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Package 374/419HostnameOS / ArchBUILDCHECKBUILD BIN
SIM 1.18.0
Maarten van Iterson
Snapshot Date: 2011-04-06 23:24:01 -0700 (Wed, 06 Apr 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/SIM
Last Changed Rev: 50293 / Revision: 54588
Last Changed Date: 2010-10-17 22:34:23 -0700 (Sun, 17 Oct 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 

Summary

Package: SIM
Version: 1.18.0
Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings SIM_1.18.0.tar.gz
StartedAt: 2011-04-07 09:03:11 -0700 (Thu, 07 Apr 2011)
EndedAt: 2011-04-07 09:04:37 -0700 (Thu, 07 Apr 2011)
EllapsedTime: 85.6 seconds
RetCode: 0
Status:  OK 
CheckDir: SIM.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/SIM.Rcheck’
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SIM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SIM’ version ‘1.18.0’
* 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) and $(LAPACK_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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.7-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c withinWindow.c -o withinWindow.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o SIM.so withinWindow.o -L/home/biocbuild/bbs-2.7-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.7-bioc/meat/SIM.Rcheck/SIM/libs
** 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-package16.437 0.06016.516
acgh.data0.0040.0000.002
assemble.data0.0280.0040.031
chrom.table0.0040.0000.003
expr.data0.0040.0000.002
getoverlappingregions000
impute.nas.by.surrounding000
integrated.analysis13.417 0.01213.430
link.metadata000
samples0.0040.0000.001
sim.plot.overlapping.indep.dep.features0.0800.0040.086
sim.plot.pvals.on.genome0.2800.0200.302
sim.plot.pvals.on.region0.0080.0000.007
sim.plot.zoom.in0.6280.0000.626
sim.plot.zscore.heatmap0.7320.0080.741
sim.update.chrom.table000
tabulate.pvals0.0040.0000.007
tabulate.top.dep.features0.0280.0000.030
tabulate.top.indep.features0.0200.0040.023