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Package 211/514HostnameOS / ArchBUILDCHECKBUILD BIN
genoset 1.2.0
Peter M. Haverty
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/genoset
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: genoset
Version: 1.2.0
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings genoset_1.2.0.tar.gz
StartedAt: 2012-03-24 00:38:16 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 00:41:09 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 172.9 seconds
RetCode: 0
Status:  OK 
CheckDir: genoset.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/genoset.Rcheck’
* using R version 2.14.2 (2012-02-29)
* 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 ‘1.2.0’
* 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 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                old_size new_size compress
  genoset.RData    142Kb     32Kb       xz
* 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 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’ ...23,26d22
< Error in !all.equal(rownames(calls), rownames(baf)) : 
<   invalid argument type
< Error in checkEquals(gcCorrect(input.vector, gc), output.vector) : 
<   Mean relative difference: 1
 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-2.9-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-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/genoset.Rcheck/genoset/libs
** R
** data
** inst
** preparing package for lazy loading
** 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
BAFSet0.8960.0160.909
BAFSet.to.ExpressionSets0.1440.0040.148
CNSet0.1160.0000.114
GenoSet0.1040.0000.103
baf0.0240.0080.030
baf2mbaf0.0240.0000.027
bafset-class0.1880.0000.216
boundingIndices0.0000.0000.001
boundingIndices2000
chr-methods0.1040.0000.114
chrIndices-methods0.0120.0040.014
chrInfo0.0280.0040.029
chrOrder0.0000.0000.001
cn0.0240.0080.030
cnset-class0.1080.0000.110
colMeans0.0080.0000.013
convertToBigMatrix000
gcCorrect0.0040.0080.010
genoPlot0.0680.0040.074
genoPos-methods0.0400.0080.048
genomeAxis0.0400.0000.041
genomeorder0.6360.0000.638
genoset-class0.1000.0000.099
genoset-methods0.4840.0080.494
initGenoSet0.1080.0000.106
isGenomeOrder0.0240.0000.023
locData0.0320.0000.033
lrr0.0280.0080.034
modeCenter0.0080.0000.007
orderedChrs0.1200.0000.118
pos0.1160.0000.114
rangeSampleMeans0.0760.0000.077
readGenoSet000
runCBS2.3880.0002.396
segTable-methods2.1840.0002.194
segs2Rle2.1050.0082.124
segs2RleDataFrame2.0480.0042.075
subsetAssayData0.0120.0000.013
uniqueChrs0.1080.0000.107
universe0.0160.0000.014