BioC 3.3: CHECK report for genoset on morelia

Package: genoset

Version: 1.27.37

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genoset_1.27.37.tar.gz

StartedAt: 2016-04-21 03:05:13 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 03:07:41 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 148.4 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_1.27.37.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/genoset.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.27.37’
* 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 ... [21s/23s] WARNING
Found the following significant warnings:
  Warning: multiple methods tables found for ‘colMeans’
  Warning: multiple methods tables found for ‘colSums’
  Warning: multiple methods tables found for ‘rowMeans’
  Warning: multiple methods tables found for ‘rowSums’
See ‘/Users/biocbuild/bbs-3.3-bioc/meat/genoset.Rcheck/00install.out’ for details.
* 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 ... NOTE
Warning: multiple methods tables found for ‘colMeans’
Warning: multiple methods tables found for ‘colSums’
Warning: multiple methods tables found for ‘rowMeans’
Warning: multiple methods tables found for ‘rowSums’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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 ... WARNING
Undocumented code objects:
  ‘colMeans’ ‘colSums’ ‘rowMeans’ ‘rowSums’
Undocumented S4 methods:
  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 ... [10s/11s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘prove.R’ [15s/14s]
  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
< 
< 
< 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
41,57c34,37
< The genoset class has transitioned to the
< RangedSummarizedExperiment API from the eSet API (e.g. use colnames instead of sampleNames). ***
< 
< Attaching package: 'genoset'
< 
< The following object is masked from 'package:GenomicRanges':
< 
<     pos
< 
< The following objects are masked from 'package:S4Vectors':
< 
<     colMeans, colSums, rowMeans, rowSums
< 
< The following objects are masked from 'package:base':
< 
<     colMeans, colSums, rowMeans, rowSums
< 
---
> 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). ***
59,63d38
< Warning messages:
< 1: multiple methods tables found for 'colMeans' 
< 2: multiple methods tables found for 'colSums' 
< 3: multiple methods tables found for 'rowMeans' 
< 4: multiple methods tables found for 'rowSums' 
76c51,52
< 
---
> Working on segmentation for sample number 2 : a2
> Using mclapply for segmentation ...
81c57
< RUNIT TEST PROTOCOL -- Thu Apr 21 03:07:38 2016 
---
> RUNIT TEST PROTOCOL -- Sat Sep 12 10:57:59 2015 
83c59
< Number of test functions: 32 
---
> Number of test functions: 36 
89,90c65,66
< 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 
92a69
> There were 19 warnings (use warnings() to see them)
Warning message:
In readLines(from) : line 101 appears to contain an embedded nul
 [16s/14s] 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-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-3.3-bioc/meat/genoset.Rcheck/genoset/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘colMeans’ in package ‘genoset’
Creating a new generic function for ‘colSums’ in package ‘genoset’
Creating a new generic function for ‘rowMeans’ in package ‘genoset’
Creating a new generic function for ‘rowSums’ in package ‘genoset’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: multiple methods tables found for ‘colMeans’
Warning: multiple methods tables found for ‘colSums’
Warning: multiple methods tables found for ‘rowMeans’
Warning: multiple methods tables found for ‘rowSums’
* DONE (genoset)

name	user	system	elapsed
GenoSet-class	0.096	0.002	0.098
RleDataFrame-class	0.237	0.003	0.241
RleDataFrame-views	0.071	0.001	0.073
baf2mbaf	0.055	0.005	0.060
boundingIndices	0.002	0.000	0.001
calcGC	0.001	0.000	0.001
calcGC2	0.001	0.000	0.001
chr-methods	0.027	0.008	0.035
chrIndices-methods	0.020	0.003	0.022
chrInfo-methods	0.038	0.002	0.039
chrNames-methods	0.023	0.002	0.024
chrOrder	0.001	0.000	0.002
gcCorrect	0.005	0.000	0.006
genoPlot-methods	0.055	0.004	0.061
genoPos-methods	0.027	0.002	0.029
genome	0.023	0.003	0.026
genomeAxis	0.065	0.004	0.069
genoset-methods	0.037	0.001	0.038
genoset-subset	0.276	0.003	0.280
isGenomeOrder-methods	0.019	0.002	0.021
modeCenter	0.006	0.000	0.006
pos-methods	0.019	0.008	0.028
rangeSampleMeans	0.034	0.002	0.036
readGenoSet	0	0	0
runCBS	1.333	0.011	1.374
segPairTable-methods	0.013	0.001	0.013
segTable-methods	0.994	0.004	0.999
segs2Rle	0.942	0.004	0.950
segs2RleDataFrame	1.042	0.005	1.049
toGenomeOrder	0.049	0.002	0.052