Package: clippda

Version: 1.34.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:clippda.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings clippda_1.34.0.tar.gz

StartedAt: 2019-10-16 00:34:33 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 00:38:54 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 260.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: clippda.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:clippda.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings clippda_1.34.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/clippda.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.34.0’
* 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 ... 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ZvaluescasesVcontrolsPlots: no visible global function definition for
  ‘plot’
ZvaluescasesVcontrolsPlots: no visible global function definition for
  ‘lines’
ZvaluescasesVcontrolsPlots: no visible global function definition for
  ‘legend’
ZvaluesfrommultinomPlots: no visible global function definition for
  ‘rmultinom’
ZvaluesfrommultinomPlots: no visible global function definition for
  ‘density’
ZvaluesfrommultinomPlots: no visible global function definition for
  ‘plot’
ZvaluesfrommultinomPlots: no visible global function definition for
  ‘lines’
ZvaluesfrommultinomPlots: no visible global function definition for
  ‘legend’
ZvaluesfrommultinomPlots: no visible global function definition for
  ‘cloud’
ZvaluesfrommultinomPlots: no visible global function definition for
  ‘var’
Undefined global functions or variables:
  cloud density legend lines plot rmultinom var
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "density", "rmultinom", "var")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
clippda-package          95.479  0.144  95.710
sampleSize               58.341  0.024  58.380
sampleSizeParameters     31.037  0.056  31.533
sample_technicalVariance  8.460  0.008   8.470
replicateCorrelations     5.740  0.000   5.742
* 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-3.9-bioc/meat/clippda.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL clippda
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘clippda’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (clippda)

name	user	system	elapsed
ZvaluescasesVcontrolsPlots	0.025	0.000	0.025
ZvaluesfrommultinomPlots	0.631	0.028	0.659
aclinicalProteomicsData-class	0.091	0.000	0.091
aclinicalProteomicsData-methods	0.419	0.196	0.615
betweensampleVariance	2.268	0.024	2.292
checkNo.replicates	0.118	0.000	0.118
clippda-package	95.479	0.144	95.710
f	0.000	0.001	0.001
fisherInformation	0.118	0.001	0.119
liverRawData	0.005	0.000	0.006
liver_pheno	0.002	0.000	0.002
liverdata	1.841	0.004	1.846
mostSimilarTwo	0.002	0.000	0.003
negativeIntensitiesCorrection	0.39	0.00	0.39
phenoDataFrame	0.097	0.000	0.097
pheno_urine	0.002	0.000	0.002
preProcRepeatedPeakData	0.862	0.004	0.866
proteomicsExprsData	0.263	0.000	0.263
proteomicspData	0.06	0.00	0.06
replicateCorrelations	5.740	0.000	5.742
sampleClusteredData	0.372	0.000	0.372
sampleSize	58.341	0.024	58.380
sampleSize3DscatterPlots	0.023	0.000	0.023
sampleSizeContourPlots	0.025	0.000	0.025
sampleSizeParameters	31.037	0.056	31.533
sample_technicalVariance	8.460	0.008	8.470
spectrumFilter	0.948	0.000	0.948
ztwo	0	0	0