BioC 2.13: CHECK report for clippda on zin1

Package: clippda

Version: 1.12.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings clippda_1.12.0.tar.gz

StartedAt: 2014-04-05 00:20:41 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 00:25:53 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 311.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: clippda.Rcheck

Warnings: 1

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/clippda.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (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 ... [4s/4s] 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 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 ... [266s/267s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
clippda-package          115.211  0.100 115.651
sampleSize                71.704  0.060  71.940
sampleSizeParameters      35.986  0.016  36.100
sample_technicalVariance   7.741  0.016   7.767
replicateCorrelations      6.248  0.000   6.259
liverdata                  6.201  0.004   6.235
preProcRepeatedPeakData    5.052  0.016   5.073
spectrumFilter             5.060  0.008   5.074
* 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 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/clippda.Rcheck/00check.log’
for details.

* installing *source* package ‘clippda’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (clippda)

name	user	system	elapsed
ZvaluescasesVcontrolsPlots	0.016	0.000	0.013
ZvaluesfrommultinomPlots	1.044	0.004	1.052
aclinicalProteomicsData-class	0.068	0.004	0.100
aclinicalProteomicsData-methods	0.268	0.144	0.413
betweensampleVariance	4.220	0.004	4.235
checkNo.replicates	0.388	0.000	0.389
clippda-package	115.211	0.100	115.651
f	0.004	0.000	0.004
fisherInformation	0.172	0.004	0.174
liverRawData	0.008	0.000	0.006
liver_pheno	0.004	0.000	0.002
liverdata	6.201	0.004	6.235
mostSimilarTwo	0.000	0.000	0.003
negativeIntensitiesCorrection	1.940	0.000	1.942
phenoDataFrame	0.072	0.000	0.071
pheno_urine	0.004	0.000	0.002
preProcRepeatedPeakData	5.052	0.016	5.073
proteomicsExprsData	0.204	0.000	0.206
proteomicspData	0.080	0.000	0.079
replicateCorrelations	6.248	0.000	6.259
sampleClusteredData	2.085	0.000	2.086
sampleSize	71.704	0.060	71.940
sampleSize3DscatterPlots	0.028	0.000	0.030
sampleSizeContourPlots	0.048	0.000	0.046
sampleSizeParameters	35.986	0.016	36.100
sample_technicalVariance	7.741	0.016	7.767
spectrumFilter	5.060	0.008	5.074
ztwo	0.000	0.000	0.003