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BioC 3.2: CHECK report for clippda on oaxaca

This page was generated on 2016-04-23 10:24:28 -0700 (Sat, 23 Apr 2016).

Package 180/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clippda 1.20.0
Stephen Nyangoma
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/clippda
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: clippda
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings clippda_1.20.0.tar.gz
StartedAt: 2016-04-22 22:47:23 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 22:52:15 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 292.6 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_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/clippda.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clippda/DESCRIPTION’ ... OK
* this is package ‘clippda’ version ‘1.20.0’
* 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 ... [5s/5s] WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.2-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
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 ... [242s/243s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
clippda-package          105.012  4.517 109.688
sampleSize                61.837  2.856  64.746
sampleSizeParameters      31.684  1.295  33.010
sample_technicalVariance   8.088  0.386   8.486
replicateCorrelations      5.414  0.220   5.659
* 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-3.2-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
ZvaluescasesVcontrolsPlots0.0150.0010.016
ZvaluesfrommultinomPlots0.7270.0310.780
aclinicalProteomicsData-class0.0690.0040.073
aclinicalProteomicsData-methods0.5520.2290.781
betweensampleVariance2.5980.0862.686
checkNo.replicates0.2160.0180.235
clippda-package105.012 4.517109.688
f0.0020.0000.002
fisherInformation0.0720.0030.075
liverRawData0.0050.0010.006
liver_pheno0.0020.0020.003
liverdata4.2170.0794.306
mostSimilarTwo0.0030.0000.002
negativeIntensitiesCorrection1.3710.0111.384
phenoDataFrame0.0670.0020.070
pheno_urine0.0020.0010.003
preProcRepeatedPeakData3.4630.0803.546
proteomicsExprsData0.2000.0060.207
proteomicspData0.0570.0030.060
replicateCorrelations5.4140.2205.659
sampleClusteredData1.2950.0241.319
sampleSize61.837 2.85664.746
sampleSize3DscatterPlots0.0890.0130.102
sampleSizeContourPlots0.0350.0010.035
sampleSizeParameters31.684 1.29533.010
sample_technicalVariance8.0880.3868.486
spectrumFilter3.4710.0503.528
ztwo0.0010.0000.000