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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: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings SIM_1.20.0.tar.gz
StartedAt: 2011-10-20 14:31:51 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 14:33:37 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 105.5 seconds
RetCode: 0
Status:  OK 
CheckDir: SIM.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/SIM.Rcheck’
* using R version 2.13.2 (2011-09-30)
* 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 ‘1.20.0’
* 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 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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-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-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/SIM.Rcheck/SIM/libs
** 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.ID000
SIM-package19.481 0.08820.075
acgh.data0.0040.0000.003
assemble.data0.1560.0080.165
chrom.table0.0000.0000.004
expr.data0.0000.0000.002
getoverlappingregions000
impute.nas.by.surrounding000
integrated.analysis15.513 0.00815.593
link.metadata000
samples0.0040.0000.003
sim.plot.overlapping.indep.dep.features0.0880.0080.115
sim.plot.pvals.on.genome0.3280.0440.451
sim.plot.pvals.on.region0.0080.0040.011
sim.plot.zoom.in0.6040.0080.776
sim.plot.zscore.heatmap0.8240.0041.356
sim.update.chrom.table0.0000.0000.001
tabulate.pvals0.0080.0000.008
tabulate.top.dep.features0.0360.0000.035
tabulate.top.indep.features0.0280.0040.031