BioC 2.14: CHECK report for ampliQueso on morelia

Package: ampliQueso

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ampliQueso_1.2.0.tar.gz

StartedAt: 2014-10-07 21:08:35 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 21:13:50 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 314.6 seconds

RetCode: 0

Status:  OK

CheckDir: ampliQueso.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ampliQueso_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/ampliQueso.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ampliQueso/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ampliQueso’ version ‘1.2.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘rnaSeqMap’ ‘knitr’ ‘rgl’ ‘ggplot2’ ‘gplots’ ‘parallel’ ‘doParallel’
  ‘foreach’ ‘VariantAnnotation’ ‘genefilter’ ‘statmod’ ‘xtable’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘ampliQueso’ can be installed ... [29s/29s] 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
Namespace in Imports field not imported from: ‘samr’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘VariantAnnotation’ ‘doParallel’ ‘foreach’ ‘genefilter’ ‘ggplot2’
  ‘gplots’ ‘knitr’ ‘rgl’ ‘statmod’ ‘xtable’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘rnaSeqMap:::newSeqReads’
  See the note in ?`:::` about the use of this operator.
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [28s/28s] OK
* 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
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/ampliQueso.Rcheck/00check.log’
for details.

* installing *source* package ‘ampliQueso’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
* DONE (ampliQueso)

name	user	system	elapsed
camelSampleTable	0.003	0.000	0.003