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BioC 3.5: CHECK report for ArrayTV on tokay2

This page was generated on 2017-08-16 13:22:39 -0400 (Wed, 16 Aug 2017).

Package 66/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ArrayTV 1.14.0
Eitan Halper-Stromberg
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ArrayTV
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ArrayTV
Version: 1.14.0
Command: rm -rf ArrayTV.buildbin-libdir ArrayTV.Rcheck && mkdir ArrayTV.buildbin-libdir ArrayTV.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ArrayTV.buildbin-libdir ArrayTV_1.14.0.tar.gz >ArrayTV.Rcheck\00install.out 2>&1 && cp ArrayTV.Rcheck\00install.out ArrayTV-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ArrayTV.buildbin-libdir --install="check:ArrayTV-install.out" --force-multiarch --no-vignettes --timings ArrayTV_1.14.0.tar.gz
StartedAt: 2017-08-15 22:02:51 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:07:39 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 288.1 seconds
RetCode: 0
Status:  OK  
CheckDir: ArrayTV.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ArrayTV.buildbin-libdir ArrayTV.Rcheck && mkdir ArrayTV.buildbin-libdir ArrayTV.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ArrayTV.buildbin-libdir ArrayTV_1.14.0.tar.gz >ArrayTV.Rcheck\00install.out 2>&1 && cp ArrayTV.Rcheck\00install.out ArrayTV-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ArrayTV.buildbin-libdir --install="check:ArrayTV-install.out" --force-multiarch --no-vignettes --timings ArrayTV_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/ArrayTV.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 'ArrayTV/DESCRIPTION' ... OK
* this is package 'ArrayTV' version '1.14.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'doMC'
* 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 'ArrayTV' 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
* 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
.rescaleGC: no visible global function definition for 'mad'
CorrectM: no visible global function definition for 'mad'
CorrectM: no visible binding for global variable 'mad'
CorrectM: no visible global function definition for 'GRanges'
CorrectM: no visible global function definition for 'IRanges'
CorrectM: no visible global function definition for 'acf'
CorrectM: no visible binding for global variable 'median'
calctvScore: no visible global function definition for 'quantile'
gcFracOneRange: no visible global function definition for
  'letterFrequencyInSlidingView'
gcModel: no visible global function definition for 'rowData'
gcModel: no visible global function definition for
  'letterFrequencyInSlidingView'
gcModelSeq: no visible global function definition for 'genome'
gcModelSeq: no visible global function definition for 'rowData'
gcModelSeq: no visible global function definition for
  'letterFrequencyInSlidingView'
priorFracs: no visible global function definition for 'quantile'
priorFracsRestOfGenome: no visible global function definition for
  'letterFrequencyInSlidingView'
priorFracsRestOfGenome: no visible global function definition for
  'quantile'
Undefined global functions or variables:
  GRanges IRanges acf genome letterFrequencyInSlidingView mad median
  quantile rowData
Consider adding
  importFrom("stats", "acf", "mad", "median", "quantile")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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-3.5-bioc/meat/ArrayTV.Rcheck/00check.log'
for details.


ArrayTV.Rcheck/00install.out:


install for i386

* installing *source* package 'ArrayTV' ...
** R
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery

install for x64

* installing *source* package 'ArrayTV' ...
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* MD5 sums
packaged installation of 'ArrayTV' as ArrayTV_1.14.0.zip
* DONE (ArrayTV)

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

nameusersystemelapsed
gcCorrect-methods000
gcCorrectMain000
methods-computeGC000

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

nameusersystemelapsed
gcCorrect-methods000
gcCorrectMain000
methods-computeGC000