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BioC 3.1: CHECK report for ExiMiR on moscato2

This page was generated on 2015-10-09 09:29:05 -0700 (Fri, 09 Oct 2015).

Package 306/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ExiMiR 2.10.0
Sylvain Gubian
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/ExiMiR
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ExiMiR
Version: 2.10.0
Command: rm -rf ExiMiR.buildbin-libdir ExiMiR.Rcheck && mkdir ExiMiR.buildbin-libdir ExiMiR.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ExiMiR.buildbin-libdir ExiMiR_2.10.0.tar.gz >ExiMiR.Rcheck\00install.out 2>&1 && cp ExiMiR.Rcheck\00install.out ExiMiR-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=ExiMiR.buildbin-libdir --install="check:ExiMiR-install.out" --force-multiarch --no-vignettes --timings ExiMiR_2.10.0.tar.gz
StartedAt: 2015-10-09 01:32:47 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 01:34:55 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 128.7 seconds
RetCode: 0
Status:  OK  
CheckDir: ExiMiR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ExiMiR.buildbin-libdir ExiMiR.Rcheck && mkdir ExiMiR.buildbin-libdir ExiMiR.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ExiMiR.buildbin-libdir ExiMiR_2.10.0.tar.gz >ExiMiR.Rcheck\00install.out 2>&1 && cp ExiMiR.Rcheck\00install.out ExiMiR-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=ExiMiR.buildbin-libdir --install="check:ExiMiR-install.out" --force-multiarch --no-vignettes --timings ExiMiR_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/ExiMiR.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ExiMiR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ExiMiR' version '2.10.0'
* 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 'ExiMiR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biobase'
A package should be listed in only one of these fields.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
Namespaces in Imports field not imported from:
  'Biobase' 'affyio' 'preprocessCore'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'Biobase' 'affy' 'limma'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NormiR.bgcorrect.methods: no visible global function definition for
  'bgcorrect.methods'
NormiR.pmcorrect.methods: no visible global function definition for
  'mm'
NormiR.pmcorrect.methods: no visible global function definition for
  'pmcorrect.methods'
NormiR.summary.methods: no visible global function definition for
  'generateExprSet.methods'
ReadExi: no visible global function definition for 'readTargets'
ReadExi: no visible global function definition for 'read.maimages'
ReadExi: no visible global function definition for 'readGAL'
ReadExi: no visible global function definition for 'getLayout'
bg.correct.miR: no visible global function definition for 'exprs'
bg.correct.miR: no visible global function definition for 'se.exprs'
bg.correct.miR: no visible global function definition for
  'backgroundCorrect.matrix'
bg.correct.miR: no visible global function definition for 'exprs<-'
bg.correct.miR: no visible global function definition for 'se.exprs<-'
bg.correct.miR: no visible global function definition for
  'bgcorrect.methods'
bg.correct.miR: no visible global function definition for 'bg.correct'
create.gal.env: no visible global function definition for 'multiassign'
createAB: no visible global function definition for 'notes<-'
createAB: no visible global function definition for 'notes'
createAB: no visible global function definition for 'pData<-'
get.bg.ab: no visible global function definition for 'se.exprs'
get.bg.ab: no visible global function definition for 'exprs'
get.bg.ab: no visible global function definition for 'cdfName'
get.bg.ab: no visible global function definition for 'phenoData'
get.bg.ab: no visible global function definition for 'annotation'
get.bg.ab: no visible global function definition for 'protocolData'
get.bg.ab: no visible global function definition for 'description'
get.bg.ab: no visible global function definition for 'notes'
has.bg: no visible global function definition for 'notes'
is.dual: no visible global function definition for 'notes'
is.from.createAB: no visible global function definition for 'notes'
make.gal.env: no visible global function definition for 'readGAL'
make.gal.env: no visible global function definition for 'getLayout'
meannorm: no visible global function definition for 'exprs'
meannorm: no visible global function definition for 'sampleNames'
mediannorm: no visible global function definition for 'exprs'
mediannorm: no visible global function definition for 'sampleNames'
norm.miR: no visible global function definition for 'getCdfInfo'
norm.miR: no visible global function definition for 'exprs'
norm.miR: no visible global function definition for
  'normalizeQuantiles'
norm.miR: no visible global function definition for 'normalize'
norm.miR: no visible global function definition for 'exprs<-'
read.annotation.fromfile: no visible global function definition for
  'read.maimages'
spikeinnorm: no visible global function definition for 'getCdfInfo'
spikeinnorm: no visible global function definition for 'exprs'
spikeinnorm: no visible global function definition for 'sampleNames'
summarize.miR: no visible global function definition for 'mm'
summarize.miR: no visible global function definition for
  'computeExprSet'
* 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' ... [31s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
NormiR         13.00   0.15   13.19
summarize.miR  10.13   0.00   10.12
bg.correct.miR  4.98   0.03    5.01
** running examples for arch 'x64' ... [43s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
NormiR        19.33   0.20   19.55
summarize.miR 14.94   0.01   14.97
* 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: 4 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/ExiMiR.Rcheck/00check.log'
for details.


ExiMiR.Rcheck/00install.out:


install for i386

* installing *source* package 'ExiMiR' ...
** 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 'ExiMiR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ExiMiR' as ExiMiR_2.10.0.zip
* DONE (ExiMiR)

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

nameusersystemelapsed
NormiR13.00 0.1513.19
ReadExi000
bg.correct.miR4.980.035.01
make.gal.env000
norm.miR1.420.051.47
summarize.miR10.13 0.0010.12

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

nameusersystemelapsed
NormiR19.33 0.2019.55
ReadExi000
bg.correct.miR4.950.034.97
make.gal.env000
norm.miR1.700.131.83
summarize.miR14.94 0.0114.97