BioC 3.2: CHECK report for Rcade on perceval

Package: Rcade

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-examples Rcade_1.12.0.tar.gz

StartedAt: 2015-11-10 08:39:25 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 08:41:40 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 135.4 seconds

RetCode: 0

Status:  OK

CheckDir: Rcade.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-examples Rcade_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/Rcade.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using options ‘--no-examples --no-vignettes’
* checking for file ‘Rcade/DESCRIPTION’ ... OK
* this is package ‘Rcade’ version ‘1.12.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rcade’ can be installed ... [12s/12s] OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   5.2Mb
* 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
Namespaces in Imports field not imported from:
  ‘graphics’ ‘plotrix’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘baySeq’ ‘GenomicRanges’ ‘methods’ ‘Rsamtools’
  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 ... NOTE
constructRcadeTable: no visible global function definition for
  ‘elementMetadata’
countReads: no visible global function definition for ‘ScanBamParam’
countReads: no visible global function definition for ‘seqlevels’
countReads: no visible global function definition for ‘scanBam’
countReads: no visible global function definition for ‘seqlevels<-’
countReads: no visible global function definition for ‘strand’
countReads: no visible global function definition for ‘start<-’
countReads: no visible global function definition for ‘width<-’
countReads: no visible global function definition for ‘countOverlaps’
defineBins: no visible global function definition for ‘IRanges’
defineBins: no visible global function definition for ‘GRanges’
defineBins: no visible global function definition for ‘DataFrame’
defineBins: no visible global function definition for ‘values<-’
describeGR: no visible global function definition for ‘elementMetadata’
diffCountsBaySeq: no visible global function definition for ‘width’
diffCountsBaySeq: no visible binding for global variable ‘getLibsizes’
diffCountsBaySeq: no visible global function definition for
  ‘libsizes<-’
diffCountsBaySeq: no visible binding for global variable ‘getPriors.NB’
diffCountsBaySeq: no visible binding for global variable
  ‘getLikelihoods’
getBamChrs: no visible global function definition for ‘scanBamHeader’
RcadeAnalysis: no visible global function definition for ‘values’
plotBBB,Rcade : .local: no visible global function definition for
  ‘decorate3d’
plotMM,Rcade : .local: no visible global function definition for
  ‘color.legend’
* 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 ... SKIPPED
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [8s/8s]
 [8s/9s] 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
* DONE

Status: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/Rcade.Rcheck/00check.log’
for details.

* installing *source* package ‘Rcade’ ...
** 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 (Rcade)