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BioC 2.12: CHECK report for SpeCond on moscato2

This page was generated on 2013-10-09 09:38:44 -0700 (Wed, 09 Oct 2013).

Package 610/671HostnameOS / ArchBUILDCHECKBUILD BIN
SpeCond 1.14.0
Florence Cavalli
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/SpeCond
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ WARNINGS ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: SpeCond
Version: 1.14.0
Command: rm -rf SpeCond.buildbin-libdir && mkdir SpeCond.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SpeCond.buildbin-libdir SpeCond_1.14.0.tar.gz >SpeCond-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=SpeCond.buildbin-libdir --install="check:SpeCond-install.out" --force-multiarch --no-vignettes --timings SpeCond_1.14.0.tar.gz && mv SpeCond.buildbin-libdir/* SpeCond.Rcheck/ && rmdir SpeCond.buildbin-libdir
StartedAt: 2013-10-09 04:18:20 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 04:22:59 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 278.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: SpeCond.Rcheck
Warnings: 1

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/SpeCond.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SpeCond/DESCRIPTION' ... OK
* this is package 'SpeCond' version '1.14.0'
* 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 ... WARNING
Found the following significant warnings:
  Warning: package 'fields' was built under R version 3.0.2
  Warning: package 'fields' was built under R version 3.0.2
  Warning: package 'fields' was built under R version 3.0.2
See 'E:/biocbld/bbs-2.12-bioc/meat/SpeCond.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package 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
* 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 for unstated dependencies in R code ... OK
* 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'
* 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 examples ...
** running examples for arch 'i386' ... [86s] OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
getFullHtmlSpeCondResult         10.25   0.49   11.32
getGeneHtmlPage                   9.58   0.39   10.20
writeSpeCondResult                8.07   0.02    8.08
SpeCond                           7.88   0.07    7.94
getProfile                        7.82   0.00    7.82
writeUniqueProfileSpecificResult  7.82   0.00    7.82
writeGeneResult                   7.31   0.01    7.33
getSpecificResult                 7.15   0.02    7.16
fitNoPriorWithExclusion           6.51   0.01    6.53
** running examples for arch 'x64' ... [90s] OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
getGeneHtmlPage                  10.24   0.32   10.59
getFullHtmlSpeCondResult         10.00   0.39   10.88
SpeCond                           9.30   0.03    9.33
writeUniqueProfileSpecificResult  8.30   0.07    8.38
fitNoPriorWithExclusion           8.24   0.00    8.24
writeSpeCondResult                8.05   0.00    8.07
getProfile                        7.11   0.03    7.15
getSpecificResult                 6.79   0.00    6.78
writeGeneResult                   6.71   0.02    6.73
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  'E:/biocbld/bbs-2.12-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
Warning: package 'fields' was built under R version 3.0.2
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: package 'fields' was built under R version 3.0.2

install for x64

* installing *source* package 'SpeCond' ...
** testing if installed package can be loaded
Warning: package 'fields' was built under R version 3.0.2
* MD5 sums
packaged installation of 'SpeCond' as SpeCond_1.14.0.zip
* DONE (SpeCond)