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BioC 2.13: CHECK report for clippda on zin1

This page was generated on 2014-04-05 09:47:47 -0700 (Sat, 05 Apr 2014).

Package 142/750HostnameOS / ArchBUILDCHECKBUILD BIN
clippda 1.12.0
Stephen Nyangoma
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/clippda
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ WARNINGS ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS  OK 

Summary

Package: clippda
Version: 1.12.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings clippda_1.12.0.tar.gz
StartedAt: 2014-04-05 00:20:41 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 00:25:53 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 311.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: clippda.Rcheck
Warnings: 1

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/clippda.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clippda/DESCRIPTION’ ... OK
* this is package ‘clippda’ version ‘1.12.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ... [4s/4s] 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.
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 installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘clippda.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [266s/267s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
clippda-package          115.211  0.100 115.651
sampleSize                71.704  0.060  71.940
sampleSizeParameters      35.986  0.016  36.100
sample_technicalVariance   7.741  0.016   7.767
replicateCorrelations      6.248  0.000   6.259
liverdata                  6.201  0.004   6.235
preProcRepeatedPeakData    5.052  0.016   5.073
spectrumFilter             5.060  0.008   5.074
* 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
  ‘/home/biocbuild/bbs-2.13-bioc/meat/clippda.Rcheck/00check.log’
for details.

clippda.Rcheck/00install.out:

* installing *source* package ‘clippda’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (clippda)

clippda.Rcheck/clippda-Ex.timings:

nameusersystemelapsed
ZvaluescasesVcontrolsPlots0.0160.0000.013
ZvaluesfrommultinomPlots1.0440.0041.052
aclinicalProteomicsData-class0.0680.0040.100
aclinicalProteomicsData-methods0.2680.1440.413
betweensampleVariance4.2200.0044.235
checkNo.replicates0.3880.0000.389
clippda-package115.211 0.100115.651
f0.0040.0000.004
fisherInformation0.1720.0040.174
liverRawData0.0080.0000.006
liver_pheno0.0040.0000.002
liverdata6.2010.0046.235
mostSimilarTwo0.0000.0000.003
negativeIntensitiesCorrection1.9400.0001.942
phenoDataFrame0.0720.0000.071
pheno_urine0.0040.0000.002
preProcRepeatedPeakData5.0520.0165.073
proteomicsExprsData0.2040.0000.206
proteomicspData0.0800.0000.079
replicateCorrelations6.2480.0006.259
sampleClusteredData2.0850.0002.086
sampleSize71.704 0.06071.940
sampleSize3DscatterPlots0.0280.0000.030
sampleSizeContourPlots0.0480.0000.046
sampleSizeParameters35.986 0.01636.100
sample_technicalVariance7.7410.0167.767
spectrumFilter5.0600.0085.074
ztwo0.0000.0000.003