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BioC 3.2: CHECK report for Pviz on moscato1

This page was generated on 2016-04-23 10:20:28 -0700 (Sat, 23 Apr 2016).

Package 816/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pviz 1.4.0
Renan Sauteraud
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Pviz
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  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: rm -rf Pviz.buildbin-libdir Pviz.Rcheck && mkdir Pviz.buildbin-libdir Pviz.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Pviz.buildbin-libdir Pviz_1.4.0.tar.gz >Pviz.Rcheck\00install.out 2>&1 && cp Pviz.Rcheck\00install.out Pviz-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=Pviz.buildbin-libdir --install="check:Pviz-install.out" --force-multiarch --no-vignettes --timings Pviz_1.4.0.tar.gz
StartedAt: 2016-04-23 06:15:00 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 06:22:51 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 471.2 seconds
RetCode: 0
Status:  OK  
CheckDir: Pviz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Pviz.buildbin-libdir Pviz.Rcheck && mkdir Pviz.buildbin-libdir Pviz.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Pviz.buildbin-libdir Pviz_1.4.0.tar.gz >Pviz.Rcheck\00install.out 2>&1 && cp Pviz.Rcheck\00install.out Pviz-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=Pviz.buildbin-libdir --install="check:Pviz-install.out" --force-multiarch --no-vignettes --timings Pviz_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/Pviz.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'Pviz' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [26s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
ProbeTrack 5.96      0    5.96
** running examples for arch 'x64' ... [29s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
ProbeTrack 6.52   0.01    7.24
* 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
  'D:/biocbld/bbs-3.2-bioc/meat/Pviz.Rcheck/00check.log'
for details.


Pviz.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'Pviz' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Pviz' as Pviz_1.4.0.zip
* DONE (Pviz)

Pviz.Rcheck/examples_i386/Pviz-Ex.timings:

nameusersystemelapsed
ATrack1.820.011.84
CladeTrack0.280.000.50
DTrack0.110.000.11
ProbeTrack5.960.005.96
ProteinAxisTrack0.240.000.24
ProteinSequenceTrack0.250.000.25
plot_clade1.000.031.03
plot_inter0.830.000.86

Pviz.Rcheck/examples_x64/Pviz-Ex.timings:

nameusersystemelapsed
ATrack2.430.052.48
CladeTrack0.280.000.28
DTrack0.120.000.12
ProbeTrack6.520.017.24
ProteinAxisTrack0.290.000.28
ProteinSequenceTrack0.420.000.44
plot_clade1.130.021.14
plot_inter1.120.001.12