BioC 3.2: CHECK report for CGHbase on oaxaca
This page was generated on 2016-04-23 10:24:04 -0700 (Sat, 23 Apr 2016).
CGHbase 1.30.0 Mark van de Wiel
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/CGHbase | Last Changed Rev: 109589 / Revision: 116712 | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | | |
moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | OK | OK | |
oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
Summary
Package: CGHbase |
Version: 1.30.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CGHbase_1.30.0.tar.gz |
StartedAt: 2016-04-22 22:31:17 -0700 (Fri, 22 Apr 2016) |
EndedAt: 2016-04-22 22:31:59 -0700 (Fri, 22 Apr 2016) |
EllapsedTime: 42.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CGHbase.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 CGHbase_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/CGHbase.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CGHbase/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CGHbase’ version ‘1.30.0’
* 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 ‘CGHbase’ can be installed ... [4s/4s] OK
* checking installed package size ... OK
* checking package 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 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.
':::' call which should be '::': ‘Biobase:::assayDataElement’
See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: ‘Biobase:::assayDataDims’
See the note in ?`:::` about the use of this operator.
* 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 examples ... [2s/2s] OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.2-bioc/meat/CGHbase.Rcheck/00check.log’
for details.
CGHbase.Rcheck/00install.out:
* installing *source* package ‘CGHbase’ ...
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (CGHbase)
CGHbase.Rcheck/CGHbase-Ex.timings:
name | user | system | elapsed
|
class.cghCall | 0.099 | 0.005 | 0.104 |
|
class.cghRaw | 0.353 | 0.026 | 0.379 |
|
class.cghRegions | 0.310 | 0.003 | 0.313 |
|
class.cghSeg | 0.057 | 0.000 | 0.057 |
|
copynumber | 0.047 | 0.004 | 0.051 |
|
frequencyPlot | 0.001 | 0.000 | 0.001 |
|
frequencyPlotCalls | 0.001 | 0.000 | 0.001 |
|
make_cghRaw | 0.157 | 0.002 | 0.158 |
|
summaryPlot | 0.001 | 0.000 | 0.001 |
|