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CHECK report for clippda on malbec2

This page was generated on 2018-10-17 08:22:50 -0400 (Wed, 17 Oct 2018).

Package 253/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clippda 1.30.0
Stephen Nyangoma
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/clippda
Branch: RELEASE_3_7
Last Commit: 6d0a35f
Last Changed Date: 2018-04-30 10:35:11 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: clippda
Version: 1.30.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:clippda.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings clippda_1.30.0.tar.gz
StartedAt: 2018-10-15 23:16:48 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 23:20:05 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 197.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: clippda.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:clippda.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings clippda_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/clippda.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.30.0’
* 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          73.952  0.100  74.106
sampleSize               43.060  0.076  43.166
sampleSizeParameters     21.548  0.028  21.590
sample_technicalVariance  5.812  0.012   5.829
* 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-3.7-bioc/meat/clippda.Rcheck/00check.log’
for details.



Installation output

clippda.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL clippda
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘clippda’ ...
** 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
* DONE (clippda)

Tests output


Example timings

clippda.Rcheck/clippda-Ex.timings

nameusersystemelapsed
ZvaluescasesVcontrolsPlots0.0200.0000.019
ZvaluesfrommultinomPlots0.4240.0000.422
aclinicalProteomicsData-class0.0520.0000.052
aclinicalProteomicsData-methods0.2600.1080.372
betweensampleVariance1.3840.0241.411
checkNo.replicates0.0680.0000.070
clippda-package73.952 0.10074.106
f0.0000.0000.001
fisherInformation0.0760.0000.073
liverRawData0.020.000.02
liver_pheno0.0000.0000.003
liverdata1.5600.0121.575
mostSimilarTwo0.0040.0000.003
negativeIntensitiesCorrection0.2560.0000.257
phenoDataFrame0.0560.0000.057
pheno_urine0.0000.0000.001
preProcRepeatedPeakData0.8480.0000.850
proteomicsExprsData0.2960.0000.302
proteomicspData0.0880.0000.090
replicateCorrelations4.0560.0044.065
sampleClusteredData0.2320.0000.231
sampleSize43.060 0.07643.166
sampleSize3DscatterPlots0.0200.0000.018
sampleSizeContourPlots0.0280.0000.027
sampleSizeParameters21.548 0.02821.590
sample_technicalVariance5.8120.0125.829
spectrumFilter0.8760.0000.876
ztwo0.0000.0000.001