BioC 3.4: CHECK report for genoset on morelia

Package: genoset

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genoset_1.30.0.tar.gz

StartedAt: 2017-04-15 02:49:09 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 02:51:57 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 167.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: genoset.Rcheck

Warnings: 3

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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_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/genoset.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.30.0’
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 ... WARNING
Rd files with duplicated name 'isGenomeOrder':
  ‘isGenomeOrder-methods.Rd’ ‘isGenomeOrder.Rd’
Rd files with duplicated alias 'isGenomeOrder':
  ‘isGenomeOrder-methods.Rd’ ‘isGenomeOrder.Rd’
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'GenoSet,ANY,ANY,ANY'
  generic 'locData' and siglist 'GenoSet'
  generic 'locData<-' and siglist 'GenoSet'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'GenoSet'
  ‘object’ ‘...’ ‘value’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘prove.R’
  Comparing ‘prove.Rout’ to ‘prove.Rout.save’ ...20,31c20,24
<     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
<     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
<     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
<     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
<     unique, unsplit, which, which.max, which.min
< 
< 
< Attaching package: 'S4Vectors'
< 
< The following objects are masked from 'package:base':
< 
<     colMeans, colSums, expand.grid, rowMeans, rowSums
---
>     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
38a32,37
> 
> *** Genoset API Changes ***
> The genoset class is transitioning to extending 
> RangedSummarizedExperiment rather than eSet. For this release, 
> please use the RSE API as the eSet API has been deprecated
>  (e.g. colnames instead of sampleNames). ***
58c57
< RUNIT TEST PROTOCOL -- Sat Apr 15 02:51:55 2017 
---
> RUNIT TEST PROTOCOL -- Sat Sep 12 10:57:59 2015 
60c59
< Number of test functions: 32 
---
> Number of test functions: 36 
66,67c65,66
< genoset RUnit Tests - 32 test functions, 0 errors, 0 failures
< Number of test functions: 32 
---
> genoset RUnit Tests - 36 test functions, 0 errors, 0 failures
> Number of test functions: 36 
69a69
> There were 19 warnings (use warnings() to see them)
 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/genoset.Rcheck/00check.log’
for details.

* installing *source* package ‘genoset’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c bounds.c -o bounds.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c init.c -o init.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c rangeSummaries.c -o rangeSummaries.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c utils.c -o utils.o
clang -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 -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-3.4-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	0.069	0.001	0.070
RleDataFrame-class	0.254	0.023	0.276
RleDataFrame-views	0.048	0.007	0.055
baf2mbaf	0.047	0.008	0.055
boundingIndices	0.001	0.001	0.002
calcGC	0.000	0.000	0.001
calcGC2	0	0	0
chr-methods	0.019	0.007	0.026
chrIndices-methods	0.016	0.003	0.019
chrInfo-methods	0.050	0.006	0.056
chrNames-methods	0.025	0.003	0.028
chrOrder	0.001	0.000	0.001
gcCorrect	0.003	0.001	0.003
genoPlot-methods	0.059	0.003	0.064
genoPos-methods	0.028	0.002	0.031
genome	0.016	0.003	0.019
genomeAxis	0.043	0.003	0.047
genoset-methods	0.039	0.001	0.040
genoset-subset	0.184	0.006	0.191
isGenomeOrder-methods	0.021	0.002	0.024
isGenomeOrder	0.018	0.003	0.020
modeCenter	0.005	0.000	0.006
pos-methods	0.012	0.006	0.018
rangeSampleMeans	0.030	0.003	0.034
readGenoSet	0.001	0.000	0.001
runCBS	1.121	0.004	1.144
segPairTable-methods	0.015	0.000	0.016
segTable-methods	0.914	0.006	0.921
segs2Rle	1.009	0.005	1.016
segs2RleDataFrame	0.946	0.004	0.950
toGenomeOrder	0.033	0.003	0.035