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BioC 2.14: CHECK report for clippda on morelia

This page was generated on 2014-10-08 09:04:03 -0700 (Wed, 08 Oct 2014).

Package 154/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clippda 1.14.0
Stephen Nyangoma
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/clippda
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK 

Summary

Package: clippda
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch clippda_1.14.0.tar.gz
StartedAt: 2014-10-07 22:00:04 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 22:06:31 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 387.2 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_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/clippda.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clippda/DESCRIPTION’ ... OK
* this is package ‘clippda’ version ‘1.14.0’
* checking package namespace information ... OK
* 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] 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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... [318s/319s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
clippda-package          136.245  4.255 140.699
sampleSize                84.809  2.463  87.456
sampleSizeParameters      42.638  1.219  43.908
sample_technicalVariance   9.663  0.372  10.045
replicateCorrelations      6.867  0.215   7.098
liverdata                  5.944  0.072   6.021
spectrumFilter             5.098  0.078   5.180
preProcRepeatedPeakData    5.021  0.082   5.113
* 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

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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
ZvaluescasesVcontrolsPlots0.0600.0010.062
ZvaluesfrommultinomPlots0.8340.0300.870
aclinicalProteomicsData-class0.0630.0030.067
aclinicalProteomicsData-methods0.5640.2160.781
betweensampleVariance4.2300.0634.294
checkNo.replicates0.5110.0210.533
clippda-package136.245 4.255140.699
f0.0020.0000.002
fisherInformation0.0900.0020.092
liverRawData0.0050.0000.005
liver_pheno0.0010.0000.002
liverdata5.9440.0726.021
mostSimilarTwo0.0030.0000.003
negativeIntensitiesCorrection2.0480.0142.077
phenoDataFrame0.0650.0020.066
pheno_urine0.0020.0000.003
preProcRepeatedPeakData5.0210.0825.113
proteomicsExprsData0.2580.0060.264
proteomicspData0.0630.0050.069
replicateCorrelations6.8670.2157.098
sampleClusteredData1.9480.0211.976
sampleSize84.809 2.46387.456
sampleSize3DscatterPlots0.0190.0010.021
sampleSizeContourPlots0.0360.0020.038
sampleSizeParameters42.638 1.21943.908
sample_technicalVariance 9.663 0.37210.045
spectrumFilter5.0980.0785.180
ztwo0.0010.0000.001