BioC 2.13: CHECK report for MinimumDistance on moscato1

Package: MinimumDistance

Version: 1.6.0

Command: rm -rf MinimumDistance.buildbin-libdir && mkdir MinimumDistance.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MinimumDistance.buildbin-libdir MinimumDistance_1.6.0.tar.gz >MinimumDistance-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=MinimumDistance.buildbin-libdir --install="check:MinimumDistance-install.out" --force-multiarch --no-vignettes --timings MinimumDistance_1.6.0.tar.gz && mv MinimumDistance.buildbin-libdir/* MinimumDistance.Rcheck/ && rmdir MinimumDistance.buildbin-libdir

StartedAt: 2014-04-05 05:09:41 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 05:25:13 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 931.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MinimumDistance.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/MinimumDistance.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MinimumDistance/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MinimumDistance' version '1.6.0'
* 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 whether package 'MinimumDistance' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'BiocGenerics'
A package should be listed in only one of these fields.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Package in Depends field not imported from: 'IRanges'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'VanillaICE:::rescale'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'Biobase:::annotatedDataFrameFromMatrix' 'Biobase:::assayDataDim'
  'Biobase:::assayDataEnvLock' 'oligoClasses:::.checkOrder'
  'oligoClasses:::.getArm' 'oligoClasses:::setSequenceLengths'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'initializeLrrAndBafArrays' 'narrowRangeForChromosome'
  'originalNames' 'read.bsfiles2' 'stackListByColIndex'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.map_trioSet: no visible global function definition for 'ocSamples'
.map_trioSet: no visible binding for global variable 'i'
.map_trioSetList: no visible global function definition for 'ocSamples'
.map_trioSetList: no visible binding for global variable 'i'
computeBayesFactorTrioSet: no visible global function definition for
  'joint4'
close,TrioSet: no visible global function definition for 'isFF'
open,TrioSet: no visible global function definition for 'isFF'
* 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 'Pedigree,ANY,ANY,ANY'
  generic '[' and siglist 'TrioSet,ANY,ANY,ANY'
  generic '[' and siglist 'TrioSetList,ANY,ANY,ANY'
  generic '[' and siglist 'ff_array,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [95s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
computeBayesFactor 40.35   0.69   41.07
callDenovoSegments 17.43   0.03   17.54
narrow              5.50   0.03    5.54
** running examples for arch 'x64' ... [116s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
computeBayesFactor 46.59   1.07   47.68
callDenovoSegments 21.00   0.11   21.11
narrow              9.05   0.01    9.06
TrioSetListLD       5.54   0.11    5.65
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'doRUnit.R' [222s]
 [222s] OK
** running tests for arch 'x64'
  Running 'doRUnit.R' [179s]
 [179s] 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

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/MinimumDistance.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'MinimumDistance' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'xyplot' from package 'lattice' in package 'MinimumDistance'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'MinimumDistance' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MinimumDistance' as MinimumDistance_1.6.0.zip
* DONE (MinimumDistance)

name	user	system	elapsed
Pedigree-class	0.02	0.00	0.02
Pedigree	0.33	0.00	0.33
TrioSet-class	3.50	0.08	3.57
TrioSet	3.06	0.00	3.58
TrioSetList-class	0.55	0.02	0.56
TrioSetListLD	3.16	0.05	3.29
calculateMindist	0.46	0.01	0.47
callDenovoSegments	17.43	0.03	17.54
computeBayesFactor	40.35	0.69	41.07
isDenovo	0.05	0.00	0.05
lrr.segs	0.02	0.00	0.02
mad2	0.5	0.0	0.5
narrow	5.50	0.03	5.54
phenoData	0.48	0.00	0.49
segment2	0.08	0.00	0.07
stackRangedDataList	0.3	0.0	0.3
trioSetList	2.74	0.03	2.78
trioSetListExample	0.37	0.02	0.39
xyplotTrio	1.42	0.01	1.43

name	user	system	elapsed
Pedigree-class	0.48	0.00	0.48
Pedigree	0.03	0.01	0.04
TrioSet-class	3.97	0.10	4.07
TrioSet	3.81	0.05	3.85
TrioSetList-class	0.45	0.01	0.47
TrioSetListLD	5.54	0.11	5.65
calculateMindist	0.51	0.08	0.59
callDenovoSegments	21.00	0.11	21.11
computeBayesFactor	46.59	1.07	47.68
isDenovo	0.11	0.00	0.11
lrr.segs	0	0	0
mad2	0.54	0.02	0.55
narrow	9.05	0.01	9.06
phenoData	0.42	0.00	0.42
segment2	0	0	0
stackRangedDataList	0.37	0.00	0.38
trioSetList	3.21	0.02	3.24
trioSetListExample	0.50	0.03	0.53
xyplotTrio	2.50	0.03	2.52