Package: SIM

Version: 1.21.0

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch SIM_1.21.0.tar.gz

StartedAt: 2011-07-07 03:36:25 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 03:38:09 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 103.9 seconds

RetCode: 0

Status:  OK

CheckDir: SIM.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/SIM.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SIM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SIM' version '1.21.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'SIM' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
assemble.data: no visible binding for global variable 'chrom.table'
convertGenomicRegion: no visible binding for global variable
  'chrom.table'
link.metadata: no visible binding for global variable 'expr.data'
link.metadata: no visible binding for global variable 'hgu133plus2CHR'
link.metadata: no visible binding for global variable
  'hgu133plus2CHRLOC'
link.metadata: no visible binding for global variable
  'hgu133plus2SYMBOL'
plotCytobands: no visible binding for global variable 'chrom.table'
sim.plot.pvals.on.genome: no visible binding for global variable
  'chrom.table'
sim.update.chrom.table: no visible global function definition for
  'dbConnect'
sim.update.chrom.table: no visible global function definition for
  'MySQL'
sim.update.chrom.table: no visible global function definition for
  'dbGetQuery'
* 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 examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'RColorBrewer'
* 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

* installing *source* package 'SIM' ...
** libs
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c withinWindow.c -o withinWindow.o
gcc -shared -s -static-libgcc -o SIM.dll tmp.def withinWindow.o -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/SIM.Rcheck/SIM/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Loading required package: SparseM
Package SparseM (0.89) loaded.
	   To cite, see citation("SparseM")


Attaching package: 'SparseM'

The following object(s) are masked from 'package:base':

    backsolve

Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'SIM.Rnw' using 'latin1' 
** testing if installed package can be loaded

* DONE (SIM)

name	user	system	elapsed
RESOURCERER.annotation.to.ID	0	0	0
SIM-package	17.44	0.11	17.67
acgh.data	0.01	0.00	0.02
assemble.data	0.05	0.00	0.04
chrom.table	0	0	0
expr.data	0	0	0
getoverlappingregions	0	0	0
impute.nas.by.surrounding	0	0	0
integrated.analysis	13.52	0.02	13.56
link.metadata	0	0	0
samples	0.01	0.00	0.02
sim.plot.overlapping.indep.dep.features	0.10	0.00	0.11
sim.plot.pvals.on.genome	0.31	0.14	0.45
sim.plot.pvals.on.region	0	0	0
sim.plot.zoom.in	0.58	0.00	0.58
sim.plot.zscore.heatmap	0.82	0.00	0.83
sim.update.chrom.table	0	0	0
tabulate.pvals	0	0	0
tabulate.top.dep.features	0.04	0.00	0.03
tabulate.top.indep.features	0.02	0.00	0.01