BioC 2.13: CHECK report for DriverNet on zin1
This page was generated on 2014-04-05 09:48:30 -0700 (Sat, 05 Apr 2014).
DriverNet 1.2.0 Jiarui Ding
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/DriverNet | Last Changed Rev: 81642 / Revision: 88450 | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| 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: DriverNet |
Version: 1.2.0 |
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings DriverNet_1.2.0.tar.gz |
StartedAt: 2014-04-05 00:52:43 -0700 (Sat, 05 Apr 2014) |
EndedAt: 2014-04-05 00:53:48 -0700 (Sat, 05 Apr 2014) |
EllapsedTime: 65.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DriverNet.Rcheck |
Warnings: 0 |
Command output
* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/DriverNet.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 ‘DriverNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DriverNet’ version ‘1.2.0’
* 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 ‘DriverNet’ can be installed ... [1s/1s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... NOTE
Package in Depends field not imported from: ‘methods’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘DriverNet-Overview.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [52s/52s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
DriverNet-package 24.481 0.048 24.576
computeDrivers 17.449 0.036 17.585
computeRandomizedResult 8.577 0.008 8.597
* 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 2 notes.
See
‘/home/biocbuild/bbs-2.13-bioc/meat/DriverNet.Rcheck/00check.log’
for details.
DriverNet.Rcheck/00install.out:
* installing *source* package ‘DriverNet’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DriverNet)
DriverNet.Rcheck/DriverNet-Ex.timings:
name | user | system | elapsed
|
DriverNet-package | 24.481 | 0.048 | 24.576 |
|
DriverNetResult-class | 0.012 | 0.004 | 0.017 |
|
actualEvents | 0.048 | 0.028 | 0.073 |
|
computeDrivers | 17.449 | 0.036 | 17.585 |
|
computeRandomizedResult | 8.577 | 0.008 | 8.597 |
|
drivers | 0.040 | 0.024 | 0.066 |
|
getPatientOutlierMatrix | 0.192 | 0.000 | 0.193 |
|
preprocessMatrices | 0.160 | 0.004 | 0.161 |
|
resultSummary | 0.176 | 0.008 | 0.185 |
|
sampleDriversList | 0.016 | 0.000 | 0.017 |
|
sampleGeneNames | 0.024 | 0.000 | 0.025 |
|
sampleInfluenceGraph | 0.136 | 0.012 | 0.149 |
|
samplePatientExpressionMatrix | 0.080 | 0.000 | 0.081 |
|
samplePatientMutationMatrix | 0.008 | 0.000 | 0.011 |
|
samplePatientOutlierMatrix | 0.008 | 0.004 | 0.012 |
|
sampleRandomDriversResult | 0.000 | 0.000 | 0.002 |
|
totalEvents | 0.016 | 0.004 | 0.020 |
|