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BioC 3.0: CHECK report for clippda on perceval

This page was generated on 2015-04-10 09:54:40 -0700 (Fri, 10 Apr 2015).

Package 161/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clippda 1.16.0
Stephen Nyangoma
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/clippda
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ WARNINGS ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: clippda
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch clippda_1.16.0.tar.gz
StartedAt: 2015-04-09 23:56:52 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-10 00:05:12 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 500.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: clippda.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch clippda_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/clippda.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clippda/DESCRIPTION’ ... OK
* this is package ‘clippda’ version ‘1.16.0’
* 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 ... [6s/8s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [404s/408s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
clippda-package          176.984  8.638 186.033
sampleSize               102.796  4.574 107.555
sampleSizeParameters      52.251  2.329  55.287
sample_technicalVariance  11.831  0.631  12.658
replicateCorrelations      9.050  0.460   9.529
betweensampleVariance      6.589  0.072   6.682
liverdata                  6.155  0.185   6.711
preProcRepeatedPeakData    5.045  0.163   5.213
spectrumFilter             4.882  0.178   5.151
* 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

WARNING: There was 1 warning.
NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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 in fun(libname, pkgname) : error in rgl_init
** 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 in fun(libname, pkgname) : error in rgl_init
* DONE (clippda)

clippda.Rcheck/clippda-Ex.timings:

nameusersystemelapsed
ZvaluescasesVcontrolsPlots0.0150.0040.026
ZvaluesfrommultinomPlots1.1900.0501.288
aclinicalProteomicsData-class0.0730.0040.077
aclinicalProteomicsData-methods0.8460.3511.209
betweensampleVariance6.5890.0726.682
checkNo.replicates0.5950.0230.618
clippda-package176.984 8.638186.033
f0.0010.0000.002
fisherInformation0.0900.0040.132
liverRawData0.0190.0040.045
liver_pheno0.0020.0000.003
liverdata6.1550.1856.711
mostSimilarTwo0.0030.0000.004
negativeIntensitiesCorrection1.9720.0662.046
phenoDataFrame0.0640.0010.066
pheno_urine0.0020.0000.002
preProcRepeatedPeakData5.0450.1635.213
proteomicsExprsData0.6770.0150.720
proteomicspData0.0740.0120.130
replicateCorrelations9.0500.4609.529
sampleClusteredData2.0400.0132.052
sampleSize102.796 4.574107.555
sampleSize3DscatterPlots0.0250.0030.243
sampleSizeContourPlots0.0430.0030.441
sampleSizeParameters52.251 2.32955.287
sample_technicalVariance11.831 0.63112.658
spectrumFilter4.8820.1785.151
ztwo0.0010.0000.001