BioC 3.5: CHECK report for genoset on oaxaca

Package: genoset

Version: 1.31.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genoset_1.31.3.tar.gz

StartedAt: 2017-03-04 03:35:36 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 03:39:01 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 205.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: genoset.Rcheck

Warnings: 1

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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_1.31.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/genoset.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.31.3’
* 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 ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'GenoSet,ANY,ANY,ANY'
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 ... 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 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’ ...15c15
<     IQR, mad, sd, var, xtabs
---
>     IQR, mad, xtabs
20,32c20,24
<     as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
<     setdiff, sort, table, tapply, union, unique, unsplit, which,
<     which.max, which.min
< 
< 
< Attaching package: 'S4Vectors'
< 
< The following object is masked from 'package:base':
< 
<     expand.grid
---
>     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
40,64d31
< matrixStats v0.51.0 (2016-10-08) successfully loaded. See ?matrixStats for help.
< 
< Attaching package: 'matrixStats'
< 
< The following objects are masked from 'package:Biobase':
< 
<     anyMissing, rowMedians
< 
< 
< Attaching package: 'DelayedArray'
< 
< The following objects are masked from 'package:matrixStats':
< 
<     colMaxs, rowMaxs
< 
< The following object is masked from 'package:base':
< 
<     apply
< 
< 
< Attaching package: 'SummarizedExperiment'
< 
< The following object is masked from 'package:matrixStats':
< 
<     rowRanges
65a33,37
> *** 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). ***
69d40
< Working on segmentation for sample number 2 : a2
70a42
> Working on segmentation for sample number 2 : a2
78d49
< Working on segmentation for sample number 2 : a2
79a51
> Working on segmentation for sample number 2 : a2
85c57
< RUNIT TEST PROTOCOL -- Sat Mar  4 03:38:51 2017 
---
> RUNIT TEST PROTOCOL -- Sat Sep 12 10:57:59 2015 
87c59
< Number of test functions: 32 
---
> Number of test functions: 36 
93,94c65,66
< 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 
96a69
> 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-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-3.5-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	0.246	0.009	0.255
RleDataFrame-class	0.897	0.016	0.913
RleDataFrame-views	0.045	0.002	0.047
baf2mbaf	0.037	0.007	0.044
boundingIndices	0.001	0.000	0.001
calcGC	0.001	0.000	0.000
calcGC2	0	0	0
chr-methods	0.016	0.005	0.022
chrIndices-methods	0.014	0.002	0.016
chrInfo-methods	0.029	0.003	0.033
chrNames-methods	0.041	0.005	0.047
chrOrder	0.001	0.000	0.001
gcCorrect	0.003	0.000	0.003
genoPlot-methods	0.078	0.010	0.089
genoPos-methods	0.022	0.003	0.025
genome	0.086	0.006	0.091
genomeAxis	0.038	0.002	0.039
genoset-methods	0.085	0.001	0.086
genoset-subset	0.270	0.005	0.276
isGenomeOrder	0.024	0.002	0.025
modeCenter	0.005	0.000	0.005
pos-methods	0.012	0.005	0.017
rangeSampleMeans	0.023	0.002	0.025
readGenoSet	0.001	0.000	0.000
runCBS	1.557	0.008	1.585
segPairTable-methods	0.009	0.000	0.009
segTable-methods	0.867	0.004	0.872
segs2Rle	0.871	0.006	0.876
segs2RleDataFrame	0.708	0.005	0.713
toGenomeOrder	0.044	0.002	0.045