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BioC 3.4: CHECK report for Clonality on moscato1

This page was generated on 2016-09-21 03:43:17 -0700 (Wed, 21 Sep 2016).

Package 208/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Clonality 1.21.0
Irina Ostrovnaya
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Clonality
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  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  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: Clonality
Version: 1.21.0
Command: rm -rf Clonality.buildbin-libdir Clonality.Rcheck && mkdir Clonality.buildbin-libdir Clonality.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Clonality.buildbin-libdir Clonality_1.21.0.tar.gz >Clonality.Rcheck\00install.out 2>&1 && cp Clonality.Rcheck\00install.out Clonality-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=Clonality.buildbin-libdir --install="check:Clonality-install.out" --force-multiarch --no-vignettes --timings Clonality_1.21.0.tar.gz
StartedAt: 2016-09-20 05:52:48 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 05:58:20 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 331.5 seconds
RetCode: 0
Status:  OK  
CheckDir: Clonality.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Clonality.buildbin-libdir Clonality.Rcheck && mkdir Clonality.buildbin-libdir Clonality.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Clonality.buildbin-libdir Clonality_1.21.0.tar.gz >Clonality.Rcheck\00install.out 2>&1 && cp Clonality.Rcheck\00install.out Clonality-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=Clonality.buildbin-libdir --install="check:Clonality-install.out" --force-multiarch --no-vignettes --timings Clonality_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/Clonality.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 'Clonality/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Clonality' version '1.21.0'
* 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
Malformed Description field: should contain one or more complete sentences.
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
** 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 ... 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 chapter 'System and foreign language interfaces' in 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' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
clonality.analysis  79.26   0.19   79.68
LRtesting3or4tumors 28.27   0.00   28.27
LOHclonality        16.46   0.01   16.47
ECMtesting          10.95   0.00   10.96
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
clonality.analysis  90.93   0.20   91.42
LRtesting3or4tumors 28.64   0.02   28.66
LOHclonality        20.35   0.01   20.35
ECMtesting          14.35   0.00   14.36
* 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/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_1.21.0.zip
* DONE (Clonality)

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

nameusersystemelapsed
ECMtesting10.95 0.0010.96
LOHclonality16.46 0.0116.47
LRtesting3or4tumors28.27 0.0028.27
ave.adj.probes1.230.001.23
chromosomePlots000
clonality.analysis79.26 0.1979.68
genomewidePlots000
histogramPlot000
splitChromosomes0.020.000.02

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

nameusersystemelapsed
ECMtesting14.35 0.0014.36
LOHclonality20.35 0.0120.35
LRtesting3or4tumors28.64 0.0228.66
ave.adj.probes1.590.001.59
chromosomePlots000
clonality.analysis90.93 0.2091.42
genomewidePlots000
histogramPlot000
splitChromosomes000