BioC 2.13: CHECK report for clippda on perceval

Package: clippda

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch clippda_1.12.0.tar.gz

StartedAt: 2014-04-05 00:23:32 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 00:32:10 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 517.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: clippda.Rcheck

Warnings: 1

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/clippda.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.12.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘clippda’ can be installed ... [6s/6s] 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 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.
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’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘clippda.pdf’ from 1615Kb to 341Kb
  consider running tools::compactPDF() on these files
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘clippda.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [435s/443s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
clippda-package          183.460 11.901 199.786
sampleSize               112.383  7.320 121.671
sampleSizeParameters      54.528  3.767  59.439
sample_technicalVariance  11.628  1.058  13.011
replicateCorrelations      9.409  0.726  10.230
betweensampleVariance      7.656  0.116   7.776
liverdata                  6.054  0.341   6.599
preProcRepeatedPeakData    5.574  0.269   5.935
spectrumFilter             5.318  0.230   5.623
* 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

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	0.025	0.002	0.028
ZvaluesfrommultinomPlots	1.955	0.076	2.038
aclinicalProteomicsData-class	0.088	0.010	0.099
aclinicalProteomicsData-methods	0.813	0.345	1.161
betweensampleVariance	7.656	0.116	7.776
checkNo.replicates	0.464	0.050	0.514
clippda-package	183.460	11.901	199.786
f	0.011	0.008	0.019
fisherInformation	0.129	0.022	0.151
liverRawData	0.007	0.002	0.009
liver_pheno	0.009	0.002	0.011
liverdata	6.054	0.341	6.599
mostSimilarTwo	0.005	0.005	0.010
negativeIntensitiesCorrection	2.058	0.102	2.166
phenoDataFrame	0.107	0.026	0.134
pheno_urine	0.004	0.004	0.008
preProcRepeatedPeakData	5.574	0.269	5.935
proteomicsExprsData	0.767	0.035	0.813
proteomicspData	0.078	0.015	0.094
replicateCorrelations	9.409	0.726	10.230
sampleClusteredData	2.038	0.053	2.108
sampleSize	112.383	7.320	121.671
sampleSize3DscatterPlots	0.047	0.011	0.058
sampleSizeContourPlots	0.075	0.018	0.093
sampleSizeParameters	54.528	3.767	59.439
sample_technicalVariance	11.628	1.058	13.011
spectrumFilter	5.318	0.230	5.623
ztwo	0.003	0.003	0.006