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BioC 3.4: CHECK report for ssviz on morelia

This page was generated on 2016-09-21 03:53:23 -0700 (Wed, 21 Sep 2016).

Package 1165/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ssviz 1.7.2
Diana Low
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ssviz
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ssviz
Version: 1.7.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ssviz_1.7.2.tar.gz
StartedAt: 2016-09-20 13:33:44 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 13:35:23 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 99.6 seconds
RetCode: 0
Status:  OK 
CheckDir: ssviz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ssviz_1.7.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/ssviz.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 ‘ssviz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ssviz’ version ‘1.7.2’
* 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 ‘ssviz’ can be installed ... 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 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
ntfreq,DataFrame-numeric : fun: no visible global function definition
  for ‘aggregate’
plotDistro,list: no visible global function definition for ‘aggregate’
plotRegion,list-character: no visible global function definition for
  ‘txtProgressBar’
plotRegion,list-character: no visible global function definition for
  ‘setTxtProgressBar’
plotRegion,list-character: no visible global function definition for
  ‘hist’
plotRegion,list-character: no visible global function definition for
  ‘density’
Undefined global functions or variables:
  aggregate density hist setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "aggregate", "density")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
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
Examples with CPU or elapsed time > 5s
          user system elapsed
pingpong 8.279  0.029   8.309
plotPP   8.260  0.015   8.277
* 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-3.4-bioc/meat/ssviz.Rcheck/00check.log’
for details.


ssviz.Rcheck/00install.out:

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

ssviz.Rcheck/ssviz-Ex.timings:

nameusersystemelapsed
getCountMatrix0.1740.0110.185
logicalORmissing-class0.0000.0000.001
ntfreq0.4800.0140.494
pingpong8.2790.0298.309
plotDistro0.2710.0090.281
plotFreq0.6450.0110.657
plotPP8.2600.0158.277
plotRegion0.6520.0130.665
readBam0.2170.0110.228