BioC 3.2: CHECK report for genoset on perceval

Package: genoset

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genoset_1.24.0.tar.gz

StartedAt: 2015-11-10 05:18:54 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 05:21:43 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 168.6 seconds

RetCode: 0

Status:  OK

CheckDir: genoset.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genoset_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/genoset.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genoset/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genoset’ version ‘1.24.0’
* 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 ... [22s/23s] 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
  .Call("RleViews_viewMaxs", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewMeans", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewMins", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewSums", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewWhichMaxs", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewWhichMins", ..., PACKAGE = "IRanges")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* 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 compiled code ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/13s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘prove.R’ [21s/19s]
  Comparing ‘prove.Rout’ to ‘prove.Rout.save’ ...19,24c19,24
<     anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
<     do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,
<     intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget,
<     order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
<     rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
<     union, unique, unlist, unsplit
---
>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
>     as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
>     eval, evalq, get, grep, grepl, intersect, is.unsorted, 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, unsplit
49a50
> Working on segmentation for sample number 1 : a1
51c52
< 
---
> Using mclapply for segmentation ...
56c57
< RUNIT TEST PROTOCOL -- Tue Nov 10 05:21:37 2015 
---
> RUNIT TEST PROTOCOL -- Sat Sep 12 10:57:59 2015 
68c69
< There were 16 warnings (use warnings() to see them)
---
> There were 19 warnings (use warnings() to see them)
Warning message:
In readLines(from) : line 76 appears to contain an embedded nul
 [21s/19s] OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/genoset.Rcheck/00check.log’
for details.

* 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 -Wall  -c bounds.c -o bounds.o
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 -Wall  -c init.c -o init.o
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 -Wall  -c rangeSummaries.c -o rangeSummaries.o
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 -Wall  -c utils.c -o utils.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/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o genoset.so bounds.o init.o rangeSummaries.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-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
GenoSet-class	0.357	0.001	0.358
GenoSet	0.044	0.006	0.050
RleDataFrame-class	0.254	0.015	0.270
RleDataFrame-views	0.058	0.001	0.060
baf2mbaf	0.042	0.010	0.053
boundingIndices	0.001	0.001	0.001
calcGC	0.001	0.000	0.000
calcGC2	0.001	0.000	0.000
chr-methods	0.025	0.014	0.038
chrIndices-methods	0.013	0.008	0.021
chrInfo-methods	0.023	0.008	0.030
chrNames-methods	0.020	0.008	0.028
chrOrder	0.001	0.000	0.002
colnames	0.011	0.008	0.020
gcCorrect	0.004	0.001	0.005
genoPlot-methods	0.053	0.010	0.064
genoPos-methods	0.022	0.007	0.029
genome-methods	0.013	0.008	0.022
genome	0.012	0.008	0.020
genomeAxis	0.034	0.009	0.043
genoset-subset	0.210	0.010	0.219
initGenoSet	0.059	0.008	0.068
isGenomeOrder-methods	0.015	0.007	0.022
locData-methods	0.012	0.005	0.017
modeCenter	0.006	0.001	0.007
pos-methods	0.015	0.012	0.028
rangeSampleMeans	0.026	0.006	0.034
readGenoSet	0.000	0.000	0.001
rownames-methods	0.012	0.007	0.018
runCBS	1.733	0.004	1.737
segPairTable-methods	0.012	0.000	0.012
segTable-methods	1.374	0.009	1.383
segs2Rle	1.333	0.008	1.340
segs2RleDataFrame	1.351	0.008	1.359
toGenomeOrder-methods	0.111	0.009	0.119