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 3.1: CHECK report for clippda on moscato2

This page was generated on 2015-10-09 09:28:37 -0700 (Fri, 09 Oct 2015).

Package 172/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clippda 1.18.0
Stephen Nyangoma
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/clippda
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  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: 1.18.0
Command: rm -rf clippda.buildbin-libdir clippda.Rcheck && mkdir clippda.buildbin-libdir clippda.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clippda.buildbin-libdir clippda_1.18.0.tar.gz >clippda.Rcheck\00install.out 2>&1 && cp clippda.Rcheck\00install.out clippda-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=clippda.buildbin-libdir --install="check:clippda-install.out" --force-multiarch --no-vignettes --timings clippda_1.18.0.tar.gz
StartedAt: 2015-10-09 00:23:35 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 00:33:13 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 578.2 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 && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=clippda.buildbin-libdir clippda_1.18.0.tar.gz >clippda.Rcheck\00install.out 2>&1 && cp clippda.Rcheck\00install.out clippda-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=clippda.buildbin-libdir --install="check:clippda-install.out" --force-multiarch --no-vignettes --timings clippda_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/clippda.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.18.0'
* 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
ZvaluesfrommultinomPlots: no visible global function definition for
  'cloud'
* 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' ... [262s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
clippda-package          113.32   0.33  113.64
sampleSize                69.64   0.15   69.80
sampleSizeParameters      34.39   0.11   34.51
sample_technicalVariance  12.06   0.00   12.06
spectrumFilter             6.29   0.00    6.29
liverdata                  5.56   0.01    5.56
replicateCorrelations      5.50   0.00    5.51
** running examples for arch 'x64' ... [242s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
clippda-package          108.94   0.28  109.22
sampleSize                62.65   0.07   62.76
sampleSizeParameters      31.07   0.00   31.07
sample_technicalVariance   7.71   0.02    7.74
replicateCorrelations      5.45   0.00    5.44
liverdata                  5.40   0.00    5.40
* 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
  'E:/biocbld/bbs-3.1-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_1.18.0.zip
* DONE (clippda)

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

nameusersystemelapsed
ZvaluescasesVcontrolsPlots0.070.000.20
ZvaluesfrommultinomPlots0.860.020.87
aclinicalProteomicsData-class0.10.00.1
aclinicalProteomicsData-methods0.350.030.39
betweensampleVariance2.130.012.13
checkNo.replicates0.170.000.18
clippda-package113.32 0.33113.64
f000
fisherInformation0.150.020.17
liverRawData000
liver_pheno0.010.000.02
liverdata5.560.015.56
mostSimilarTwo000
negativeIntensitiesCorrection1.950.021.97
phenoDataFrame0.090.000.09
pheno_urine0.020.000.02
preProcRepeatedPeakData4.490.004.49
proteomicsExprsData0.230.000.24
proteomicspData0.100.000.09
replicateCorrelations5.500.005.51
sampleClusteredData2.530.002.52
sampleSize69.64 0.1569.80
sampleSize3DscatterPlots0.020.020.03
sampleSizeContourPlots0.030.000.03
sampleSizeParameters34.39 0.1134.51
sample_technicalVariance12.06 0.0012.06
spectrumFilter6.290.006.29
ztwo000

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

nameusersystemelapsed
ZvaluescasesVcontrolsPlots0.090.000.10
ZvaluesfrommultinomPlots0.980.000.99
aclinicalProteomicsData-class0.080.010.09
aclinicalProteomicsData-methods0.310.080.39
betweensampleVariance2.690.002.68
checkNo.replicates0.230.020.25
clippda-package108.94 0.28109.22
f000
fisherInformation0.120.000.12
liverRawData000
liver_pheno000
liverdata5.40.05.4
mostSimilarTwo000
negativeIntensitiesCorrection1.900.001.91
phenoDataFrame0.080.010.09
pheno_urine000
preProcRepeatedPeakData4.760.024.77
proteomicsExprsData0.230.000.24
proteomicspData0.090.020.11
replicateCorrelations5.450.005.44
sampleClusteredData1.890.001.89
sampleSize62.65 0.0762.76
sampleSize3DscatterPlots0.120.000.12
sampleSizeContourPlots0.050.000.05
sampleSizeParameters31.07 0.0031.07
sample_technicalVariance7.710.027.74
spectrumFilter4.340.004.34
ztwo000