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BioC 3.2: CHECK report for Pviz on perceval

This page was generated on 2015-10-27 17:36:27 -0400 (Tue, 27 Oct 2015).

Package 816/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pviz 1.4.0
Renan Sauteraud
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Pviz
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Pviz
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Pviz_1.4.0.tar.gz
StartedAt: 2015-10-27 11:14:28 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 11:19:18 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 289.6 seconds
RetCode: 0
Status:  OK 
CheckDir: Pviz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Pviz_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/Pviz.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Pviz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pviz’ version ‘1.4.0’
* 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 ‘Pviz’ can be installed ... [28s/28s] 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 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
drawGD,ProbeTrack : .local: no visible global function definition for
  ‘pushViewport’
drawGD,ProbeTrack : .local: no visible global function definition for
  ‘viewport’
drawGD,ProbeTrack : .local: no visible global function definition for
  ‘popViewport’
drawGD,ProbeTrack : .local: no visible global function definition for
  ‘unit’
drawGD,ProbeTrack : .local: no visible global function definition for
  ‘gpar’
drawGD,ProbeTrack : .local: no visible global function definition for
  ‘convertWidth’
drawGD,ProbeTrack : .local: no visible global function definition for
  ‘stringWidth’
drawGD,ProbeTrack : .local: no visible global function definition for
  ‘stringHeight’
drawGD,ProbeTrack : .local: no visible global function definition for
  ‘grid.text’
drawGD,ProbeTrack : .local: no visible global function definition for
  ‘grid.rect’
drawGD,ProbeTrack : .local: no visible global function definition for
  ‘dataViewport’
drawGD,ProbeTrack : .local : <anonymous>: no visible global function
  definition for ‘grid.rect’
drawGD,ProbeTrack : .local : <anonymous>: no visible global function
  definition for ‘gpar’
drawGD,ProbeTrack : .local : <anonymous>: no visible global function
  definition for ‘grid.text’
drawGD,ProteinAxisTrack : .local: no visible global function definition
  for ‘pushViewport’
drawGD,ProteinAxisTrack : .local: no visible global function definition
  for ‘dataViewport’
drawGD,ProteinAxisTrack : .local: no visible global function definition
  for ‘convertHeight’
drawGD,ProteinAxisTrack : .local: no visible global function definition
  for ‘stringHeight’
drawGD,ProteinAxisTrack : .local: no visible global function definition
  for ‘popViewport’
drawGD,ProteinAxisTrack : .local: no visible global function definition
  for ‘.getGapPos’
drawGD,ProteinAxisTrack : .local: no visible global function definition
  for ‘gaps’
drawGD,ProteinAxisTrack : .local: no visible global function definition
  for ‘viewport’
drawGD,ProteinAxisTrack : .local: no visible global function definition
  for ‘grid.segments’
drawGD,ProteinAxisTrack : .local: no visible global function definition
  for ‘gpar’
drawGD,ProteinAxisTrack : .local: no visible global function definition
  for ‘coord2ext’
drawGD,ProteinAxisTrack : .local: no visible global function definition
  for ‘grid.text’
drawGD,ProteinAxisTrack : .local: no visible global function definition
  for ‘convertWidth’
drawGD,ProteinAxisTrack : .local: no visible global function definition
  for ‘stringWidth’
drawGD,ProteinSequenceTrack : .local: no visible global function
  definition for ‘pushViewport’
drawGD,ProteinSequenceTrack : .local: no visible global function
  definition for ‘dataViewport’
drawGD,ProteinSequenceTrack : .local: no visible global function
  definition for ‘gpar’
drawGD,ProteinSequenceTrack : .local: no visible global function
  definition for ‘popViewport’
drawGD,ProteinSequenceTrack : .local: no visible global function
  definition for ‘convertUnit’
drawGD,ProteinSequenceTrack : .local: no visible global function
  definition for ‘stringWidth’
drawGD,ProteinSequenceTrack : .local: no visible global function
  definition for ‘grid.lines’
drawGD,ProteinSequenceTrack : .local: no visible global function
  definition for ‘unit’
drawGD,ProteinSequenceTrack : .local: no visible global function
  definition for ‘grid.text’
drawGD,ProteinSequenceTrack : .local: no visible global function
  definition for ‘grid.rect’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [25s/25s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
ProbeTrack 5.554   0.02   5.575
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/Pviz.Rcheck/00check.log’
for details.


Pviz.Rcheck/00install.out:

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

Pviz.Rcheck/Pviz-Ex.timings:

nameusersystemelapsed
ATrack2.0770.0462.123
CladeTrack0.3390.0090.364
DTrack0.0670.0020.069
ProbeTrack5.5540.0205.575
ProteinAxisTrack0.3640.0020.386
ProteinSequenceTrack0.3400.0090.353
plot_clade1.1760.0101.187
plot_inter1.4270.0581.486