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BioC 3.3: CHECK report for TarSeqQC on zin2

This page was generated on 2016-10-13 12:46:03 -0700 (Thu, 13 Oct 2016).

Package 1147/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TarSeqQC 1.2.0
Gabriela Merino
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/TarSeqQC
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TarSeqQC
Version: 1.2.0
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings TarSeqQC_1.2.0.tar.gz
StartedAt: 2016-10-13 07:19:54 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 07:22:16 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 141.6 seconds
RetCode: 0
Status:  OK 
CheckDir: TarSeqQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings TarSeqQC_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/TarSeqQC.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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
  ‘/home/biocbuild/bbs-3.3-bioc/meat/TarSeqQC.Rcheck/00check.log’
for details.


TarSeqQC.Rcheck/00install.out:

* 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)

TarSeqQC.Rcheck/TarSeqQC-Ex.timings:

nameusersystemelapsed
TargetExperiment-biasExploration0.0460.0040.049
TargetExperiment-buildFeaturePanel0.0010.0000.001
TargetExperiment-buildReport0.3880.0160.415
TargetExperiment-constructor0.0010.0000.002
TargetExperiment-getters0.1170.0160.132
TargetExperiment-initialize0.0010.0000.001
TargetExperiment-plot0.0010.0000.000
TargetExperiment-plotAttrExpl0.0010.0000.000
TargetExperiment-plotAttrPerform0.0320.0000.031
TargetExperiment-plotFeatPerform0.0010.0000.001
TargetExperiment-plotFeature0.0020.0000.001
TargetExperiment-plotGeneAttrPerFeat0.0010.0000.001
TargetExperiment-plotMetaDataExpl0.0390.0000.039
TargetExperiment-plotNtdPercentage0.0000.0040.001
TargetExperiment-plotRegion0.0000.0000.002
TargetExperiment-print0.0370.0000.037
TargetExperiment-readFrequencies0.2150.0371.632
TargetExperiment-setters0.0050.0000.005
TargetExperiment-show0.0320.0000.032
TargetExperiment-statistics0.0280.0080.035
TargetExperiment-summarizePanel0.0460.0191.410
pileupCounts0.1230.0482.860
plotInOutFeatures0.1710.0241.618