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BioC 3.6: CHECK report for Rcade on tokay1

This page was generated on 2017-08-16 13:30:52 -0400 (Wed, 16 Aug 2017).

Package 1087/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rcade 1.19.0
Jonathan Cairns
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rcade
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rcade
Version: 1.19.0
Command: rm -rf Rcade.buildbin-libdir Rcade.Rcheck && mkdir Rcade.buildbin-libdir Rcade.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rcade.buildbin-libdir Rcade_1.19.0.tar.gz >Rcade.Rcheck\00install.out 2>&1 && cp Rcade.Rcheck\00install.out Rcade-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Rcade.buildbin-libdir --install="check:Rcade-install.out" --force-multiarch --no-vignettes --timings Rcade_1.19.0.tar.gz
StartedAt: 2017-08-16 01:52:05 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:57:24 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 318.5 seconds
RetCode: 0
Status:  OK  
CheckDir: Rcade.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Rcade.buildbin-libdir Rcade.Rcheck && mkdir Rcade.buildbin-libdir Rcade.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rcade.buildbin-libdir Rcade_1.19.0.tar.gz >Rcade.Rcheck\00install.out 2>&1 && cp Rcade.Rcheck\00install.out Rcade-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Rcade.buildbin-libdir --install="check:Rcade-install.out" --force-multiarch --no-vignettes --timings Rcade_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Rcade.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rcade/DESCRIPTION' ... OK
* this is package 'Rcade' version '1.19.0'
* 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 whether package 'Rcade' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   5.2Mb
* 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
constructRcadeTable: no visible binding for global variable 'p.DE'
constructRcadeTable: no visible binding for global variable 'p.ChIP'
plotBBB,Rcade: no visible global function definition for 'decorate3d'
Undefined global functions or variables:
  decorate3d p.ChIP p.DE
* 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
diffCountsBaySeq 6.53   0.02    6.55
RcadeAnalysis    6.36   0.11    6.52
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
diffCountsBaySeq 9.36   0.00    9.36
RcadeAnalysis    8.30   0.01    8.31
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/Rcade.Rcheck/00check.log'
for details.


Rcade.Rcheck/00install.out:


install for i386

* installing *source* package 'Rcade' ...
** R
** data
** 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 'Rcade' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rcade' as Rcade_1.19.0.zip
* DONE (Rcade)

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

nameusersystemelapsed
Rcade-class1.030.091.12
RcadeAnalysis6.360.116.52
RcadeSTAT10.010.000.02
constructRcadeTable0.130.020.14
countReads2.560.042.61
defineBins0.020.000.01
diffCountsBaySeq6.530.026.55
exportRcade-methods000

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

nameusersystemelapsed
Rcade-class1.390.041.42
RcadeAnalysis8.300.018.31
RcadeSTAT1000
constructRcadeTable0.200.000.21
countReads3.220.033.25
defineBins0.010.000.02
diffCountsBaySeq9.360.009.36
exportRcade-methods0.000.020.01