Package: genoset

Version: 1.8.7

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genoset_1.8.7.tar.gz

StartedAt: 2012-06-21 00:20:51 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 00:24:43 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 231.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: genoset.Rcheck

Warnings: 2

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/genoset.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'genoset/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genoset' version '1.8.7'
* 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 ... WARNING
Found the following significant warnings:
  Warning: subclass "SimpleRangesList" of class "RangesList" is not local and cannot be updated for new inheritance information; consider setClassUnion()
  Warning: subclass "IRangesList" of class "RangesList" is not local and cannot be updated for new inheritance information; consider setClassUnion()
  Warning: subclass "MaskCollection" of class "RangesList" is not local and cannot be updated for new inheritance information; consider setClassUnion()
  Warning: subclass "SimpleIRangesList" of class "RangesList" is not local and cannot be updated for new inheritance information; consider setClassUnion()
  Warning: subclass "CompressedIRangesList" of class "RangesList" is not local and cannot be updated for new inheritance information; consider setClassUnion()
  Warning: subclass "NormalIRangesList" of class "RangesList" is not local and cannot be updated for new inheritance information; consider setClassUnion()
  Warning: subclass "CompressedNormalIRangesList" of class "RangesList" is not local and cannot be updated for new inheritance information; consider setClassUnion()
  Warning: subclass "SimpleNormalIRangesList" of class "RangesList" is not local and cannot be updated for new inheritance information; consider setClassUnion()
See '/Users/biocbuild/bbs-2.11-bioc/meat/genoset.Rcheck/00install.out' for details.
* 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 ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'GenoSet,ANY'
  generic '[' and siglist 'GenoSet,RangedDataOrRangesListOrGRanges'
  generic '[' and siglist 'GenoSet,character'
  generic 'featureNames<-' and siglist 'GRanges'
  generic 'featureNames<-' and siglist 'RangedData'
  generic 'locData<-' and siglist 'GenoSet,RangedDataOrGRanges'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'prove.R'
  Comparing 'prove.Rout' to 'prove.Rout.save' ...26a27,32
> 
> **************************************************************************
>    The plan to change the data format for CNA object has been postponed   
>  in order to ensure backward compatibility with older versions of DNAcopy 
> **************************************************************************
> 
39c45
< RUNIT TEST PROTOCOL -- Thu Jun 21 00:24:36 2012 
---
> RUNIT TEST PROTOCOL -- Mon May 21 16:20:50 2012 
51c57
< There were 28 warnings (use warnings() to see them)
---
> There were 26 warnings (use warnings() to see them)
 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

WARNING: There were 2 warnings.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/genoset.Rcheck/00check.log'
for details.

* installing *source* package 'genoset' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c genoset.c -o genoset.o
gcc -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-2.11-bioc/meat/genoset.Rcheck/genoset/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: subclass "SimpleRangesList" of class "RangesList" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Warning: subclass "IRangesList" of class "RangesList" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Warning: subclass "MaskCollection" of class "RangesList" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Warning: subclass "SimpleIRangesList" of class "RangesList" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Warning: subclass "CompressedIRangesList" of class "RangesList" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Warning: subclass "SimpleIRangesList" of class "RangesList" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Warning: subclass "NormalIRangesList" of class "RangesList" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Warning: subclass "CompressedNormalIRangesList" of class "RangesList" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Warning: subclass "SimpleNormalIRangesList" of class "RangesList" is not local and cannot be updated for new inheritance information; consider setClassUnion()
** help
*** installing help indices
** building package indices
** installing vignettes
   'genoset.Rnw' 
** testing if installed package can be loaded

* DONE (genoset)

name	user	system	elapsed
BAFSet-class	0.528	0.006	0.537
BAFSet	0.330	0.006	0.337
BAFSet.to.ExpressionSets	0.221	0.010	0.231
CNSet-class	0.124	0.000	0.125
CNSet	0.112	0.000	0.118
GenoSet-class	0.120	0.001	0.121
GenoSet	0.111	0.001	0.113
baf	0.046	0.019	0.065
baf2mbaf	0.038	0.003	0.042
boundingIndices	0.001	0.001	0.002
boundingIndices2	0.001	0.000	0.001
chr-methods	0.113	0.001	0.113
chrIndices-methods	0.031	0.002	0.032
chrInfo	0.040	0.002	0.042
chrNames	0.112	0.001	0.112
chrOrder	0.002	0.000	0.001
cn	0.044	0.019	0.064
colMeans	0.010	0.000	0.011
featureNames	0.127	0.003	0.130
gcCorrect	0.013	0.002	0.015
genoPlot-methods	0.099	0.008	0.108
genoPos-methods	0.058	0.020	0.078
genomeAxis	0.057	0.003	0.061
genoset-methods	0.643	0.021	0.665
initGenoSet	0.112	0.001	0.112
isGenomeOrder-methods	0.033	0.002	0.036
locData-methods	0.063	0.002	0.065
lrr	0.044	0.019	0.062
modeCenter	0.010	0.002	0.012
pos	0.124	0.001	0.125
rangeSampleMeans	0.114	0.003	0.116
readGenoSet	0	0	0
runCBS	4.024	0.025	4.071
segPairTable-methods	0.025	0.001	0.027
segTable-methods	3.426	0.019	3.455
segs2Rle	3.003	0.016	3.075
segs2RleDataFrame	3.561	0.025	3.607
subsetAssayData	0.028	0.002	0.031
toGenomeOrder-methods	0.554	0.005	0.560