BioC 3.2: CHECK report for genomation on moscato1

Package: genomation

Version: 1.1.12

Command: rm -rf genomation.buildbin-libdir genomation.Rcheck && mkdir genomation.buildbin-libdir genomation.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genomation.buildbin-libdir genomation_1.1.12.tar.gz >genomation.Rcheck\00install.out 2>&1 && cp genomation.Rcheck\00install.out genomation-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=genomation.buildbin-libdir --install="check:genomation-install.out" --force-multiarch --no-vignettes --timings genomation_1.1.12.tar.gz

StartedAt: 2015-08-20 04:52:52 -0700 (Thu, 20 Aug 2015)

EndedAt: 2015-08-20 04:59:17 -0700 (Thu, 20 Aug 2015)

EllapsedTime: 384.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: genomation.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf genomation.buildbin-libdir genomation.Rcheck && mkdir genomation.buildbin-libdir genomation.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genomation.buildbin-libdir genomation_1.1.12.tar.gz >genomation.Rcheck\00install.out 2>&1 && cp genomation.Rcheck\00install.out genomation-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=genomation.buildbin-libdir --install="check:genomation-install.out" --force-multiarch --no-vignettes --timings genomation_1.1.12.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.2-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 '1.1.12'
* 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
* 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
Unexported objects imported by ':::' calls:
  'BiocGenerics:::testPackage' 'GenomicAlignments:::invertRleStrand'
  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
gffToGRanges: no visible global function definition for 'seqlevels<-'
heatMeta: no visible binding for global variable 'a'
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 ... WARNING
Codoc mismatches from documentation object 'gffToGRanges':
gffToGRanges
  Code: function(gff.file, filter = NULL, zero.based = FALSE, ensembl =
                 FALSE)
  Docs: function(gff.file, track.line = FALSE, split.group = FALSE,
                 split.char = ";", filter = NULL, zero.based = FALSE,
                 ensembl = FALSE)
  Argument names in docs not in code:
    track.line split.group split.char
  Mismatches in argument names:
    Position: 2 Code: filter Docs: track.line
    Position: 3 Code: zero.based Docs: split.group
    Position: 4 Code: ensembl Docs: split.char

* 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' ... [13s] OK
** running examples for arch 'x64' ... [15s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'genomation_unit_tests.R' [26s]
 [26s] OK
** running tests for arch 'x64' ...
  Running 'genomation_unit_tests.R' [31s]
 [32s] 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, 3 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/genomation.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'genomation' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'genomation' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genomation' as genomation_1.1.12.zip
* DONE (genomation)

name	user	system	elapsed
AnnotationByGeneParts-methods	0.80	0.00	1.01
ScoreMatrix-methods	0	0	0
ScoreMatrixBin-methods	0	0	0
ScoreMatrixList-methods	0	0	0
annotateWithFeature-methods	0.06	0.00	0.06
annotateWithFeatureFlank-methods	0.26	0.00	0.26
annotateWithGeneParts-methods	0	0	0
binMatrix-methods	0	0	0
convertBed2Exons-methods	0.08	0.02	0.10
convertBed2Introns-methods	0.11	0.00	0.11
findFeatureComb-methods	0.42	0.03	0.45
getFeatsWithTargetsStats-methods	0.66	0.00	0.66
getFlanks-methods	0.19	0.00	0.19
getRandomEnrichment-methods	0	0	0
getTargetAnnotationStats-methods	0.62	0.00	0.65
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	0.89	0.00	0.89
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	0.97	0.00	1.26
ScoreMatrix-methods	0	0	0
ScoreMatrixBin-methods	0	0	0
ScoreMatrixList-methods	0	0	0
annotateWithFeature-methods	0.04	0.00	0.05
annotateWithFeatureFlank-methods	0.36	0.00	0.36
annotateWithGeneParts-methods	0	0	0
binMatrix-methods	0	0	0
convertBed2Exons-methods	0.13	0.00	0.12
convertBed2Introns-methods	0.11	0.00	0.11
findFeatureComb-methods	0.61	0.01	0.62
getFeatsWithTargetsStats-methods	0.60	0.02	0.62
getFlanks-methods	0.18	0.00	0.17
getRandomEnrichment-methods	0	0	0
getTargetAnnotationStats-methods	0.62	0.01	0.64
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	0.54	0.00	0.54
readBed	0	0	0
readBroadPeak	0.02	0.00	0.02
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