BioC 2.13: CHECK report for Clonality on zin1
This page was generated on 2014-04-05 09:48:00 -0700 (Sat, 05 Apr 2014).
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: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings Clonality_1.10.1.tar.gz |
StartedAt: 2014-04-05 00:22:33 -0700 (Sat, 05 Apr 2014) |
EndedAt: 2014-04-05 00:25:16 -0700 (Sat, 05 Apr 2014) |
EllapsedTime: 163.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Clonality.Rcheck |
Warnings: 0 |
Command output
* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/Clonality.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-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 ‘1.10.1’
* 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 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
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 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 ... [139s/143s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
clonality.analysis 56.703 0.388 59.799
LRtesting3or4tumors 39.155 0.004 39.427
LOHclonality 28.302 0.052 28.446
ECMtesting 14.300 0.008 14.356
* 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
‘/home/biocbuild/bbs-2.13-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:
name | user | system | elapsed
|
ECMtesting | 14.300 | 0.008 | 14.356 |
|
LOHclonality | 28.302 | 0.052 | 28.446 |
|
LRtesting3or4tumors | 39.155 | 0.004 | 39.427 |
|
ave.adj.probes | 0.000 | 0.008 | 0.007 |
|
chromosomePlots | 0.028 | 0.004 | 0.035 |
|
clonality.analysis | 56.703 | 0.388 | 59.799 |
|
genomewidePlots | 0.012 | 0.004 | 0.016 |
|
histogramPlot | 0.016 | 0.000 | 0.016 |
|
splitChromosomes | 0.012 | 0.004 | 0.018 |
|