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Package 415/467HostnameOS / ArchBUILDCHECKBUILD BIN
SIM 1.20.0
Maarten van Iterson
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/SIM
Last Changed Rev: 54800 / Revision: 59457
Last Changed Date: 2011-04-13 15:27:35 -0700 (Wed, 13 Apr 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: SIM
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SIM_1.20.0.tar.gz
StartedAt: 2011-10-20 17:24:32 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 17:26:48 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 136.4 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 2.13.2 (2011-09-30)
* 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 '1.20.0'
* checking package namespace 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 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 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
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 sizes of PDF files under inst/doc ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'SIM.pdf' from 742Kb to 285Kb
  consider running tools::compactPDF() on these files
* 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

SIM.Rcheck/00install.out:

* installing *source* package 'SIM' ...
** libs
*** arch - i386
gcc-4.2 -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-4.2 -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
** 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.ID0.0000.0000.001
SIM-package24.668 0.44925.352
acgh.data0.0040.0010.005
assemble.data0.0460.0070.056
chrom.table0.0040.0000.005
expr.data0.0050.0010.006
getoverlappingregions0.0000.0000.001
impute.nas.by.surrounding000
integrated.analysis20.135 0.17420.515
link.metadata000
samples0.0020.0010.003
sim.plot.overlapping.indep.dep.features0.1270.0110.140
sim.plot.pvals.on.genome0.4330.0730.516
sim.plot.pvals.on.region0.0100.0010.012
sim.plot.zoom.in0.6740.1280.809
sim.plot.zscore.heatmap0.8230.1450.974
sim.update.chrom.table0.0000.0000.001
tabulate.pvals0.0100.0010.010
tabulate.top.dep.features0.0430.0050.049
tabulate.top.indep.features0.0320.0030.035