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Package 258/658HostnameOS / ArchBUILDCHECKBUILD BIN
GeneSelector 2.9.0
Martin Slawski
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneSelector
Last Changed Rev: 70052 / Revision: 74774
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: GeneSelector
Version: 2.9.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneSelector_2.9.0.tar.gz
StartedAt: 2013-03-25 02:40:02 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 02:41:38 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 95.7 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneSelector.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GeneSelector.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GeneSelector/DESCRIPTION' ... OK
* this is package 'GeneSelector' version '2.9.0'
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'GeneSelector' can be installed ... [7s/7s] OK
* 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
* 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
HeatmapRankings,RepeatedRanking: warning in heatmap(Rmat[ind, , drop =
  FALSE], hclustfun = hclust, labCol = colnames(Rmat), scale = "none",
  labRow = character(), col = terrain.colors(20), mar = c(8, 8)):
  partial argument match of 'mar' to 'margins'
RankingPermutation,matrix-numeric: no visible binding for global
  variable 'test'
RepeatRanking,GeneRanking-BootMatrix-missing-missing-missing: no
  visible binding for global variable 'RankingBstat'
RepeatRanking,GeneRanking-FoldMatrix-ANY-missing-missing: no visible
  binding for global variable 'RankingBstat'
RepeatRanking,GeneRanking-missing-missing-ANY-ANY: no visible binding
  for global variable 'RankingBstat'
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'preamble.tex'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [29s/29s] OK
* 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

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/GeneSelector.Rcheck/00check.log'
for details.

GeneSelector.Rcheck/00install.out:

* installing *source* package 'GeneSelector' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c kendall.c -o kendall.o
kendall.c: In function 'kendall':
kendall.c:3: warning: 'tau' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c mcfour.c -o mcfour.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c mct.c -o mct.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GeneSelector.so kendall.o mcfour.o mct.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/GeneSelector.Rcheck/GeneSelector/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'GeneSelector.rnw' 
** testing if installed package can be loaded
* DONE (GeneSelector)

GeneSelector.Rcheck/GeneSelector-Ex.timings:

nameusersystemelapsed
AggregateMC0.7850.1370.933
AggregatePenalty0.8870.1421.039
AggregateSVD0.4220.1390.571
AggregateSimple0.4530.1300.610
GeneSelector3.4860.6664.232
GenerateBootMatrix0.1100.0150.130
GenerateFoldMatrix0.0980.0170.116
GetStabilityDistance0.2940.1390.446
GetStabilityOverlap0.3840.1540.552
GetStabilityUnion0.3930.1880.605
HeatmapRankings2.7780.5473.399
MergeMethods3.0270.5433.636
RankingBaldiLong0.1280.0220.151
RankingEbam0.7680.1750.960
RankingFC0.0920.0210.124
RankingFoxDimmic0.0580.0180.079
RankingLimma0.9690.0551.034
RankingPermutation1.4460.0271.477
RankingSam2.2960.4912.834
RankingShrinkageT0.1270.0170.146
RankingSoftthresholdT0.1850.0240.212
RankingTstat0.0290.0180.056
RankingWelchT0.0350.0230.059
RankingWilcEbam0.5290.0360.567
RankingWilcoxon0.2810.0210.302
RepeatRanking2.3440.5472.949
toydata0.0180.0100.029