BioC 3.1: CHECK report for genomation on moscato2

Package: genomation

Version: 1.0.0

Command: rm -rf genomation.buildbin-libdir genomation.Rcheck && mkdir genomation.buildbin-libdir genomation.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genomation.buildbin-libdir genomation_1.0.0.tar.gz >genomation.Rcheck\00install.out 2>&1 && cp genomation.Rcheck\00install.out genomation-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=genomation.buildbin-libdir --install="check:genomation-install.out" --force-multiarch --no-vignettes --timings genomation_1.0.0.tar.gz

StartedAt: 2015-10-09 02:06:52 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:11:41 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 288.4 seconds

RetCode: 0

Status:  OK

CheckDir: genomation.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf genomation.buildbin-libdir genomation.Rcheck && mkdir genomation.buildbin-libdir genomation.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genomation.buildbin-libdir genomation_1.0.0.tar.gz >genomation.Rcheck\00install.out 2>&1 && cp genomation.Rcheck\00install.out genomation-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=genomation.buildbin-libdir --install="check:genomation-install.out" --force-multiarch --no-vignettes --timings genomation_1.0.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/genomation.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'genomation/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genomation' version '1.0.0'
* package encoding: latin1
* 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 'genomation' 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
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 ... OK
* checking R code for possible problems ... NOTE
plotGeneAnnotation,list: no visible binding for global variable
  'SampleName'
plotGeneAnnotation,list: no visible binding for global variable 'value'
randomizeFeature,GRanges : <anonymous>: no visible global function
  definition for 'Rle'
randomizeFeature,GRanges: no visible global function definition for
  'runValue'
* 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 Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... NOTE
The following directory looks like a leftover from 'knitr':
  'cache'
Please remove from your package.
* checking examples ...
** running examples for arch 'i386' ... [10s] OK
** running examples for arch 'x64' ... [11s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'genomation_unit_tests.R' [18s]
 [18s] OK
** running tests for arch 'x64' ...
  Running 'genomation_unit_tests.R' [21s]
 [21s] 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 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/genomation.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'genomation' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'genomation' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'genomation' as genomation_1.0.0.zip
* DONE (genomation)

name	user	system	elapsed
AnnotationByGeneParts-methods	0.75	0.01	0.77
ScoreMatrix-methods	0	0	0
ScoreMatrixBin-methods	0	0	0
ScoreMatrixList-methods	0	0	0
annotateWithFeature-methods	0.07	0.00	0.08
annotateWithFeatureFlank-methods	0.28	0.00	0.28
annotateWithGeneParts-methods	0	0	0
binMatrix-methods	0	0	0
convertBed2Exons-methods	0.10	0.00	0.09
convertBed2Introns-methods	0.09	0.00	0.10
findFeatureComb-methods	0.49	0.00	0.48
getFeatsWithTargetsStats-methods	0.73	0.00	0.73
getFlanks-methods	0.2	0.0	0.2
getRandomEnrichment-methods	0	0	0
getTargetAnnotationStats-methods	0.75	0.00	0.75
gffToGRanges	0	0	0
heatMatrix	0	0	0
heatMeta	0	0	0
intersectScoreMatrixList-methods	0	0	0
multiHeatMatrix	0.02	0.00	0.02
orderBy-methods	0	0	0
plotGeneAnnotation-methods	0	0	0
plotMeta	0	0	0
plotTargetAnnotation-methods	0.73	0.02	0.75
readBed	0	0	0
readBroadPeak	0	0	0
readFeatureFlank-methods	0	0	0
readGeneric	0	0	0
readNarrowPeak	0	0	0
readTranscriptFeatures-methods	0	0	0
scaleScoreMatrix-methods	0	0	0
scaleScoreMatrixList	0	0	0

name	user	system	elapsed
AnnotationByGeneParts-methods	0.93	0.00	0.94
ScoreMatrix-methods	0	0	0
ScoreMatrixBin-methods	0	0	0
ScoreMatrixList-methods	0.02	0.00	0.01
annotateWithFeature-methods	0.03	0.00	0.03
annotateWithFeatureFlank-methods	0.25	0.00	0.25
annotateWithGeneParts-methods	0	0	0
binMatrix-methods	0	0	0
convertBed2Exons-methods	0.11	0.00	0.11
convertBed2Introns-methods	0.11	0.00	0.11
findFeatureComb-methods	0.45	0.00	0.45
getFeatsWithTargetsStats-methods	0.55	0.00	0.55
getFlanks-methods	0.16	0.00	0.15
getRandomEnrichment-methods	0	0	0
getTargetAnnotationStats-methods	0.51	0.00	0.52
gffToGRanges	0	0	0
heatMatrix	0	0	0
heatMeta	0	0	0
intersectScoreMatrixList-methods	0	0	0
multiHeatMatrix	0.02	0.00	0.01
orderBy-methods	0	0	0
plotGeneAnnotation-methods	0	0	0
plotMeta	0	0	0
plotTargetAnnotation-methods	0.51	0.00	0.52
readBed	0	0	0
readBroadPeak	0	0	0
readFeatureFlank-methods	0	0	0
readGeneric	0	0	0
readNarrowPeak	0	0	0
readTranscriptFeatures-methods	0	0	0
scaleScoreMatrix-methods	0.02	0.00	0.01
scaleScoreMatrixList	0	0	0