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BioC 2.14: CHECK report for flowType on petty

This page was generated on 2014-10-08 08:59:37 -0700 (Wed, 08 Oct 2014).

Package 295/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowType 2.2.0
Nima Aghaeepour
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/flowType
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: flowType
Version: 2.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowType_2.2.0.tar.gz
StartedAt: 2014-10-07 22:00:31 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 22:03:48 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 197.2 seconds
RetCode: 0
Status:  OK 
CheckDir: flowType.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowType_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/flowType.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowType/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowType’ version ‘2.2.0’
* 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 ‘flowType’ can be installed ... [32s/33s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘BH’ ‘Rcpp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [11s/11s] 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/flowType.Rcheck/00check.log’
for details.

flowType.Rcheck/00install.out:

* installing *source* package ‘flowType’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c countsAndMeans.cpp -o countsAndMeans.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c flowType.cpp -o flowType.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c numberGenerator.cpp -o numberGenerator.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o flowType.so countsAndMeans.o flowType.o numberGenerator.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/flowType.Rcheck/flowType/libs
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
Creating a generic function for ‘summary’ from package ‘base’ in package ‘flowType’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
* DONE (flowType)

flowType.Rcheck/flowType-Ex.timings:

nameusersystemelapsed
DLBCLExample0.0130.0100.023
HIVData0.1610.0180.191
HIVMetaData0.0030.0010.004
Phenotypes0.0040.0010.003
calcNumPops0.0020.0000.002
decodePhenotype-methods0.0030.0010.003
encodePhenotype0.0010.0000.002
flowType-package1.1710.0151.197
flowType1.0980.0121.114
getLabels0.0010.0000.001
plot0.0010.0000.002
summary-methods0.0010.0010.001