BioC 3.3: CHECK report for clippda on oaxaca

Package: clippda

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings clippda_1.22.0.tar.gz

StartedAt: 2016-10-13 00:15:48 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 00:20:29 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 280.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: clippda.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings clippda_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/clippda.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clippda/DESCRIPTION’ ... OK
* this is package ‘clippda’ version ‘1.22.0’
* checking package namespace information ... NOTE
  Namespaces with empty importFrom:
  ‘Biobase’ ‘tools’
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘limma’ ‘statmod’ ‘rgl’ ‘lattice’ ‘scatterplot3d’ ‘Biobase’ ‘tools’
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 ‘clippda’ can be installed ... WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.3-bioc/meat/clippda.Rcheck/00install.out’ for details.
* 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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
  Error in bibentry(bibtype = entry, textVersion = textVersion, header = header,     footer = footer, ...): argument "textVersion" is missing, with no default
* 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 to packages already attached by Depends:
  ‘lattice’ ‘limma’ ‘rgl’ ‘scatterplot3d’ ‘statmod’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘lattice’ ‘rgl’
  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
ZvaluescasesVcontrolsPlots: no visible global function definition for
  ‘plot’
ZvaluescasesVcontrolsPlots: no visible global function definition for
  ‘lines’
ZvaluescasesVcontrolsPlots: no visible global function definition for
  ‘legend’
ZvaluesfrommultinomPlots: no visible global function definition for
  ‘rmultinom’
ZvaluesfrommultinomPlots: no visible global function definition for
  ‘density’
ZvaluesfrommultinomPlots: no visible global function definition for
  ‘plot’
ZvaluesfrommultinomPlots: no visible global function definition for
  ‘lines’
ZvaluesfrommultinomPlots: no visible global function definition for
  ‘legend’
ZvaluesfrommultinomPlots: no visible global function definition for
  ‘cloud’
ZvaluesfrommultinomPlots: no visible global function definition for
  ‘var’
Undefined global functions or variables:
  cloud density legend lines plot rmultinom var
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "density", "rmultinom", "var")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
clippda-package          95.599  4.625 100.563
sampleSize               56.643  2.708  59.510
sampleSizeParameters     28.060  1.348  29.494
sample_technicalVariance  7.546  0.382   7.953
replicateCorrelations     4.785  0.217   5.010
* 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: 2 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/clippda.Rcheck/00check.log’
for details.

* installing *source* package ‘clippda’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** 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: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (clippda)

name	user	system	elapsed
ZvaluescasesVcontrolsPlots	0.013	0.001	0.042
ZvaluesfrommultinomPlots	0.659	0.028	1.951
aclinicalProteomicsData-class	0.052	0.003	0.054
aclinicalProteomicsData-methods	0.549	0.233	1.099
betweensampleVariance	2.114	0.082	2.200
checkNo.replicates	0.141	0.011	0.153
clippda-package	95.599	4.625	100.563
f	0.001	0.000	0.001
fisherInformation	0.076	0.003	0.079
liverRawData	0.005	0.001	0.006
liver_pheno	0.001	0.001	0.002
liverdata	3.506	0.068	3.579
mostSimilarTwo	0.004	0.000	0.003
negativeIntensitiesCorrection	1.234	0.021	1.256
phenoDataFrame	0.047	0.001	0.048
pheno_urine	0.002	0.002	0.004
preProcRepeatedPeakData	2.936	0.080	3.021
proteomicsExprsData	0.171	0.008	0.179
proteomicspData	0.049	0.003	0.052
replicateCorrelations	4.785	0.217	5.010
sampleClusteredData	1.245	0.022	1.270
sampleSize	56.643	2.708	59.510
sampleSize3DscatterPlots	0.021	0.002	0.024
sampleSizeContourPlots	0.035	0.002	0.084
sampleSizeParameters	28.060	1.348	29.494
sample_technicalVariance	7.546	0.382	7.953
spectrumFilter	3.011	0.053	3.070
ztwo	0.001	0.000	0.000