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BioC 3.2: CHECK report for SpeCond on windows1.bioconductor.org

This page was generated on 2015-10-27 17:29:00 -0400 (Tue, 27 Oct 2015).

Package 1002/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpeCond 1.24.0
Florence Cavalli
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/SpeCond
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SpeCond
Version: 1.24.0
Command: rm -rf SpeCond.buildbin-libdir SpeCond.Rcheck && mkdir SpeCond.buildbin-libdir SpeCond.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SpeCond.buildbin-libdir SpeCond_1.24.0.tar.gz >SpeCond.Rcheck\00install.out 2>&1 && cp SpeCond.Rcheck\00install.out SpeCond-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=SpeCond.buildbin-libdir --install="check:SpeCond-install.out" --force-multiarch --no-vignettes --timings SpeCond_1.24.0.tar.gz
StartedAt: 2015-10-27 05:49:36 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 05:51:52 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 135.1 seconds
RetCode: 0
Status:  OK  
CheckDir: SpeCond.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SpeCond.buildbin-libdir SpeCond.Rcheck && mkdir SpeCond.buildbin-libdir SpeCond.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SpeCond.buildbin-libdir SpeCond_1.24.0.tar.gz >SpeCond.Rcheck\00install.out 2>&1 && cp SpeCond.Rcheck\00install.out SpeCond-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=SpeCond.buildbin-libdir --install="check:SpeCond-install.out" --force-multiarch --no-vignettes --timings SpeCond_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/SpeCond.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SpeCond/DESCRIPTION' ... OK
* this is package 'SpeCond' version '1.24.0'
* 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 'SpeCond' 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 ... OK
* 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
Packages in Depends field not imported from:
  'Biobase' 'fields' 'hwriter' 'mclust' 'methods'
  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
SpeCond: warning in getSpecificOutliersStep1(expressionMatrix, fit =
  fit1, param.detection = param.detection, multitest.correction.method
  = "BY", prefix.file = prefix.file, print.hist.pv = FALSE): partial
  argument match of 'fit' to 'fit1'
SpeCond: warning in getSpecificResult(expressionMatrix, fit = fit2,
  specificOutlierStep1 = specificOutlierStep1, param.detection =
  param.detection, multitest.correction.method =
  multitest.correction.method, prefix.file = prefix.file, print.hist.pv
  = print.hist.pv): partial argument match of 'fit' to 'fit2'
createSingleGeneHtmlPage: warning in matrix(c("color:#000DFE", NA), nr
  = 1, nc = 2): partial argument match of 'nr' to 'nrow'
createSingleGeneHtmlPage: warning in matrix(c("color:#000DFE", NA), nr
  = 1, nc = 2): partial argument match of 'nc' to 'ncol'
getExpressionpatternLegend: warning in matrix(" ", nr = 2, nc =
  1): partial argument match of 'nr' to 'nrow'
getExpressionpatternLegend: warning in matrix(" ", nr = 2, nc =
  1): partial argument match of 'nc' to 'ncol'
getHeatmap: warning in heatmap(M_values, scale = "none", margin = c(8,
  8), col = colors): partial argument match of 'margin' to 'margins'
getHeatmap: warning in heatmap(M_values, scale = "none", margin = c(8,
  8), col = colors, RowSideColors = colRowSide): partial argument match
  of 'margin' to 'margins'
getHeatmap: warning in heatmap(M_values[rownames(M_values) %in%
  probe_set, ], scale = "none", margin = c(8, 8), col = colors):
  partial argument match of 'margin' to 'margins'
getProfileHeatmap: warning in heatmap(M_profile, scale = "none", margin
  = c(8, 8), col = colors): partial argument match of 'margin' to
  'margins'
callMclustInStep2: no visible global function definition for 'Mclust'
callMclustInStep2: no visible global function definition for
  'priorControl'
createSingleGeneHtmlPage: no visible global function definition for
  'openPage'
createSingleGeneHtmlPage: no visible global function definition for
  'hwrite'
createSingleGeneHtmlPage: no visible global function definition for
  'closePage'
fitNoPriorWithExclusion : <anonymous>: no visible global function
  definition for 'Mclust'
fitPrior : <anonymous>: no visible global function definition for
  'Mclust'
fitPrior : <anonymous>: no visible global function definition for
  'priorControl'
getExpressionpatternLegend: no visible global function definition for
  'hwrite'
getFullHtmlSpeCondResult: no visible global function definition for
  'openPage'
getFullHtmlSpeCondResult: no visible global function definition for
  'hwrite'
getFullHtmlSpeCondResult: no visible global function definition for
  'hwriteImage'
getFullHtmlSpeCondResult: no visible global function definition for
  'closePage'
getGeneHtmlPage: no visible global function definition for 'openPage'
getGeneHtmlPage: no visible global function definition for 'hwrite'
getGeneHtmlPage: no visible global function definition for 'closePage'
getHeatmap: no visible global function definition for 'colorbar.plot'
getMatrixFromExpressionSet: no visible global function definition for
  'exprs'
plotNormalMixture: no visible global function definition for
  'hwriteImage'
* 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' ... [39s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
getGeneHtmlPage 5.02    0.3    5.31
** running examples for arch 'x64' ... [44s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
getFullHtmlSpeCondResult 4.94   0.37    5.39
getGeneHtmlPage          4.84   0.24    5.11
* 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: 2 NOTEs
See
  'C:/biocbld/bbs-3.2-bioc/meat/SpeCond.Rcheck/00check.log'
for details.


SpeCond.Rcheck/00install.out:


install for i386

* installing *source* package 'SpeCond' ...
** 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 'SpeCond' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SpeCond' as SpeCond_1.24.0.zip
* DONE (SpeCond)

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

nameusersystemelapsed
SpeCond3.470.033.50
createParameterMatrix000
expSetSpeCondExample0.020.000.01
expressionSpeCondExample000
fitNoPriorWithExclusion2.950.002.96
fitPrior1.920.001.92
getDefaultParameter000
getFullHtmlSpeCondResult4.530.454.98
getGeneHtmlPage5.020.305.31
getMatrixFromExpressionSet0.180.000.19
getProfile3.600.013.61
getSpecificOutliersStep12.030.022.05
getSpecificResult3.060.003.06
simulatedSpeCondData000
writeGeneResult3.270.003.27
writeSpeCondResult3.480.003.48
writeUniqueProfileSpecificResult3.140.003.14

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

nameusersystemelapsed
SpeCond4.090.024.14
createParameterMatrix000
expSetSpeCondExample000
expressionSpeCondExample000
fitNoPriorWithExclusion3.480.003.48
fitPrior2.330.002.33
getDefaultParameter000
getFullHtmlSpeCondResult4.940.375.39
getGeneHtmlPage4.840.245.11
getMatrixFromExpressionSet0.270.000.27
getProfile3.860.003.86
getSpecificOutliersStep12.40.02.4
getSpecificResult4.020.004.02
simulatedSpeCondData000
writeGeneResult3.690.003.69
writeSpeCondResult3.890.003.89
writeUniqueProfileSpecificResult3.730.003.73