BioC 2.12: CHECK report for genoset on pelham

Package: genoset

Version: 1.11.26

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genoset_1.11.26.tar.gz

StartedAt: 2013-03-24 05:41:15 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 05:45:43 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 267.6 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 3.0.0 beta (2013-03-21 r62346)
* 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 '1.11.26'
* 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 ... [32s/33s] 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 installed files from 'inst/doc' ... OK
* checking examples ... [25s/25s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'prove.R' [52s/47s]
  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' 
44d45
< Working on segmentation for sample number 2 : a2
45a47
> Working on segmentation for sample number 2 : a2
46a49
> Working on segmentation for sample number 1 : a1
48c51,52
< 
---
> Using mclapply for segmentation ...
> Working on segmentation for sample number 1 : a1
50c54
< 
---
> Using mclapply for segmentation ...
58d61
< 
59a63
> Using mclapply for segmentation ...
60a65
> Working on segmentation for sample number 2 : a2
63c68
< RUNIT TEST PROTOCOL -- Sun Mar 24 05:45:37 2013 
---
> RUNIT TEST PROTOCOL -- Thu Oct 25 19:26:26 2012 
75c80
< There were 50 or more warnings (use warnings() to see the first 50)
---
> There were 37 warnings (use warnings() to see them)
 [52s/48s] 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 -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
   'genoset.Rnw' 
** testing if installed package can be loaded
* DONE (genoset)

name	user	system	elapsed
BAFSet-class	0.316	0.015	0.334
BAFSet	0.480	0.015	0.499
BAFSet.to.ExpressionSets	0.185	0.017	0.206
CNSet-class	0.098	0.001	0.099
CNSet	0.327	0.003	0.330
GenoSet-class	0.082	0.003	0.086
GenoSet	0.287	0.003	0.289
baf	0.046	0.023	0.070
baf2mbaf	0.045	0.009	0.053
boundingIndices	0.009	0.000	0.010
boundingIndices2	0.009	0.002	0.010
chr-methods	0.402	0.003	0.406
chrIndices-methods	0.036	0.012	0.049
chrInfo	0.045	0.006	0.050
chrNames	0.805	0.011	0.821
chrOrder	0.010	0.002	0.012
cn	0.047	0.035	0.083
colMeans	0.024	0.001	0.025
featureNames	0.094	0.006	0.101
gcCorrect	0.022	0.001	0.023
genoPlot-methods	0.116	0.016	0.134
genoPos-methods	0.057	0.007	0.065
genomeAxis	0.072	0.008	0.080
genoset-methods	0.470	0.037	0.510
initGenoSet	0.314	0.013	0.328
isGenomeOrder-methods	0.043	0.011	0.054
locData-methods	0.034	0.007	0.043
lrr	0.048	0.024	0.073
modeCenter	0.013	0.003	0.017
pos	0.595	0.006	0.605
rangeSampleMeans	0.095	0.015	0.112
readGenoSet	0.010	0.002	0.012
runCBS	2.815	0.018	2.849
sampleNames	0.032	0.006	0.038
segPairTable-methods	0.047	0.003	0.051
segTable-methods	2.152	0.016	2.168
segs2Rle	2.092	0.019	2.122
segs2RleDataFrame	2.109	0.017	2.137
subsetAssayData	0.031	0.007	0.038
toGenomeOrder-methods	0.397	0.010	0.411

Summary

Command output