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BioC 3.2: CHECK report for Clonality on zin1

This page was generated on 2015-08-24 10:47:54 -0700 (Mon, 24 Aug 2015).

Package 181/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Clonality 1.17.0
Irina Ostrovnaya
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Clonality
Last Changed Rev: 102594 / Revision: 107696
Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Clonality
Version: 1.17.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Clonality_1.17.0.tar.gz
StartedAt: 2015-08-23 22:37:57 -0700 (Sun, 23 Aug 2015)
EndedAt: 2015-08-23 22:40:35 -0700 (Sun, 23 Aug 2015)
EllapsedTime: 157.8 seconds
RetCode: 0
Status:  OK 
CheckDir: Clonality.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Clonality_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/Clonality.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Clonality/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Clonality’ version ‘1.17.0’
* 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 ‘Clonality’ can be installed ... [1s/1s] 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [140s/140s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
clonality.analysis  76.806  0.092  77.120
LRtesting3or4tumors 34.160  0.011  34.257
LOHclonality        15.595  0.036  15.625
ECMtesting          11.513  0.005  11.513
* 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
  ‘/home/biocbuild/bbs-3.2-bioc/meat/Clonality.Rcheck/00check.log’
for details.


Clonality.Rcheck/00install.out:

* 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
* DONE (Clonality)

Clonality.Rcheck/Clonality-Ex.timings:

nameusersystemelapsed
ECMtesting11.513 0.00511.513
LOHclonality15.595 0.03615.625
LRtesting3or4tumors34.160 0.01134.257
ave.adj.probes1.2810.0041.283
chromosomePlots0.0000.0000.001
clonality.analysis76.806 0.09277.120
genomewidePlots0.0010.0000.001
histogramPlot0.0000.0000.001
splitChromosomes0.0110.0000.011