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: 2013-03-25 02:41:52 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:46:08 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 256.6 seconds

RetCode: 0

Status:  OK

CheckDir: genoset.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/genoset.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '1.11.26'
* 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 ... [34s/34s] 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 ... [21s/21s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'prove.R' [52s/46s]
  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 -- Mon Mar 25 02:46:01 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)
 [52s/46s] 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
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/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-2.12-bioc/meat/genoset.Rcheck/genoset/libs/i386
** 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	0.210	0.016	0.225
BAFSet	0.441	0.018	0.462
BAFSet.to.ExpressionSets	0.146	0.013	0.160
CNSet-class	0.076	0.009	0.085
CNSet	0.273	0.012	0.286
GenoSet-class	0.072	0.009	0.081
GenoSet	0.269	0.007	0.276
baf	0.042	0.021	0.062
baf2mbaf	0.176	0.011	0.187
boundingIndices	0.006	0.006	0.013
boundingIndices2	0.008	0.007	0.015
chr-methods	0.346	0.014	0.361
chrIndices-methods	0.034	0.010	0.045
chrInfo	0.042	0.009	0.051
chrNames	0.673	0.011	0.685
chrOrder	0.007	0.004	0.011
cn	0.039	0.021	0.061
colMeans	0.017	0.006	0.024
featureNames	0.071	0.009	0.080
gcCorrect	0.017	0.009	0.026
genoPlot-methods	0.098	0.020	0.158
genoPos-methods	0.050	0.009	0.060
genomeAxis	0.064	0.012	0.085
genoset-methods	0.526	0.040	0.566
initGenoSet	0.253	0.008	0.261
isGenomeOrder-methods	0.033	0.007	0.040
locData-methods	0.033	0.008	0.041
lrr	0.039	0.020	0.060
modeCenter	0.013	0.006	0.019
pos	0.485	0.011	0.497
rangeSampleMeans	0.085	0.008	0.093
readGenoSet	0.005	0.004	0.010
runCBS	2.623	0.036	2.661
sampleNames	0.030	0.008	0.038
segPairTable-methods	0.038	0.009	0.048
segTable-methods	2.172	0.027	2.200
segs2Rle	2.017	0.019	2.037
segs2RleDataFrame	2.116	0.020	2.136
subsetAssayData	0.027	0.007	0.033
toGenomeOrder-methods	0.143	0.010	0.154