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: 2013-05-01 06:01:40 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 06:06:06 -0700 (Wed, 01 May 2013)

EllapsedTime: 266.1 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 Patched (2013-04-08 r62531)
* 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 ... [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 ... [24s/25s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'prove.R' [51s/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 -- Wed May  1 06:06:00 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)
 [51s/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
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c genoset.c -o genoset.o
genoset.c:194:22: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    init_low = low = p_subject_chr_indices[chr_start_index];
                   ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
genoset.c:195:24: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    init_high = high = p_subject_chr_indices[chr_end_index];
                     ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
genoset.c:198:26: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    for (int query_index=p_query_chr_indices[chr_start_index]; query_index <= p_query_chr_indices[chr_end_index]; query_index++, left_bound_index++, right_bound_index++) {
             ˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
3 warnings generated.
clang -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	0.236	0.008	0.250
BAFSet	0.456	0.011	0.470
BAFSet.to.ExpressionSets	0.171	0.017	0.199
CNSet-class	0.100	0.002	0.103
CNSet	0.286	0.004	0.301
GenoSet-class	0.081	0.003	0.087
GenoSet	0.290	0.003	0.299
baf	0.290	0.033	0.338
baf2mbaf	0.041	0.013	0.056
boundingIndices	0.008	0.001	0.010
boundingIndices2	0.007	0.001	0.008
chr-methods	0.387	0.011	0.410
chrIndices-methods	0.035	0.014	0.051
chrInfo	0.046	0.011	0.057
chrNames	0.843	0.009	0.876
chrOrder	0.006	0.001	0.007
cn	0.045	0.023	0.074
colMeans	0.018	0.003	0.021
featureNames	0.075	0.010	0.087
gcCorrect	0.019	0.002	0.023
genoPlot-methods	0.114	0.010	0.135
genoPos-methods	0.055	0.017	0.078
genomeAxis	0.300	0.017	0.336
genoset-methods	0.446	0.056	0.536
initGenoSet	0.287	0.004	0.304
isGenomeOrder-methods	0.036	0.006	0.044
locData-methods	0.036	0.013	0.051
lrr	0.044	0.025	0.071
modeCenter	0.016	0.002	0.018
pos	0.538	0.005	0.568
rangeSampleMeans	0.092	0.008	0.108
readGenoSet	0.005	0.001	0.005
runCBS	2.862	0.027	3.007
sampleNames	0.036	0.012	0.054
segPairTable-methods	0.051	0.003	0.056
segTable-methods	2.148	0.025	2.287
segs2Rle	2.098	0.024	2.179
segs2RleDataFrame	2.112	0.015	2.148
subsetAssayData	0.032	0.008	0.043
toGenomeOrder-methods	0.424	0.018	0.471