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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: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch SIM_1.20.0.tar.gz
StartedAt: 2011-10-20 16:41:54 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 16:43:34 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 100.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: SIM.Rcheck
Warnings: 1

Command output

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/SIM.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-pc-mingw32 (64-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 '1.20.0'
* 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 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' ... WARNING
Package vignette(s) without corresponding PDF:
   SIM.Rnw

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.8-bioc/meat/SIM.Rcheck/00check.log'
for details

SIM.Rcheck/00install.out:

* installing *source* package 'SIM' ...
** libs
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -std=gnu99 -c withinWindow.c -o withinWindow.o
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o SIM.dll tmp.def withinWindow.o -LD:/biocbld/BBS-2˜1.8-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.8-bioc/meat/SIM.Rcheck/SIM/libs/x64
** R
** data
** inst
** preparing package for lazy loading
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 ...
** testing if installed package can be loaded

* DONE (SIM)

SIM.Rcheck/SIM-Ex.timings:

nameusersystemelapsed
RESOURCERER.annotation.to.ID000
SIM-package18.38 0.0718.45
acgh.data000
assemble.data0.050.000.05
chrom.table000
expr.data000
getoverlappingregions000
impute.nas.by.surrounding000
integrated.analysis15.11 0.0015.11
link.metadata000
samples000
sim.plot.overlapping.indep.dep.features0.100.010.11
sim.plot.pvals.on.genome0.390.030.42
sim.plot.pvals.on.region000
sim.plot.zoom.in0.640.000.64
sim.plot.zscore.heatmap0.800.020.81
sim.update.chrom.table000
tabulate.pvals000
tabulate.top.dep.features0.040.000.03
tabulate.top.indep.features0.010.010.03