0.000	0.001
TargetExperiment-plotAttrExpl	0.001	0.000	0.001
TargetExperiment-plotAttrPerform	0.038	0.009	0.047
TargetExperiment-plotFeatPerform	0.001	0.000	0.002
TargetExperiment-plotFeature	0.002	0.000	0.002
TargetExperiment-plotGeneAttrPerFeat	0.001	0.000	0.001
TargetExperiment-plotMetaDataExpl	0.048	0.008	0.057
TargetExperiment-plotNtdPercentage	0.002	0.000	0.002
TargetExperiment-plotRegion	0.003	0.000	0.004
TargetExperiment-print	0.039	0.010	0.049
TargetExperiment-readFrequencies	0.244	0.073	1.719
TargetExperiment-setters	0.005	0.000	0.005
TargetExperiment-show	0.033	0.011	0.044
TargetExperiment-statistics	0.037	0.012	0.049
TargetExperiment-summarizePanel	0.060	0.065	1.556
pileupCounts	0.149	0.110	2.979
plotInOutFeatures	0.200	0.081	1.719