Back to the "Multiple platform build/check report" A  B [C] D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.5: CHECK report for clippda on tokay2

This page was generated on 2017-10-18 14:20:30 -0400 (Wed, 18 Oct 2017).

Package 227/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clippda 1.26.0
Stephen Nyangoma
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/clippda
Branch: RELEASE_3_5
Last Commit: b7ca8e8
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: clippda
Version: 1.26.0
Command: rm -rf clippda.buildbin-libdir clippda.Rcheck && mkdir clippda.buildbin-libdir clippda.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clippda.buildbin-libdir clippda_1.26.0.tar.gz >clippda.Rcheck\00install.out 2>&1 && cp clippda.Rcheck\00install.out clippda-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=clippda.buildbin-libdir --install="check:clippda-install.out" --force-multiarch --no-vignettes --timings clippda_1.26.0.tar.gz
StartedAt: 2017-10-17 22:46:27 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 22:53:52 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 445.8 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-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clippda.buildbin-libdir clippda_1.26.0.tar.gz >clippda.Rcheck\00install.out 2>&1 && cp clippda.Rcheck\00install.out clippda-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=clippda.buildbin-libdir --install="check:clippda-install.out" --force-multiarch --no-vignettes --timings clippda_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/clippda.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '1.26.0'
* 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          81.23   0.51   81.75
sampleSize               45.90   0.06   45.96
sampleSizeParameters     21.96   0.03   21.98
sample_technicalVariance  5.81   0.00    5.81
replicateCorrelations     5.53   0.02    5.55
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
clippda-package          75.04   0.29   75.35
sampleSize               45.55   0.16   45.70
sampleSizeParameters     23.29   0.20   23.50
sample_technicalVariance  6.89   0.02    6.91
liverdata                 5.09   0.00    5.09
* 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-3.5-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_1.26.0.zip
* DONE (clippda)

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

nameusersystemelapsed
ZvaluescasesVcontrolsPlots0.050.011.86
ZvaluesfrommultinomPlots0.940.050.99
aclinicalProteomicsData-class0.10.00.1
aclinicalProteomicsData-methods0.220.160.37
betweensampleVariance1.540.031.58
checkNo.replicates0.130.000.13
clippda-package81.23 0.5181.75
f000
fisherInformation0.080.000.07
liverRawData000
liver_pheno000
liverdata4.240.014.25
mostSimilarTwo000
negativeIntensitiesCorrection1.530.001.53
phenoDataFrame0.060.020.08
pheno_urine0.000.020.02
preProcRepeatedPeakData3.470.003.46
proteomicsExprsData0.150.010.18
proteomicspData0.080.000.07
replicateCorrelations5.530.025.55
sampleClusteredData1.530.001.53
sampleSize45.90 0.0645.96
sampleSize3DscatterPlots0.030.000.03
sampleSizeContourPlots0.010.020.03
sampleSizeParameters21.96 0.0321.98
sample_technicalVariance5.810.005.81
spectrumFilter3.200.003.21
ztwo000

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

nameusersystemelapsed
ZvaluescasesVcontrolsPlots0.080.000.18
ZvaluesfrommultinomPlots0.920.050.96
aclinicalProteomicsData-class0.070.010.09
aclinicalProteomicsData-methods0.240.110.35
betweensampleVariance1.890.021.90
checkNo.replicates0.190.000.19
clippda-package75.04 0.2975.35
f000
fisherInformation0.120.030.16
liverRawData0.020.000.01
liver_pheno0.000.020.02
liverdata5.090.005.09
mostSimilarTwo000
negativeIntensitiesCorrection1.310.001.31
phenoDataFrame0.060.020.08
pheno_urine0.020.000.01
preProcRepeatedPeakData3.140.013.16
proteomicsExprsData0.150.000.15
proteomicspData0.080.020.10
replicateCorrelations3.640.013.65
sampleClusteredData1.340.001.35
sampleSize45.55 0.1645.70
sampleSize3DscatterPlots0.060.000.06
sampleSizeContourPlots0.050.000.05
sampleSizeParameters23.29 0.2023.50
sample_technicalVariance6.890.026.91
spectrumFilter4.600.004.59
ztwo000