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BioC 3.5: CHECK report for metaSeq on tokay2

This page was generated on 2017-08-16 13:22:49 -0400 (Wed, 16 Aug 2017).

Package 795/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metaSeq 1.16.0
Koki Tsuyuzaki
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/metaSeq
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  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: metaSeq
Version: 1.16.0
Command: rm -rf metaSeq.buildbin-libdir metaSeq.Rcheck && mkdir metaSeq.buildbin-libdir metaSeq.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=metaSeq.buildbin-libdir metaSeq_1.16.0.tar.gz >metaSeq.Rcheck\00install.out 2>&1 && cp metaSeq.Rcheck\00install.out metaSeq-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=metaSeq.buildbin-libdir --install="check:metaSeq-install.out" --force-multiarch --no-vignettes --timings metaSeq_1.16.0.tar.gz
StartedAt: 2017-08-16 01:06:35 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:08:38 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 123.5 seconds
RetCode: 0
Status:  OK  
CheckDir: metaSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf metaSeq.buildbin-libdir metaSeq.Rcheck && mkdir metaSeq.buildbin-libdir metaSeq.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=metaSeq.buildbin-libdir metaSeq_1.16.0.tar.gz >metaSeq.Rcheck\00install.out 2>&1 && cp metaSeq.Rcheck\00install.out metaSeq-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=metaSeq.buildbin-libdir --install="check:metaSeq-install.out" --force-multiarch --no-vignettes --timings metaSeq_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/metaSeq.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 'metaSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'metaSeq' version '1.16.0'
* 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 whether package 'metaSeq' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
* 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
** 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 ... 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 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/metaSeq.Rcheck/00check.log'
for details.


metaSeq.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'metaSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'metaSeq' as metaSeq_1.16.0.zip
* DONE (metaSeq)

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

nameusersystemelapsed
BreastCancer0.110.000.11
Fisher.test1.640.031.68
Result.Meta0.150.020.17
Stouffer.test1.220.071.30
StudyA0.190.000.19
meta.oneside.noiseq1.380.021.39
meta.readData1.430.001.44
other.oneside.pvalues0.030.000.03
pvals1.470.021.48

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

nameusersystemelapsed
BreastCancer0.130.000.12
Fisher.test2.650.062.72
Result.Meta0.160.000.16
Stouffer.test1.420.031.45
StudyA0.170.000.17
meta.oneside.noiseq1.600.021.61
meta.readData1.790.011.82
other.oneside.pvalues0.050.000.04
pvals1.750.051.80