BioC 3.1: CHECK report for clippda on zin2

Package: clippda

Version: 1.18.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings clippda_1.18.0.tar.gz

StartedAt: 2015-10-08 23:34:58 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:39:48 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 289.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: clippda.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings clippda_1.18.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/clippda.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clippda/DESCRIPTION’ ... OK
* this is package ‘clippda’ version ‘1.18.0’
* 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 ... [3s/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 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 ... [199s/245s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
clippda-package          88.079  0.079 108.857
sampleSize               53.933  0.040  65.533
sampleSizeParameters     26.715  0.019  33.776
sample_technicalVariance  7.089  0.000   8.195
replicateCorrelations     4.714  0.004   6.058
* 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
  ‘/home/biocbuild/bbs-3.1-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	0.014	0.000	0.017
ZvaluesfrommultinomPlots	0.658	0.012	0.848
aclinicalProteomicsData-class	0.065	0.000	0.097
aclinicalProteomicsData-methods	0.291	0.121	0.509
betweensampleVariance	1.966	0.015	2.738
checkNo.replicates	0.175	0.000	0.234
clippda-package	88.079	0.079	108.857
f	0.001	0.000	0.001
fisherInformation	0.136	0.004	0.204
liverRawData	0.004	0.000	0.004
liver_pheno	0.002	0.000	0.002
liverdata	3.816	0.004	4.914
mostSimilarTwo	0.003	0.000	0.002
negativeIntensitiesCorrection	1.311	0.000	1.462
phenoDataFrame	0.063	0.000	0.119
pheno_urine	0.002	0.000	0.001
preProcRepeatedPeakData	3.217	0.000	3.795
proteomicsExprsData	0.142	0.003	0.146
proteomicspData	0.062	0.000	0.077
replicateCorrelations	4.714	0.004	6.058
sampleClusteredData	1.323	0.000	1.872
sampleSize	53.933	0.040	65.533
sampleSize3DscatterPlots	0.084	0.000	0.083
sampleSizeContourPlots	0.026	0.004	0.031
sampleSizeParameters	26.715	0.019	33.776
sample_technicalVariance	7.089	0.000	8.195
spectrumFilter	3.271	0.000	4.046
ztwo	0.000	0.000	0.001