BioC 3.2: CHECK report for clippda on linux1.bioconductor.org

Package: clippda

Version: 1.20.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings clippda_1.20.0.tar.gz

StartedAt: 2015-10-27 02:09:03 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:13:22 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 258.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: clippda.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings clippda_1.20.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-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 ‘1.20.0’
* 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 ... [3s/3s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [220s/220s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
clippda-package          99.079  0.091  99.239
sampleSize               59.153  0.048  59.220
sampleSizeParameters     28.543  0.016  28.569
sample_technicalVariance  8.266  0.008   8.276
liverdata                 5.097  0.012   5.111
* 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-3.2-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	0.012	0.000	0.011
ZvaluesfrommultinomPlots	0.564	0.004	0.567
aclinicalProteomicsData-class	0.058	0.000	0.058
aclinicalProteomicsData-methods	0.209	0.116	0.326
betweensampleVariance	2.682	0.016	2.698
checkNo.replicates	0.158	0.004	0.162
clippda-package	99.079	0.091	99.239
f	0.001	0.000	0.001
fisherInformation	0.115	0.000	0.116
liverRawData	0.005	0.000	0.006
liver_pheno	0.002	0.000	0.002
liverdata	5.097	0.012	5.111
mostSimilarTwo	0.003	0.000	0.003
negativeIntensitiesCorrection	1.657	0.000	1.656
phenoDataFrame	0.090	0.004	0.093
pheno_urine	0.002	0.000	0.002
preProcRepeatedPeakData	3.882	0.000	3.884
proteomicsExprsData	0.125	0.000	0.125
proteomicspData	0.055	0.000	0.055
replicateCorrelations	4.692	0.000	4.697
sampleClusteredData	1.352	0.000	1.355
sampleSize	59.153	0.048	59.220
sampleSize3DscatterPlots	0.011	0.004	0.016
sampleSizeContourPlots	0.025	0.000	0.025
sampleSizeParameters	28.543	0.016	28.569
sample_technicalVariance	8.266	0.008	8.276
spectrumFilter	2.858	0.000	2.860
ztwo	0.000	0.000	0.001