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Package 625/658HostnameOS / ArchBUILDCHECKBUILD BIN
tilingArray 1.37.0
Zhenyu Xu
Snapshot Date: 2013-03-23 17:02:20 -0700 (Sat, 23 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/tilingArray
Last Changed Rev: 70052 / Revision: 74756
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: tilingArray
Version: 1.37.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch tilingArray_1.37.0.tar.gz
StartedAt: 2013-03-24 10:48:59 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 10:52:13 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 194.6 seconds
RetCode: 0
Status:  OK 
CheckDir: tilingArray.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/tilingArray.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'tilingArray/DESCRIPTION' ... OK
* this is package 'tilingArray' version '1.37.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'tilingArray' can be installed ... [19s/20s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ... OK
* 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 compiled code ... OK
* checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'Makefile'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [12s/12s] OK
* checking for unstated dependencies in vignettes ... OK
* 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/tilingArray.Rcheck/00check.log'
for details.

tilingArray.Rcheck/00install.out:

* installing *source* package 'tilingArray' ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c findsegments.c -o findsegments.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c sampleStep.c -o sampleStep.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o tilingArray.so findsegments.o sampleStep.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/tilingArray.Rcheck/tilingArray/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'assessNorm.Rnw' 
   'costMatrix.Rnw' 
   'findsegments.Rnw' 
   'plotAlongChrom.Rnw' 
   'segmentation.Rnw' 
** testing if installed package can be loaded
* DONE (tilingArray)

tilingArray.Rcheck/tilingArray-Ex.timings:

nameusersystemelapsed
PMindex0.0100.0040.015
class-segmentation0.1050.0090.115
comparisonPlot0.0050.0030.009
costMatrix0.1150.0230.140
findsegments0.0070.0020.009
gffSub0.2130.0160.229
normalizeByReference0.0080.0030.011
otherStrand0.0070.0030.011
plotAlongChrom0.3360.0170.353
plotAlongChromLegend0.0060.0000.006
plotSegmentationHeatmap0.1750.0120.190
plotpenLL0.0660.0060.078
posMin0.0130.0030.016
qcPlots0.0130.0030.016
readCel2eSet0.0200.0050.025
sampleStep0.0160.0030.019
segChrom0.0120.0020.014
segment0.0120.0020.014
segnf0.4660.0080.476