BioC 3.3: CHECK report for clippda on moscato2

Package: clippda

Version: 1.22.0

Command: rm -rf clippda.buildbin-libdir clippda.Rcheck && mkdir clippda.buildbin-libdir clippda.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clippda.buildbin-libdir clippda_1.22.0.tar.gz >clippda.Rcheck\00install.out 2>&1 && cp clippda.Rcheck\00install.out clippda-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=clippda.buildbin-libdir --install="check:clippda-install.out" --force-multiarch --no-vignettes --timings clippda_1.22.0.tar.gz

StartedAt: 2016-10-13 02:10:53 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 02:22:36 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 703.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: clippda.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf clippda.buildbin-libdir clippda.Rcheck && mkdir clippda.buildbin-libdir clippda.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clippda.buildbin-libdir clippda_1.22.0.tar.gz >clippda.Rcheck\00install.out 2>&1 && cp clippda.Rcheck\00install.out clippda-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=clippda.buildbin-libdir --install="check:clippda-install.out" --force-multiarch --no-vignettes --timings clippda_1.22.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/clippda.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'clippda/DESCRIPTION' ... OK
* this is package 'clippda' version '1.22.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
clippda-package          146.52   0.44  147.28
sampleSize                79.14   0.06   79.20
sampleSizeParameters      42.03   0.02   42.48
sample_technicalVariance  10.97   0.01   10.99
liverdata                  8.31   0.02    8.33
replicateCorrelations      7.77   0.00    7.76
preProcRepeatedPeakData    7.70   0.02    7.71
spectrumFilter             6.14   0.00    6.14
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
clippda-package          116.34   0.25  116.77
sampleSize                70.00   0.31   70.31
sampleSizeParameters      35.01   0.10   35.11
sample_technicalVariance   9.87   0.04    9.91
liverdata                  6.84   0.03    6.87
replicateCorrelations      6.73   0.00    6.72
preProcRepeatedPeakData    6.15   0.00    6.15
* 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
  'E:/biocbld/bbs-3.3-bioc/meat/clippda.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'clippda' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clippda' as clippda_1.22.0.zip
* DONE (clippda)

name	user	system	elapsed
ZvaluescasesVcontrolsPlots	0.09	0.02	0.13
ZvaluesfrommultinomPlots	1.04	0.00	1.05
aclinicalProteomicsData-class	0.16	0.02	0.17
aclinicalProteomicsData-methods	0.53	0.15	0.69
betweensampleVariance	2.98	0.02	2.99
checkNo.replicates	0.23	0.01	0.25
clippda-package	146.52	0.44	147.28
f	0	0	0
fisherInformation	0.18	0.02	0.20
liverRawData	0.00	0.01	0.02
liver_pheno	0.02	0.00	0.02
liverdata	8.31	0.02	8.33
mostSimilarTwo	0	0	0
negativeIntensitiesCorrection	2.63	0.01	2.63
phenoDataFrame	0.10	0.00	0.11
pheno_urine	0	0	0
preProcRepeatedPeakData	7.70	0.02	7.71
proteomicsExprsData	0.32	0.01	0.34
proteomicspData	0.13	0.00	0.13
replicateCorrelations	7.77	0.00	7.76
sampleClusteredData	2.23	0.02	2.25
sampleSize	79.14	0.06	79.20
sampleSize3DscatterPlots	0.04	0.00	0.05
sampleSizeContourPlots	0.07	0.00	0.28
sampleSizeParameters	42.03	0.02	42.48
sample_technicalVariance	10.97	0.01	10.99
spectrumFilter	6.14	0.00	6.14
ztwo	0	0	0

name	user	system	elapsed
ZvaluescasesVcontrolsPlots	0.10	0.01	0.17
ZvaluesfrommultinomPlots	1.07	0.00	1.37
aclinicalProteomicsData-class	0.14	0.00	0.14
aclinicalProteomicsData-methods	0.56	0.10	0.66
betweensampleVariance	2.34	0.01	2.35
checkNo.replicates	0.18	0.00	0.17
clippda-package	116.34	0.25	116.77
f	0	0	0
fisherInformation	0.17	0.00	0.17
liverRawData	0.02	0.00	0.02
liver_pheno	0.01	0.00	0.01
liverdata	6.84	0.03	6.87
mostSimilarTwo	0	0	0
negativeIntensitiesCorrection	2.66	0.02	2.68
phenoDataFrame	0.16	0.02	0.17
pheno_urine	0.01	0.00	0.01
preProcRepeatedPeakData	6.15	0.00	6.15
proteomicsExprsData	0.24	0.01	0.24
proteomicspData	0.09	0.03	0.13
replicateCorrelations	6.73	0.00	6.72
sampleClusteredData	2.83	0.02	2.86
sampleSize	70.00	0.31	70.31
sampleSize3DscatterPlots	0.03	0.00	0.03
sampleSizeContourPlots	0.05	0.02	0.30
sampleSizeParameters	35.01	0.10	35.11
sample_technicalVariance	9.87	0.04	9.91
spectrumFilter	4.78	0.01	4.79
ztwo	0	0	0