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BioC 2.14: CHECK report for Clonality on moscato2

This page was generated on 2014-06-28 08:19:21 -0700 (Sat, 28 Jun 2014).

Package 157/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Clonality 1.12.0
Irina Ostrovnaya
Snapshot Date: 2014-06-27 17:20:31 -0700 (Fri, 27 Jun 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/Clonality
Last Changed Rev: 88838 / Revision: 91969
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.2) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: Clonality
Version: 1.12.0
Command: rm -rf Clonality.buildbin-libdir && mkdir Clonality.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Clonality.buildbin-libdir Clonality_1.12.0.tar.gz >Clonality-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=Clonality.buildbin-libdir --install="check:Clonality-install.out" --force-multiarch --no-vignettes --timings Clonality_1.12.0.tar.gz
StartedAt: 2014-06-27 23:27:36 -0700 (Fri, 27 Jun 2014)
EndedAt: 2014-06-27 23:32:54 -0700 (Fri, 27 Jun 2014)
EllapsedTime: 318.9 seconds
RetCode: 0
Status:  OK  
CheckDir: Clonality.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Clonality.buildbin-libdir && mkdir Clonality.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Clonality.buildbin-libdir Clonality_1.12.0.tar.gz >Clonality-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=Clonality.buildbin-libdir --install="check:Clonality-install.out" --force-multiarch --no-vignettes --timings Clonality_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/Clonality.Rcheck'
* using R version 3.1.0 RC (2014-04-02 r65358)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Clonality/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Clonality' version '1.12.0'
* 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 'Clonality' 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:
  'DNAcopy'
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 ... NOTE
Foreign function call to a different package:
  .Fortran("fndcpt", ..., PACKAGE = "DNAcopy")
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [140s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
clonality.analysis  39.92   0.18   74.13
LRtesting3or4tumors 30.03   0.00   30.38
LOHclonality        21.83   0.00   21.82
ECMtesting          13.48   0.00   13.48
** running examples for arch 'x64' ... [146s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
clonality.analysis  38.90   0.16   72.21
LRtesting3or4tumors 31.42   0.00   31.42
LOHclonality        25.94   0.01   25.96
ECMtesting          15.67   0.00   15.66
* 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 were 2 notes.
See
  'E:/biocbld/bbs-2.14-bioc/meat/Clonality.Rcheck/00check.log'
for details.

Clonality.Rcheck/00install.out:


install for i386

* installing *source* package 'Clonality' ...
** 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 'Clonality' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Clonality' as Clonality_1.12.0.zip
* DONE (Clonality)

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

nameusersystemelapsed
ECMtesting13.48 0.0013.48
LOHclonality21.83 0.0021.82
LRtesting3or4tumors30.03 0.0030.38
ave.adj.probes000
chromosomePlots000
clonality.analysis39.92 0.1874.13
genomewidePlots000
histogramPlot000
splitChromosomes000

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

nameusersystemelapsed
ECMtesting15.67 0.0015.66
LOHclonality25.94 0.0125.96
LRtesting3or4tumors31.42 0.0031.42
ave.adj.probes000
chromosomePlots000
clonality.analysis38.90 0.1672.21
genomewidePlots000
histogramPlot000
splitChromosomes000