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CHECK report for metaSeq on veracruz1

This page was generated on 2018-04-12 13:37:47 -0400 (Thu, 12 Apr 2018).

Package 827/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metaSeq 1.18.0
Koki Tsuyuzaki
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/metaSeq
Branch: RELEASE_3_6
Last Commit: 02d575f
Last Changed Date: 2017-10-30 12:40:09 -0400 (Mon, 30 Oct 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 [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: metaSeq
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metaSeq_1.18.0.tar.gz
StartedAt: 2018-04-12 06:10:08 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 06:11:18 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 70.1 seconds
RetCode: 0
Status:  OK 
CheckDir: metaSeq.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings metaSeq_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/metaSeq.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.18.0’
* 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 ... 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 ... 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
* 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’
* 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 global function definition for ‘data’
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 global function definition for
  ‘assignInNamespace’
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’
Reset.Accelerate.NOISeq: no visible global function definition for
  ‘assignInNamespace’
custom.MD: no visible global function definition for ‘combn’
custom.probdeg: no visible global function definition for ‘na.omit’
each.Fisher.ignore.test: no visible global function definition for
  ‘pchisq’
each.Fisher.test: no visible global function definition for ‘pchisq’
each.Stouffer.ignore.test: no visible global function definition for
  ‘qnorm’
each.Stouffer.ignore.test: no visible global function definition for
  ‘pnorm’
each.Stouffer.test: no visible global function definition for ‘qnorm’
each.Stouffer.test: no visible global function definition for ‘pnorm’
oneside.noiseq: no visible global function definition for
  ‘assignInNamespace’
original.MD: no visible global function definition for ‘combn’
original.probdeg: no visible global function definition for ‘na.omit’
original.probdeg: no visible binding for global variable ‘n.menor’
original.probdeg: no visible binding for global variable ‘busca’
Undefined global functions or variables:
  assignInNamespace busca combn data n.menor na.omit nmenor pchisq
  pnorm qnorm text.busca_unix text.busca_win text.n.menor_unix
  text.n.menor_win
Consider adding
  importFrom("stats", "na.omit", "pchisq", "pnorm", "qnorm")
  importFrom("utils", "assignInNamespace", "combn", "data")
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 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 ... 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/metaSeq.Rcheck/00check.log’
for details.



Installation output

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)

Tests output


Example timings

metaSeq.Rcheck/metaSeq-Ex.timings

nameusersystemelapsed
BreastCancer0.0860.0080.095
Fisher.test1.7190.0461.789
Result.Meta0.1560.0060.166
Stouffer.test1.4080.0241.440
StudyA0.1530.0100.165
meta.oneside.noiseq1.5960.0241.631
meta.readData1.8230.0231.883
other.oneside.pvalues0.0360.0000.038
pvals1.5130.0461.574