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BioC 2.13: CHECK report for clippda on moscato1

This page was generated on 2014-04-05 09:49:56 -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: rm -rf clippda.buildbin-libdir && mkdir clippda.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clippda.buildbin-libdir clippda_1.12.0.tar.gz >clippda-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=clippda.buildbin-libdir --install="check:clippda-install.out" --force-multiarch --no-vignettes --timings clippda_1.12.0.tar.gz && mv clippda.buildbin-libdir/* clippda.Rcheck/ && rmdir clippda.buildbin-libdir
StartedAt: 2014-04-05 03:03:34 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 03:15:33 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 719.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: clippda.Rcheck
Warnings: 1

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/clippda.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 whether package 'clippda' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... [303s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
clippda-package          133.29   0.35  133.63
sampleSize                79.06   0.11   79.17
sampleSizeParameters      38.43   0.06   38.49
sample_technicalVariance   9.23   0.02    9.26
liverdata                  8.25   0.00    8.26
preProcRepeatedPeakData    7.29   0.01    7.30
replicateCorrelations      6.58   0.00    6.59
spectrumFilter             5.64   0.00    5.65
** running examples for arch 'x64' ... [327s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
clippda-package          147.31   0.33  147.64
sampleSize                81.30   0.08   81.39
sampleSizeParameters      38.78   0.11   38.89
sample_technicalVariance  10.39   0.01   10.40
replicateCorrelations      8.93   0.02    8.94
liverdata                  7.38   0.00    7.37
preProcRepeatedPeakData    6.72   0.00    6.72
spectrumFilter             6.51   0.00    6.51
betweensampleVariance      6.21   0.00    6.21
* 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
  'D:/biocbld/bbs-2.13-bioc/meat/clippda.Rcheck/00check.log'
for details.

clippda.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'clippda' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clippda' as clippda_1.12.0.zip
* DONE (clippda)

clippda.Rcheck/examples_i386/clippda-Ex.timings:

nameusersystemelapsed
ZvaluescasesVcontrolsPlots0.100.000.17
ZvaluesfrommultinomPlots1.380.021.41
aclinicalProteomicsData-class0.100.000.11
aclinicalProteomicsData-methods0.380.030.40
betweensampleVariance3.230.013.24
checkNo.replicates0.220.000.22
clippda-package133.29 0.35133.63
f000
fisherInformation0.140.000.14
liverRawData0.010.000.01
liver_pheno000
liverdata8.250.008.26
mostSimilarTwo000
negativeIntensitiesCorrection2.960.002.97
phenoDataFrame0.170.000.17
pheno_urine000
preProcRepeatedPeakData7.290.017.30
proteomicsExprsData0.280.000.29
proteomicspData0.110.000.10
replicateCorrelations6.580.006.59
sampleClusteredData2.940.002.94
sampleSize79.06 0.1179.17
sampleSize3DscatterPlots0.030.000.03
sampleSizeContourPlots0.060.000.06
sampleSizeParameters38.43 0.0638.49
sample_technicalVariance9.230.029.26
spectrumFilter5.640.005.65
ztwo000

clippda.Rcheck/examples_x64/clippda-Ex.timings:

nameusersystemelapsed
ZvaluescasesVcontrolsPlots0.120.000.19
ZvaluesfrommultinomPlots1.950.021.97
aclinicalProteomicsData-class0.160.000.15
aclinicalProteomicsData-methods0.440.160.61
betweensampleVariance6.210.006.21
checkNo.replicates0.680.000.69
clippda-package147.31 0.33147.64
f000
fisherInformation0.120.000.12
liverRawData0.090.000.09
liver_pheno000
liverdata7.380.007.37
mostSimilarTwo000
negativeIntensitiesCorrection2.560.012.58
phenoDataFrame0.110.000.11
pheno_urine000
preProcRepeatedPeakData6.720.006.72
proteomicsExprsData0.310.000.31
proteomicspData0.160.000.16
replicateCorrelations8.930.028.94
sampleClusteredData2.730.002.73
sampleSize81.30 0.0881.39
sampleSize3DscatterPlots0.040.010.05
sampleSizeContourPlots0.040.020.06
sampleSizeParameters38.78 0.1138.89
sample_technicalVariance10.39 0.0110.40
spectrumFilter6.510.006.51
ztwo000