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BioC 2.14: CHECK report for metaSeq on morelia

This page was generated on 2014-10-08 09:07:11 -0700 (Wed, 08 Oct 2014).

Package 484/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metaSeq 1.4.0
Koki Tsuyuzaki
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/metaSeq
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: metaSeq
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch metaSeq_1.4.0.tar.gz
StartedAt: 2014-10-07 23:56:09 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 23:57:11 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 62.4 seconds
RetCode: 0
Status:  OK 
CheckDir: metaSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch metaSeq_1.4.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/metaSeq.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metaSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metaSeq’ 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 ‘metaSeq’ can be installed ... [4s/4s] OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘NOISeq:::busca’ ‘NOISeq:::n.menor’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘oneside.noiseq’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File ‘metaSeq/R/Accelerate.NOISeq.R’:
  assignInNamespace("busca", busca, ns = "NOISeq", envir = env)
  assignInNamespace("n.menor", nmenor, ns = "NOISeq", envir = env)
  assignInNamespace("busca", busca, ns = "NOISeq", envir = env)
  assignInNamespace("n.menor", nmenor, ns = "NOISeq", envir = env)
File ‘metaSeq/R/Reset.Accelerate.NOISeq.R’:
  assignInNamespace("busca", original.busca, ns = "NOISeq", envir = env)
  assignInNamespace("n.menor", original.n.menor, ns = "NOISeq", 
    envir = env)
File ‘metaSeq/R/oneside.noiseq.R’:
  assignInNamespace("probdeg", custom.probdeg, ns = "NOISeq", envir = env)
  assignInNamespace("MD", custom.MD, ns = "NOISeq", envir = env)
  assignInNamespace("probdeg", original.probdeg, ns = "NOISeq", 
    envir = env)
  assignInNamespace("MD", original.MD, ns = "NOISeq", envir = env)

Accelerate.NOISeq: no visible binding for global variable
  ‘text.n.menor_unix’
Accelerate.NOISeq: no visible binding for global variable
  ‘text.busca_unix’
Accelerate.NOISeq: no visible binding for global variable ‘busca’
Accelerate.NOISeq: no visible binding for global variable ‘nmenor’
Accelerate.NOISeq: no visible binding for global variable
  ‘text.n.menor_win’
Accelerate.NOISeq: no visible binding for global variable
  ‘text.busca_win’
original.probdeg: no visible binding for global variable ‘n.menor’
original.probdeg: no visible binding for global variable ‘busca’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
  ‘Fig1.jpeg’, ‘Fig2.png’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking files in ‘vignettes’ ... OK
* checking examples ... [15s/15s] 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

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/metaSeq.Rcheck/00check.log’
for details.

metaSeq.Rcheck/00install.out:

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

metaSeq.Rcheck/metaSeq-Ex.timings:

nameusersystemelapsed
BreastCancer0.1010.0080.108
Fisher.test2.9310.0462.980
Result.Meta0.2020.0080.210
Stouffer.test2.4950.0372.534
StudyA0.2060.0160.222
meta.oneside.noiseq2.4760.0322.510
meta.readData2.6040.0412.653
other.oneside.pvalues0.0190.0010.020
pvals1.6960.0511.753