BioC 3.2: CHECK report for clippda on perceval

Package: clippda

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings clippda_1.20.0.tar.gz

StartedAt: 2015-10-27 06:29:32 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:36:04 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 392.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: clippda.Rcheck

Warnings: 1

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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_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/clippda.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 option ‘--no-vignettes’
* checking for file ‘clippda/DESCRIPTION’ ... OK
* this is package ‘clippda’ version ‘1.20.0’
* 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 ... [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 ... 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
ZvaluesfrommultinomPlots: no visible global function definition for
  ‘cloud’
* 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 ... [332s/333s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
clippda-package          147.303  5.918 153.227
sampleSize                86.321  3.783  90.107
sampleSizeParameters      43.538  2.212  45.752
sample_technicalVariance  10.580  0.493  11.073
replicateCorrelations      7.424  0.313   7.737
* 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: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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 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 (clippda)

name	user	system	elapsed
ZvaluescasesVcontrolsPlots	0.014	0.002	0.016
ZvaluesfrommultinomPlots	0.793	0.033	0.833
aclinicalProteomicsData-class	0.072	0.004	0.075
aclinicalProteomicsData-methods	0.735	0.274	1.009
betweensampleVariance	4.331	0.078	4.410
checkNo.replicates	0.256	0.016	0.271
clippda-package	147.303	5.918	153.227
f	0.001	0.000	0.001
fisherInformation	0.084	0.002	0.087
liverRawData	0.005	0.001	0.006
liver_pheno	0.001	0.000	0.002
liverdata	4.316	0.139	4.455
mostSimilarTwo	0.003	0.000	0.002
negativeIntensitiesCorrection	1.383	0.055	1.438
phenoDataFrame	0.066	0.002	0.068
pheno_urine	0.001	0.000	0.003
preProcRepeatedPeakData	3.567	0.184	3.752
proteomicsExprsData	0.674	0.014	0.688
proteomicspData	0.064	0.001	0.066
replicateCorrelations	7.424	0.313	7.737
sampleClusteredData	1.409	0.056	1.465
sampleSize	86.321	3.783	90.107
sampleSize3DscatterPlots	0.024	0.002	0.026
sampleSizeContourPlots	0.043	0.002	0.045
sampleSizeParameters	43.538	2.212	45.752
sample_technicalVariance	10.580	0.493	11.073
spectrumFilter	3.589	0.225	3.813
ztwo	0.001	0.000	0.001