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Package 240/609HostnameOS / ArchBUILDCHECKBUILD BIN
GeneSelector 2.8.0
Martin Slawski
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/GeneSelector
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: GeneSelector
Version: 2.8.0
Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings GeneSelector_2.8.0.tar.gz
StartedAt: 2013-03-25 01:26:26 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 01:27:39 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 73.5 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneSelector.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/GeneSelector.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneSelector/DESCRIPTION’ ... OK
* this is package ‘GeneSelector’ version ‘2.8.0’
* 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 whether package ‘GeneSelector’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 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 ... 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
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/GeneSelector.Rcheck/00check.log’
for details.

GeneSelector.Rcheck/00install.out:

* installing *source* package ‘GeneSelector’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c kendall.c -o kendall.o
kendall.c: In function ‘kendall’:
kendall.c:7:10: warning: ‘tau’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c mcfour.c -o mcfour.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.11-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c mct.c -o mct.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o GeneSelector.so kendall.o mcfour.o mct.o -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-bioc/meat/GeneSelector.Rcheck/GeneSelector/libs
** 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
AggregateMC1.0360.0161.078
AggregatePenalty0.9480.0120.977
AggregateSVD0.8240.0000.836
AggregateSimple0.580.000.58
GeneSelector3.3200.0603.662
GenerateBootMatrix0.0640.0000.067
GenerateFoldMatrix0.0520.0000.054
GetStabilityDistance0.2200.0120.229
GetStabilityOverlap0.4000.0000.402
GetStabilityUnion0.3320.0040.336
HeatmapRankings2.5200.0242.549
MergeMethods2.2040.0282.233
RankingBaldiLong0.0720.0040.076
RankingEbam0.5440.0160.560
RankingFC0.0120.0000.011
RankingFoxDimmic0.0360.0000.036
RankingLimma0.5840.0040.597
RankingPermutation0.9040.0040.996
RankingSam1.5530.0201.573
RankingShrinkageT0.1160.0000.116
RankingSoftthresholdT0.1560.0000.157
RankingTstat0.0080.0040.014
RankingWelchT0.160.000.16
RankingWilcEbam0.2280.0000.228
RankingWilcoxon0.1520.0000.153
RepeatRanking1.6880.0041.697
toydata0.0080.0000.009