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BioC 3.4: CHECK report for frma on moscato1

This page was generated on 2016-09-21 03:42:55 -0700 (Wed, 21 Sep 2016).

Package 442/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
frma 1.25.0
Matthew N. McCall
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/frma
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: frma
Version: 1.25.0
Command: rm -rf frma.buildbin-libdir frma.Rcheck && mkdir frma.buildbin-libdir frma.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=frma.buildbin-libdir frma_1.25.0.tar.gz >frma.Rcheck\00install.out 2>&1 && cp frma.Rcheck\00install.out frma-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=frma.buildbin-libdir --install="check:frma-install.out" --force-multiarch --no-vignettes --timings frma_1.25.0.tar.gz
StartedAt: 2016-09-20 08:30:26 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 08:35:00 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 274.1 seconds
RetCode: 0
Status:  OK  
CheckDir: frma.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf frma.buildbin-libdir frma.Rcheck && mkdir frma.buildbin-libdir frma.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=frma.buildbin-libdir frma_1.25.0.tar.gz >frma.Rcheck\00install.out 2>&1 && cp frma.Rcheck\00install.out frma-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=frma.buildbin-libdir --install="check:frma-install.out" --force-multiarch --no-vignettes --timings frma_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/frma.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'frma/DESCRIPTION' ... OK
* this is package 'frma' version '1.25.0'
* 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 'frma' 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 ... 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
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GNUSE: no visible binding for global variable 'median'
GNUSE: no visible binding for global variable 'quantile'
GNUSE: no visible global function definition for 'boxplot'
barcode: no visible global function definition for 'pnorm'
batchFit: no visible global function definition for 'median'
coerce<-,frmaExpressionSet-ExpressionSet: no visible global function
  definition for 'slot<-'
coerce<-,frmaExpressionSet-ExpressionSet: no visible global function
  definition for 'slot'
randomeffects<-,frmaExpressionSet: no visible global function
  definition for 'validObject'
residuals<-,frmaExpressionSet: no visible global function definition
  for 'validObject'
se.exprs<-,ExpressionSet: no visible global function definition for
  'validObject'
se.exprs<-,frmaExpressionSet: no visible global function definition for
  'validObject'
weights<-,frmaExpressionSet: no visible global function definition for
  'validObject'
Undefined global functions or variables:
  boxplot median pnorm quantile slot slot<- validObject
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("methods", "slot", "slot<-", "validObject")
  importFrom("stats", "median", "pnorm", "quantile")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
GNUSE   13.85   0.35   16.27
barcode 10.79   0.03   10.92
frma    10.70   0.06   10.77
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
GNUSE   16.89   0.22   17.24
frma    12.98   0.08   13.05
barcode 12.25   0.20   12.45
* 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: 2 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/frma.Rcheck/00check.log'
for details.


frma.Rcheck/00install.out:


install for i386

* installing *source* package 'frma' ...
** R
** 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 'frma' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'frma' as frma_1.25.0.zip
* DONE (frma)

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

nameusersystemelapsed
GNUSE13.85 0.3516.27
barcode10.79 0.0310.92
frma10.70 0.0610.77
frmaExpressionSet-class0.130.000.12

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

nameusersystemelapsed
GNUSE16.89 0.2217.24
barcode12.25 0.2012.45
frma12.98 0.0813.05
frmaExpressionSet-class0.140.000.14