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BioC 3.4: CHECK report for RareVariantVis on moscato1

This page was generated on 2016-09-21 03:47:14 -0700 (Wed, 21 Sep 2016).

Package 971/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RareVariantVis 1.7.2
Tomasz Stokowy
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RareVariantVis
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: RareVariantVis
Version: 1.7.2
Command: rm -rf RareVariantVis.buildbin-libdir RareVariantVis.Rcheck && mkdir RareVariantVis.buildbin-libdir RareVariantVis.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RareVariantVis.buildbin-libdir RareVariantVis_1.7.2.tar.gz >RareVariantVis.Rcheck\00install.out 2>&1 && cp RareVariantVis.Rcheck\00install.out RareVariantVis-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=RareVariantVis.buildbin-libdir --install="check:RareVariantVis-install.out" --force-multiarch --no-vignettes --timings RareVariantVis_1.7.2.tar.gz
StartedAt: 2016-09-20 14:48:27 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 14:55:08 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 400.7 seconds
RetCode: 0
Status:  OK  
CheckDir: RareVariantVis.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RareVariantVis.buildbin-libdir RareVariantVis.Rcheck && mkdir RareVariantVis.buildbin-libdir RareVariantVis.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RareVariantVis.buildbin-libdir RareVariantVis_1.7.2.tar.gz >RareVariantVis.Rcheck\00install.out 2>&1 && cp RareVariantVis.Rcheck\00install.out RareVariantVis-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=RareVariantVis.buildbin-libdir --install="check:RareVariantVis-install.out" --force-multiarch --no-vignettes --timings RareVariantVis_1.7.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/RareVariantVis.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RareVariantVis/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RareVariantVis' 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 whether package 'RareVariantVis' 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
** checking loading without being on the library search path ... 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 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
chromosomeVis: no visible global function definition for 'read.table'
chromosomeVis: no visible global function definition for 'rowRanges'
chromosomeVis: no visible global function definition for 'png'
chromosomeVis: no visible global function definition for 'points'
chromosomeVis: no visible global function definition for 'lines'
chromosomeVis: no visible global function definition for 'abline'
chromosomeVis: no visible global function definition for 'dev.off'
chromosomeVis: no visible global function definition for 'write.table'
multipleVis: no visible binding for global variable 'read.table'
multipleVis: no visible global function definition for 'write.table'
rareVariantVis: no visible global function definition for 'read.table'
trioVis: no visible global function definition for 'read.table'
trioVis: no visible global function definition for 'write.table'
Undefined global functions or variables:
  abline dev.off lines png points read.table rowRanges write.table
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "lines", "points")
  importFrom("utils", "read.table", "write.table")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
chromosomeVis 36.41   3.92   43.76
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
chromosomeVis 41.82   3.14    45.5
* 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-3.4-bioc/meat/RareVariantVis.Rcheck/00check.log'
for details.


RareVariantVis.Rcheck/00install.out:


install for i386

* installing *source* package 'RareVariantVis' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'

install for x64

* installing *source* package 'RareVariantVis' ...
** testing if installed package can be loaded
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
* MD5 sums
packaged installation of 'RareVariantVis' as RareVariantVis_1.7.2.zip
* DONE (RareVariantVis)

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

nameusersystemelapsed
chromosomeVis36.41 3.9243.76
movingAverage000
multipleVis0.060.000.06
rareVariantVis000
trioVis0.050.022.03

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

nameusersystemelapsed
chromosomeVis41.82 3.1445.50
movingAverage000
multipleVis0.080.000.08
rareVariantVis0.010.000.01
trioVis0.050.000.05