BioC 3.4: CHECK report for Clonality on morelia
This page was generated on 2017-04-15 16:23:28 -0400 (Sat, 15 Apr 2017).
Clonality 1.22.0 Irina Ostrovnaya
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/Clonality | Last Changed Rev: 122710 / Revision: 128728 | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK |  |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK |  |
Summary
Package: Clonality |
Version: 1.22.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Clonality_1.22.0.tar.gz |
StartedAt: 2017-04-15 00:02:30 -0700 (Sat, 15 Apr 2017) |
EndedAt: 2017-04-15 00:05:50 -0700 (Sat, 15 Apr 2017) |
EllapsedTime: 200.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Clonality.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Clonality_1.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/Clonality.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.22.0’
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
clonality.analysis 84.400 0.421 85.445
LRtesting3or4tumors 58.808 0.075 58.929
LOHclonality 14.792 0.233 15.038
ECMtesting 12.064 0.032 12.106
* 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
‘/Users/biocbuild/bbs-3.4-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 | 12.064 | 0.032 | 12.106 |
|
LOHclonality | 14.792 | 0.233 | 15.038 |
|
LRtesting3or4tumors | 58.808 | 0.075 | 58.929 |
|
ave.adj.probes | 1.788 | 0.038 | 1.828 |
|
chromosomePlots | 0 | 0 | 0 |
|
clonality.analysis | 84.400 | 0.421 | 85.445 |
|
genomewidePlots | 0.000 | 0.001 | 0.001 |
|
histogramPlot | 0.000 | 0.000 | 0.001 |
|
splitChromosomes | 0.008 | 0.000 | 0.010 |
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