BioC 2.12: CHECK report for genoset on petty

Package: genoset

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genoset_1.12.0.tar.gz

StartedAt: 2013-10-08 22:33:29 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:38:38 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 309.2 seconds

RetCode: 0

Status:  OK

CheckDir: genoset.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/genoset.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'genoset/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genoset' version '1.12.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'genoset' can be installed ... [38s/39s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [27s/27s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'prove.R' [62s/57s]
  Comparing 'prove.Rout' to 'prove.Rout.save' ...7,13c7
< The following objects are masked from 'package:parallel':
< 
<     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
<     clusterExport, clusterMap, parApply, parCapply, parLapply,
<     parLapplyLB, parRapply, parSapply, parSapplyLB
< 
< The following object is masked from 'package:stats':
---
> The following object(s) are masked from 'package:stats':
17c11
< The following objects are masked from 'package:base':
---
> The following object(s) are masked from 'package:base':
19,23c13,16
<     Filter, Find, Map, Position, Reduce, anyDuplicated, as.data.frame,
<     cbind, colnames, duplicated, eval, get, intersect, lapply, mapply,
<     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
<     rbind, rep.int, rownames, sapply, setdiff, sort, table, tapply,
<     union, unique, unlist
---
>     Filter, Find, Map, Position, Reduce, anyDuplicated, cbind,
>     colnames, duplicated, eval, get, intersect, lapply, mapply, mget,
>     order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int,
>     rownames, sapply, setdiff, table, tapply, union, unique
30a24,30
> 
> Attaching package: 'Biobase'
> 
> The following object(s) are masked from 'package:BiocGenerics':
> 
>     annotation, annotation<-
> 
31a32,33
> Warning message:
> replacing previous import 'annotation' when loading 'Biobase' 
66c68
< RUNIT TEST PROTOCOL -- Tue Oct  8 22:38:29 2013 
---
> RUNIT TEST PROTOCOL -- Thu Oct 25 19:26:26 2012 
78c80
< There were 50 or more warnings (use warnings() to see the first 50)
---
> There were 37 warnings (use warnings() to see them)
 [63s/58s] 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

* installing *source* package 'genoset' ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c genoset.c -o genoset.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -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-2.12-bioc/meat/genoset.Rcheck/genoset/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (genoset)

name	user	system	elapsed
BAFSet-class	0.332	0.009	0.342
BAFSet	0.628	0.010	0.640
BAFSet.to.ExpressionSets	0.226	0.014	0.242
CNSet-class	0.132	0.002	0.134
CNSet	0.439	0.003	0.443
GenoSet-class	0.119	0.002	0.121
GenoSet	0.405	0.002	0.406
baf	0.296	0.022	0.320
baf2mbaf	0.050	0.013	0.063
boundingIndices	0.011	0.001	0.011
boundingIndices2	0.009	0.001	0.009
chr-methods	0.565	0.008	0.574
chrIndices-methods	0.042	0.014	0.056
chrInfo	0.061	0.008	0.070
chrNames	1.124	0.003	1.130
chrOrder	0.008	0.001	0.008
cn	0.053	0.027	0.080
colMeans	0.024	0.003	0.026
featureNames	0.104	0.008	0.112
gcCorrect	0.021	0.002	0.023
genoPlot-methods	0.153	0.015	0.169
genoPos-methods	0.071	0.014	0.085
genomeAxis	0.329	0.012	0.342
genoset-methods	0.605	0.061	0.669
initGenoSet	0.416	0.002	0.419
isGenomeOrder-methods	0.043	0.012	0.055
locData-methods	0.042	0.014	0.057
lrr	0.048	0.027	0.075
modeCenter	0.019	0.003	0.021
pos	0.815	0.001	0.818
rangeSampleMeans	0.132	0.007	0.139
readGenoSet	0.010	0.002	0.012
runCBS	2.647	0.015	2.701
sampleNames	0.038	0.009	0.047
segPairTable-methods	0.065	0.001	0.069
segTable-methods	2.036	0.019	2.102
segs2Rle	1.962	0.019	1.987
segs2RleDataFrame	1.969	0.015	1.986
subsetAssayData	0.035	0.008	0.043
toGenomeOrder-methods	0.517	0.012	0.530