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BioC 3.6: CHECK report for clippda on veracruz1

This page was generated on 2017-08-16 13:40:43 -0400 (Wed, 16 Aug 2017).

Package 229/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clippda 1.27.0
Stephen Nyangoma
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/clippda
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: clippda
Version: 1.27.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings clippda_1.27.0.tar.gz
StartedAt: 2017-08-16 01:13:22 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:17:39 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 257.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: clippda.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings clippda_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/clippda.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clippda/DESCRIPTION’ ... OK
* this is package ‘clippda’ version ‘1.27.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.6-bioc/meat/clippda.Rcheck/00install.out’ for details.
* 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
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
clippda-package          83.730  3.934  94.367
sampleSize               48.631  2.547  52.947
sampleSizeParameters     26.382  1.269  28.417
sample_technicalVariance  6.763  0.315   7.331
* 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: 2 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/clippda.Rcheck/00check.log’
for details.


clippda.Rcheck/00install.out:

* installing *source* package ‘clippda’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (clippda)

clippda.Rcheck/clippda-Ex.timings:

nameusersystemelapsed
ZvaluescasesVcontrolsPlots0.0220.0010.034
ZvaluesfrommultinomPlots0.7580.0310.990
aclinicalProteomicsData-class0.0670.0040.091
aclinicalProteomicsData-methods0.5400.2411.014
betweensampleVariance2.2150.0562.872
checkNo.replicates0.0910.0100.128
clippda-package83.730 3.93494.367
f0.0010.0000.002
fisherInformation0.0710.0040.075
liverRawData0.0040.0010.006
liver_pheno0.0010.0010.003
liverdata3.1810.0603.332
mostSimilarTwo0.0030.0000.002
negativeIntensitiesCorrection1.0550.0101.096
phenoDataFrame0.0510.0020.055
pheno_urine0.0010.0010.002
preProcRepeatedPeakData2.7260.0662.853
proteomicsExprsData0.1510.0050.165
proteomicspData0.0550.0050.071
replicateCorrelations4.2410.2154.606
sampleClusteredData1.2490.0231.316
sampleSize48.631 2.54752.947
sampleSize3DscatterPlots0.0320.0010.033
sampleSizeContourPlots0.0300.0020.031
sampleSizeParameters26.382 1.26928.417
sample_technicalVariance6.7630.3157.331
spectrumFilter3.2500.0583.478
ztwo0.0010.0000.001