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Package 385/436HostnameOS / ArchBUILDCHECKBUILD BIN
SIM 1.19.0
Maarten van Iterson
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SIM
Last Changed Rev: 50725 / Revision: 53255
Last Changed Date: 2010-11-06 14:29:12 -0700 (Sat, 06 Nov 2010)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.4) / i386  OK [ OK ] OK 

Summary

Package: SIM
Version: 1.19.0
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SIM_1.19.0.tar.gz
StartedAt: 2011-02-24 16:55:21 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 16:56:50 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 89.4 seconds
RetCode: 0
Status:  OK 
CheckDir: SIM.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/SIM.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'SIM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SIM' version '1.19.0'
* 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 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 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 data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

SIM.Rcheck/00install.out:

* installing *source* package 'SIM' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c withinWindow.c -o withinWindow.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 SIM.so withinWindow.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/SIM.Rcheck/SIM/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Loading required package: SparseM
Package SparseM (0.86) loaded.
	   To cite, see citation("SparseM")


Attaching package: 'SparseM'

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

    backsolve

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (SIM)

SIM.Rcheck/SIM-Ex.timings:

nameusersystemelapsed
RESOURCERER.annotation.to.ID000
SIM-package18.352 0.11718.513
acgh.data0.0030.0010.004
assemble.data0.0360.0040.040
chrom.table0.0030.0010.004
expr.data0.0030.0010.003
getoverlappingregions000
impute.nas.by.surrounding000
integrated.analysis14.913 0.05914.972
link.metadata0.0000.0010.000
samples0.0020.0000.002
sim.plot.overlapping.indep.dep.features0.0920.0040.096
sim.plot.pvals.on.genome0.3130.0280.342
sim.plot.pvals.on.region0.0080.0010.009
sim.plot.zoom.in0.5270.0080.535
sim.plot.zscore.heatmap0.6510.0140.665
sim.update.chrom.table000
tabulate.pvals0.0080.0010.008
tabulate.top.dep.features0.0310.0020.033
tabulate.top.indep.features0.0270.0020.029