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Package 192/467HostnameOS / ArchBUILDCHECKBUILD BIN
genoset 1.0.0
Peter M. Haverty
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/genoset
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: genoset
Version: 1.0.0
Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings genoset_1.0.0.tar.gz
StartedAt: 2011-10-20 12:53:36 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 12:55:33 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 116.9 seconds
RetCode: 0
Status:  OK 
CheckDir: genoset.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/genoset.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 ‘genoset/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genoset’ version ‘1.0.0’
* checking package namespace 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 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 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 -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c genoset.c -o genoset.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o genoset.so genoset.o -L/home/biocbuild/bbs-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/genoset.Rcheck/genoset/libs
** R
** data
** inst
** preparing package for lazy loading

**************************************************************************
   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 ...
** testing if installed package can be loaded

* DONE (genoset)

genoset.Rcheck/genoset-Ex.timings:

nameusersystemelapsed
BAFSet0.5440.0040.547
BAFSet.to.ExpressionSets0.1760.0000.173
CNSet0.3640.0000.364
GenoSet0.2000.0000.199
baf0.0200.0120.032
baf2mbaf0.0240.0040.025
bafset-class0.2440.0000.244
boundingIndices0.0000.0000.001
boundingIndices2000
chr-methods0.20.00.2
chrIndices-methods0.0160.0000.015
chrInfo0.0280.0000.027
chrOrder0.0000.0000.001
cn0.0200.0080.029
cnset-class0.2000.0000.199
colMeans0.0120.0000.011
gcCorrect0.0080.0000.006
genoPlot0.0640.0000.065
genoPos-methods0.0440.0040.047
genomeAxis0.0360.0000.042
genomeOrder0.0200.0040.027
genoset-class0.2120.0000.212
genoset-methods0.7560.0120.767
initGenoSet0.2080.0000.207
isGenomeOrder0.1040.0040.108
locData0.0120.0000.014
lrr0.0200.0080.029
modeCenter0.0000.0040.007
orderedChrs0.2400.0000.243
pos0.2240.0000.229
rangeSampleMeans0.2160.0000.227
runCBS2.4440.0082.509
segTable2.1600.0042.256
segs2Rle1.8280.0042.495
segs2RleDataFrame2.2490.0362.345
subsetAssayData0.0120.0000.013
uniqueChrs0.2040.0000.207
universe0.0120.0000.015