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BioC 2.13: CHECK report for Clonality on moscato1

This page was generated on 2014-04-05 09:50:14 -0700 (Sat, 05 Apr 2014).

Package 144/750HostnameOS / ArchBUILDCHECKBUILD BIN
Clonality 1.10.1
Irina Ostrovnaya
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/Clonality
Last Changed Rev: 87013 / Revision: 88450
Last Changed Date: 2014-03-04 09:59:56 -0800 (Tue, 04 Mar 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: Clonality
Version: 1.10.1
Command: rm -rf Clonality.buildbin-libdir && mkdir Clonality.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Clonality.buildbin-libdir Clonality_1.10.1.tar.gz >Clonality-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=Clonality.buildbin-libdir --install="check:Clonality-install.out" --force-multiarch --no-vignettes --timings Clonality_1.10.1.tar.gz && mv Clonality.buildbin-libdir/* Clonality.Rcheck/ && rmdir Clonality.buildbin-libdir
StartedAt: 2014-04-05 03:05:58 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 03:12:18 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 380.1 seconds
RetCode: 0
Status:  OK  
CheckDir: Clonality.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/Clonality.Rcheck'
* using R version 3.0.3 (2014-03-06)
* 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 '1.10.1'
* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'Clonality.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [166s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
clonality.analysis  40.15    0.2   81.25
LRtesting3or4tumors 33.98    0.0   33.97
LOHclonality        32.18    0.0   32.19
ECMtesting          17.95    0.0   17.97
** running examples for arch 'x64' ... [173s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
clonality.analysis  43.35   0.15   81.23
LOHclonality        36.74   0.02   36.75
LRtesting3or4tumors 32.96   0.00   32.96
ECMtesting          21.46   0.00   21.46
* 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 3 notes.
See
  'D:/biocbld/bbs-2.13-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_1.10.1.zip
* DONE (Clonality)

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

nameusersystemelapsed
ECMtesting17.95 0.0017.97
LOHclonality32.18 0.0032.19
LRtesting3or4tumors33.98 0.0033.97
ave.adj.probes000
chromosomePlots0.020.000.01
clonality.analysis40.15 0.2081.25
genomewidePlots0.030.000.03
histogramPlot0.010.000.01
splitChromosomes0.010.000.02

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

nameusersystemelapsed
ECMtesting21.46 0.0021.46
LOHclonality36.74 0.0236.75
LRtesting3or4tumors32.96 0.0032.96
ave.adj.probes0.020.000.02
chromosomePlots0.010.020.03
clonality.analysis43.35 0.1581.23
genomewidePlots0.030.000.03
histogramPlot0.030.000.03
splitChromosomes0.020.000.02