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BioC 3.4: CHECK report for clippda on tokay1

This page was generated on 2017-04-15 16:16:00 -0400 (Sat, 15 Apr 2017).

Package 212/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clippda 1.24.0
Stephen Nyangoma
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/clippda
Last Changed Rev: 123155 / Revision: 128728
Last Changed Date: 2016-10-28 13:53:44 -0400 (Fri, 28 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: clippda
Version: 1.24.0
Command: rm -rf clippda.buildbin-libdir clippda.Rcheck && mkdir clippda.buildbin-libdir clippda.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clippda.buildbin-libdir clippda_1.24.0.tar.gz >clippda.Rcheck\00install.out 2>&1 && cp clippda.Rcheck\00install.out clippda-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=clippda.buildbin-libdir --install="check:clippda-install.out" --force-multiarch --no-vignettes --timings clippda_1.24.0.tar.gz
StartedAt: 2017-04-14 21:32:23 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:39:23 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 420.4 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: clippda.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf clippda.buildbin-libdir clippda.Rcheck && mkdir clippda.buildbin-libdir clippda.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clippda.buildbin-libdir clippda_1.24.0.tar.gz >clippda.Rcheck\00install.out 2>&1 && cp clippda.Rcheck\00install.out clippda-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=clippda.buildbin-libdir --install="check:clippda-install.out" --force-multiarch --no-vignettes --timings clippda_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/clippda.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'clippda/DESCRIPTION' ... OK
* this is package 'clippda' version '1.24.0'
* 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 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
** checking loading without being on the library search path ... 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 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
ZvaluescasesVcontrolsPlots: no visible global function definition for
  'plot'
ZvaluescasesVcontrolsPlots: no visible global function definition for
  'lines'
ZvaluescasesVcontrolsPlots: no visible global function definition for
  'legend'
ZvaluesfrommultinomPlots: no visible global function definition for
  'rmultinom'
ZvaluesfrommultinomPlots: no visible global function definition for
  'density'
ZvaluesfrommultinomPlots: no visible global function definition for
  'plot'
ZvaluesfrommultinomPlots: no visible global function definition for
  'lines'
ZvaluesfrommultinomPlots: no visible global function definition for
  'legend'
ZvaluesfrommultinomPlots: no visible global function definition for
  'cloud'
ZvaluesfrommultinomPlots: no visible global function definition for
  'var'
Undefined global functions or variables:
  cloud density legend lines plot rmultinom var
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "density", "rmultinom", "var")
to your NAMESPACE file.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
clippda-package          78.67   0.41   79.08
sampleSize               51.04   0.03   51.08
sampleSizeParameters     25.12   0.06   25.18
sample_technicalVariance  7.18   0.00    7.18
preProcRepeatedPeakData   6.26   0.03    6.30
replicateCorrelations     5.36   0.01    5.37
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
clippda-package          68.28   0.47   68.75
sampleSize               42.56   0.19   42.75
sampleSizeParameters     21.33   0.06   21.39
sample_technicalVariance  7.51   0.05    7.56
spectrumFilter            5.28   0.01    5.30
* 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: 1 WARNING, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-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_1.24.0.zip
* DONE (clippda)

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

nameusersystemelapsed
ZvaluescasesVcontrolsPlots0.070.000.34
ZvaluesfrommultinomPlots0.610.060.67
aclinicalProteomicsData-class0.070.010.10
aclinicalProteomicsData-methods0.210.160.35
betweensampleVariance1.450.021.47
checkNo.replicates0.080.040.13
clippda-package78.67 0.4179.08
f000
fisherInformation0.090.020.11
liverRawData0.020.000.01
liver_pheno000
liverdata4.750.004.75
mostSimilarTwo000
negativeIntensitiesCorrection2.80.02.8
phenoDataFrame0.120.000.12
pheno_urine0.020.000.02
preProcRepeatedPeakData6.260.036.30
proteomicsExprsData0.270.010.28
proteomicspData0.110.020.13
replicateCorrelations5.360.015.37
sampleClusteredData1.570.021.58
sampleSize51.04 0.0351.08
sampleSize3DscatterPlots0.020.000.01
sampleSizeContourPlots0.030.000.04
sampleSizeParameters25.12 0.0625.18
sample_technicalVariance7.180.007.18
spectrumFilter3.780.023.79
ztwo000

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

nameusersystemelapsed
ZvaluescasesVcontrolsPlots0.070.000.06
ZvaluesfrommultinomPlots0.730.000.73
aclinicalProteomicsData-class0.090.000.10
aclinicalProteomicsData-methods0.220.090.31
betweensampleVariance1.910.001.91
checkNo.replicates0.160.000.15
clippda-package68.28 0.4768.75
f000
fisherInformation0.090.000.10
liverRawData0.020.000.01
liver_pheno000
liverdata3.50.03.5
mostSimilarTwo000
negativeIntensitiesCorrection1.260.021.28
phenoDataFrame0.080.000.08
pheno_urine000
preProcRepeatedPeakData3.410.033.44
proteomicsExprsData0.280.000.28
proteomicspData0.120.000.12
replicateCorrelations3.820.013.83
sampleClusteredData1.370.001.38
sampleSize42.56 0.1942.75
sampleSize3DscatterPlots0.020.020.03
sampleSizeContourPlots0.110.000.11
sampleSizeParameters21.33 0.0621.39
sample_technicalVariance7.510.057.56
spectrumFilter5.280.015.30
ztwo000