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Package 195/472HostnameOS / ArchBUILDCHECKBUILD BIN
genoset 1.1.0
Peter M. Haverty
Snapshot Date: 2011-06-21 19:21:48 -0700 (Tue, 21 Jun 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genoset
Last Changed Rev: 54802 / Revision: 56351
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / 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 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: genoset
Version: 1.1.0
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genoset_1.1.0.tar.gz
StartedAt: 2011-06-22 03:17:01 -0700 (Wed, 22 Jun 2011)
EndedAt: 2011-06-22 03:19:43 -0700 (Wed, 22 Jun 2011)
EllapsedTime: 161.4 seconds
RetCode: 0
Status:  OK 
CheckDir: genoset.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/genoset.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genoset/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genoset’ version ‘1.1.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘genoset’ 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 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘prove.pmh.utils.R’
  Comparing ‘prove.pmh.utils.Rout’ to ‘prove.pmh.utils.Rout.save’ ... OK
 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

genoset.Rcheck/00install.out:

* installing *source* package ‘genoset’ ...
** libs
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c genoset.c -o genoset.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 genoset.so genoset.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/genoset.Rcheck/genoset/libs/i386
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.


Attaching package: ‘IRanges’

The following object(s) are masked from ‘package:Biobase’:

    updateObject

The following object(s) are masked from ‘package:base’:

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union


**************************************************************************
   The plan to change the data format for CNA object has been postponed   
 in order to ensure backward compatibility with older versions of DNAcopy 
**************************************************************************

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘genoset.Rnw’ 
** testing if installed package can be loaded

* DONE (genoset)

genoset.Rcheck/genoset-Ex.timings:

nameusersystemelapsed
BAFSet0.6570.0070.737
BAFSet.to.ExpressionSets0.2430.0080.279
CNSet0.2870.0010.307
GenoSet0.2810.0010.298
baf0.0540.0190.093
baf2mbaf0.0400.0020.043
bafset-class0.3350.0030.369
boundingIndices0.0010.0000.002
boundingIndices20.0010.0010.001
chr-methods0.2720.0010.286
chrIndices-methods0.0310.0010.036
chrInfo0.0460.0010.049
chrOrder0.0010.0000.002
cn0.0540.0190.079
cnset-class0.2720.0010.274
colMeans0.0160.0000.016
gcCorrect0.0080.0010.009
genoPlot0.0970.0020.099
genoPos-methods0.0860.0200.113
genomeAxis0.0610.0020.064
genomeOrder0.0450.0100.056
genoset-class0.2730.0020.276
genoset-methods1.0730.0231.106
initGenoSet0.2730.0010.275
isGenomeOrder0.1520.0030.166
locData0.0280.0010.029
lrr0.0530.0190.076
modeCenter0.0100.0020.012
orderedChrs0.3240.0020.345
pos0.3800.0050.422
rangeSampleMeans0.2670.0030.274
runCBS4.0540.0254.128
segTable3.4590.0243.510
segs2Rle3.0180.0183.059
segs2RleDataFrame3.4000.0203.449
subsetAssayData0.0280.0020.030
uniqueChrs0.2660.0010.277
universe0.0300.0020.033