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BioC 3.1: CHECK report for AgiMicroRna on moscato2

This page was generated on 2015-10-09 09:28:37 -0700 (Fri, 09 Oct 2015).

Package 31/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AgiMicroRna 2.18.0
Pedro Lopez-Romero
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/AgiMicroRna
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: AgiMicroRna
Version: 2.18.0
Command: rm -rf AgiMicroRna.buildbin-libdir AgiMicroRna.Rcheck && mkdir AgiMicroRna.buildbin-libdir AgiMicroRna.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AgiMicroRna.buildbin-libdir AgiMicroRna_2.18.0.tar.gz >AgiMicroRna.Rcheck\00install.out 2>&1 && cp AgiMicroRna.Rcheck\00install.out AgiMicroRna-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=AgiMicroRna.buildbin-libdir --install="check:AgiMicroRna-install.out" --force-multiarch --no-vignettes --timings AgiMicroRna_2.18.0.tar.gz
StartedAt: 2015-10-08 23:15:09 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:23:38 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 508.8 seconds
RetCode: 0
Status:  OK  
CheckDir: AgiMicroRna.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf AgiMicroRna.buildbin-libdir AgiMicroRna.Rcheck && mkdir AgiMicroRna.buildbin-libdir AgiMicroRna.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AgiMicroRna.buildbin-libdir AgiMicroRna_2.18.0.tar.gz >AgiMicroRna.Rcheck\00install.out 2>&1 && cp AgiMicroRna.Rcheck\00install.out AgiMicroRna-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=AgiMicroRna.buildbin-libdir --install="check:AgiMicroRna-install.out" --force-multiarch --no-vignettes --timings AgiMicroRna_2.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/AgiMicroRna.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 'AgiMicroRna/DESCRIPTION' ... OK
* this is package 'AgiMicroRna' version '2.18.0'
* 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 whether package 'AgiMicroRna' 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.
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 ... 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
'library' or 'require' calls to packages already attached by Depends:
  'affy' 'affycoretools' 'preprocessCore'
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'codelink' 'gdata' 'geneplotter' 'gplots' 'gtools' 'marray'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'affy' 'affycoretools' 'limma' 'methods' 'preprocessCore'
  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 ... NOTE
Foreign function call to a different package:
  .Call("rma_c_complete_copy", ..., PACKAGE = "affy")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
DEG.print.info: no visible global function definition for 'exprs'
HeatMapMicroRna: no visible global function definition for 'maPalette'
HeatMapMicroRna: no visible global function definition for 'heatmap.2'
PCAplotMicroRna: no visible global function definition for 'exprs'
PCAplotMicroRna: no visible global function definition for 'exprs<-'
PCAplotMicroRna: no visible global function definition for 'plotPCA'
basicLimma: no visible global function definition for 'exprs'
basicLimma: no visible global function definition for 'lmFit'
basicLimma: no visible global function definition for 'contrasts.fit'
basicLimma: no visible global function definition for 'eBayes'
esetMicroRna: no visible global function definition for 'exprs'
getDecideTests: no visible global function definition for 'decideTests'
read.agiMicroRna: no visible global function definition for
  'read.columns'
rmaMicroRna: no visible global function definition for
  'rma.background.correct'
rmaMicroRna: no visible global function definition for
  'normalizeBetweenArrays'
significantMicroRna: no visible global function definition for 'exprs'
tgsNormalization: no visible global function definition for
  'normalizeBetweenArrays'
writeEset: no visible global function definition for 'exprs'
writeEset: no visible global function definition for 'featureNames'
* 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' ... [48s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
mvaMicroRna 15.37   0.05   15.48
rmaMicroRna  7.71   0.00    7.71
** running examples for arch 'x64' ... [49s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
mvaMicroRna 16.69   0.04   16.74
rmaMicroRna  8.40   0.01    8.42
* 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/AgiMicroRna.Rcheck/00check.log'
for details.


AgiMicroRna.Rcheck/00install.out:


install for i386

* installing *source* package 'AgiMicroRna' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'AgiMicroRna' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'AgiMicroRna' as AgiMicroRna_2.18.0.zip
* DONE (AgiMicroRna)

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

nameusersystemelapsed
HeatMapMicroRna0.370.001.03
PCAplotMicroRna0.150.001.22
RleMicroRna1.410.001.40
basicLimma000
boxplotMicroRna0.670.000.67
cvArray000
filterMicroRna0.620.062.39
getDecideTests0.020.000.01
hierclusMicroRna0.010.000.02
mvaBASIC1.390.051.43
mvaMicroRna15.37 0.0515.48
plotDensityMicroRna0.30.00.3
pvalHistogram000
qcPlots000
readMicroRnaAFE000
rmaMicroRna7.710.007.71
significantMicroRna0.840.001.12
tgsMicroRna0.160.010.74
tgsNormalization000
uRNAList000
writeEset000

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

nameusersystemelapsed
HeatMapMicroRna0.460.001.02
PCAplotMicroRna0.190.000.28
RleMicroRna1.760.031.80
basicLimma000
boxplotMicroRna0.870.000.87
cvArray000
filterMicroRna0.530.081.14
getDecideTests000
hierclusMicroRna0.020.000.02
mvaBASIC1.470.031.73
mvaMicroRna16.69 0.0416.74
plotDensityMicroRna0.340.040.37
pvalHistogram000
qcPlots000
readMicroRnaAFE000
rmaMicroRna8.400.018.42
significantMicroRna0.610.030.64
tgsMicroRna0.190.000.18
tgsNormalization000
uRNAList000
writeEset000