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Package 192/462HostnameOS / ArchBUILDCHECKBUILD BIN
genoset 1.1.0
Peter M. Haverty
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genoset
Last Changed Rev: 54802 / Revision: 55359
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 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: genoset
Version: 1.1.0
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings genoset_1.1.0.tar.gz
StartedAt: 2011-05-09 13:45:46 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 13:48:19 -0700 (Mon, 09 May 2011)
EllapsedTime: 152.8 seconds
RetCode: 0
Status:  OK  
CheckDir: genoset.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/genoset.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 ... NOTE
Package which this enhances but not available for checking: multicore
* 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 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 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
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include"          -O3 -Wall  -std=gnu99 -c genoset.c -o genoset.o
gcc -shared -s -static-libgcc -o genoset.dll tmp.def genoset.o -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/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
BAFSet0.480.000.49
BAFSet.to.ExpressionSets0.160.000.15
CNSet0.180.000.19
GenoSet0.180.000.17
baf0.030.000.03
baf2mbaf0.010.010.03
bafset-class0.210.000.21
boundingIndices000
boundingIndices2000
chr-methods0.170.000.18
chrIndices-methods0.030.000.04
chrInfo0.030.000.03
chrOrder000
cn0.020.000.04
cnset-class0.170.000.18
colMeans0.010.000.01
gcCorrect0.020.000.06
genoPlot0.060.000.11
genoPos-methods0.060.000.07
genomeAxis0.050.000.04
genomeOrder0.030.000.03
genoset-class0.170.000.18
genoset-methods0.640.020.65
initGenoSet0.180.000.17
isGenomeOrder0.100.000.09
locData0.010.000.02
lrr0.050.000.05
modeCenter0.000.000.06
orderedChrs0.190.000.19
pos0.180.000.18
rangeSampleMeans0.190.000.19
runCBS4.580.004.59
segTable3.860.003.88
segs2Rle3.480.003.48
segs2RleDataFrame3.720.003.77
subsetAssayData0.020.000.01
uniqueChrs0.170.000.18
universe0.010.000.01