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BioC 3.0: CHECK report for qcmetrics on zin1

This page was generated on 2015-04-10 09:41:26 -0700 (Fri, 10 Apr 2015).

Package 698/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qcmetrics 1.4.1
Laurent Gatto
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/qcmetrics
Last Changed Rev: 100963 / Revision: 102249
Last Changed Date: 2015-03-21 00:50:07 -0700 (Sat, 21 Mar 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: qcmetrics
Version: 1.4.1
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings qcmetrics_1.4.1.tar.gz
StartedAt: 2015-04-10 03:20:52 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 03:22:10 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 78.2 seconds
RetCode: 0
Status:  OK 
CheckDir: qcmetrics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings qcmetrics_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/qcmetrics.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qcmetrics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qcmetrics’ version ‘1.4.1’
* 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 ‘qcmetrics’ can be installed ... [5s/5s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘affy’ ‘ggplot2’ ‘yaqcaffy’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘yaqcaffy:::.plotQCRatios’
  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 ... NOTE
n15qc: no visible global function definition for ‘fvarLabels’
n15qc: no visible global function definition for ‘fData’
n15qc : <anonymous>: no visible global function definition for ‘ggplot’
n15qc : <anonymous>: no visible global function definition for ‘aes’
n15qc : <anonymous>: no visible global function definition for
  ‘geom_jitter’
n15qc : <anonymous>: no visible global function definition for
  ‘geom_boxplot’
n15qc : <anonymous>: no visible global function definition for
  ‘geom_hline’
n15qc : <anonymous>: no visible global function definition for ‘labs’
n15qc: no visible global function definition for ‘fData<-’
n15qc: no visible global function definition for ‘combineFeatures’
n15qc: no visible global function definition for ‘exprs’
n15qc: no visible global function definition for ‘fileNames’
n15qc: no visible global function definition for ‘experimentData’
rnadeg: no visible global function definition for ‘ReadAffy’
rnadeg: no visible global function definition for ‘AffyRNAdeg’
rnadeg : <anonymous>: no visible global function definition for
  ‘plotAffyRNAdeg’
rnadeg: no visible global function definition for ‘yaqc’
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/12s] OK
Examples with CPU or elapsed time > 5s
     user system elapsed
psm 5.116  0.204   5.452
* 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/qcmetrics.Rcheck/00check.log’
for details.

qcmetrics.Rcheck/00install.out:

* installing *source* package ‘qcmetrics’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘qcmetrics’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘qcmetrics’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (qcmetrics)

qcmetrics.Rcheck/qcmetrics-Ex.timings:

nameusersystemelapsed
QcMetadata-class0.0040.0000.004
QcMetric-class0.0120.0040.015
QcMetrics-class0.0320.0080.041
psm5.1160.2045.452
qcReport-methods1.4440.2083.330