BioC 3.1: CHECK report for copynumber on morelia
This page was generated on 2015-10-09 09:40:53 -0700 (Fri, 09 Oct 2015).
copynumber 1.8.0 Gro Nilsen
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/copynumber | Last Changed Rev: 102591 / Revision: 109384 | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |  |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |  |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK |  |
Summary
Package: copynumber |
Version: 1.8.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings copynumber_1.8.0.tar.gz |
StartedAt: 2015-10-09 00:43:12 -0700 (Fri, 09 Oct 2015) |
EndedAt: 2015-10-09 00:45:54 -0700 (Fri, 09 Oct 2015) |
EllapsedTime: 161.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: copynumber.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 copynumber_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/copynumber.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘copynumber/DESCRIPTION’ ... OK
* this is package ‘copynumber’ version ‘1.8.0’
* 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 ‘copynumber’ can be installed ... [7s/8s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... NOTE
Package in Depends field not imported from: ‘BiocGenerics’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [66s/75s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotCircle 9.352 0.654 13.881
plotFreq 5.619 0.301 5.973
plotHeatmap 4.971 0.233 5.270
plotAberration 4.175 0.356 5.430
* 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-3.1-bioc/meat/copynumber.Rcheck/00check.log’
for details.
copynumber.Rcheck/00install.out:
* installing *source* package ‘copynumber’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (copynumber)
copynumber.Rcheck/copynumber-Ex.timings:
name | user | system | elapsed
|
SNPdata | 0.018 | 0.010 | 0.027 |
|
aspcf | 2.382 | 0.181 | 2.568 |
|
callAberrations | 4.068 | 0.171 | 4.246 |
|
getGRangesFormat | 3.905 | 0.151 | 4.060 |
|
imputeMissing | 2.903 | 0.239 | 3.145 |
|
interpolate.pcf | 0.675 | 0.013 | 0.689 |
|
lymphoma | 0.002 | 0.001 | 0.003 |
|
micma | 0.002 | 0.000 | 0.002 |
|
multipcf | 0.526 | 0.011 | 0.537 |
|
pcf | 0.824 | 0.015 | 1.448 |
|
pcfPlain | 0.207 | 0.007 | 0.214 |
|
plotAberration | 4.175 | 0.356 | 5.430 |
|
plotAllele | 2.629 | 0.113 | 3.375 |
|
plotChrom | 2.580 | 0.145 | 3.320 |
|
plotCircle | 9.352 | 0.654 | 13.881 |
|
plotFreq | 5.619 | 0.301 | 5.973 |
|
plotGamma | 2.006 | 0.238 | 3.333 |
|
plotGenome | 3.514 | 0.125 | 3.747 |
|
plotHeatmap | 4.971 | 0.233 | 5.270 |
|
plotSample | 3.027 | 0.182 | 3.339 |
|
selectSegments | 1.082 | 0.103 | 1.185 |
|
subsetData | 0.003 | 0.000 | 0.004 |
|
subsetSegments | 4.247 | 0.255 | 4.519 |
|
winsorize | 0.236 | 0.005 | 0.261 |
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