BioC 3.2: CHECK report for genomation on windows1.bioconductor.org

Package: genomation

Version: 1.2.0

Command: rm -rf genomation.buildbin-libdir genomation.Rcheck && mkdir genomation.buildbin-libdir genomation.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genomation.buildbin-libdir genomation_1.2.0.tar.gz >genomation.Rcheck\00install.out 2>&1 && cp genomation.Rcheck\00install.out genomation-install.out && C:\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_1.2.0.tar.gz

StartedAt: 2015-10-20 02:10:27 -0400 (Tue, 20 Oct 2015)

EndedAt: 2015-10-20 02:15:15 -0400 (Tue, 20 Oct 2015)

EllapsedTime: 288.7 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 && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genomation.buildbin-libdir genomation_1.2.0.tar.gz >genomation.Rcheck\00install.out 2>&1 && cp genomation.Rcheck\00install.out genomation-install.out  && C:\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_1.2.0.tar.gz
###
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/genomation.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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 '1.2.0'
* 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
* 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
heatMeta: no visible binding for global variable 'a'
ScoreMatrixBin,GRanges-GRanges : .local: no visible global function
  definition for 'runValue'
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' ... [22s] OK
** running examples for arch 'x64' ... [26s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'genomation_unit_tests.R' [19s]
 [19s] OK
** running tests for arch 'x64' ...
  Running 'genomation_unit_tests.R' [24s]
 [24s] 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
  'C:/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_1.2.0.zip
* DONE (genomation)

name	user	system	elapsed
AnnotationByGeneParts-methods	0.66	0.00	0.68
ScoreMatrix-methods	2.89	0.18	3.06
ScoreMatrixBin-methods	0.57	0.01	0.58
ScoreMatrixList-methods	0.71	0.03	0.75
annotateWithFeature-methods	0.02	0.00	0.01
annotateWithFeatureFlank-methods	0.14	0.00	0.14
annotateWithGeneParts-methods	0.36	0.00	0.35
binMatrix-methods	0.19	0.01	0.21
convertBed2Exons-methods	0.08	0.00	0.08
convertBed2Introns-methods	0.06	0.00	0.06
findFeatureComb-methods	0.30	0.02	0.31
getFeatsWithTargetsStats-methods	0.36	0.00	0.36
getFlanks-methods	0.09	0.00	0.09
getRandomEnrichment-methods	0	0	0
getTargetAnnotationStats-methods	0.36	0.00	0.36
gffToGRanges	0.08	0.00	0.08
heatMatrix	1.06	0.05	1.11
heatMeta	1.08	0.03	1.11
intersectScoreMatrixList-methods	0.45	0.00	0.45
multiHeatMatrix	0.75	0.05	0.80
orderBy-methods	0.74	0.00	0.73
patternMatrix-methods	0.12	0.02	0.14
plotGeneAnnotation-methods	0.72	0.01	0.74
plotMeta	0.96	0.06	1.03
plotTargetAnnotation-methods	0.36	0.00	0.36
readBed	0.05	0.00	0.05
readBroadPeak	0.03	0.00	0.03
readFeatureFlank-methods	0.08	0.00	0.08
readGeneric	0.03	0.00	0.03
readNarrowPeak	0.03	0.00	0.03
readTranscriptFeatures-methods	0.17	0.00	0.17
scaleScoreMatrix-methods	0.19	0.02	0.21
scaleScoreMatrixList	0.75	0.02	0.76

name	user	system	elapsed
AnnotationByGeneParts-methods	0.80	0.01	0.82
ScoreMatrix-methods	3.58	0.11	3.69
ScoreMatrixBin-methods	0.64	0.00	0.64
ScoreMatrixList-methods	0.89	0.02	0.91
annotateWithFeature-methods	0.03	0.00	0.03
annotateWithFeatureFlank-methods	0.50	0.01	0.52
annotateWithGeneParts-methods	0.42	0.00	0.42
binMatrix-methods	0.21	0.02	0.22
convertBed2Exons-methods	0.06	0.00	0.06
convertBed2Introns-methods	0.06	0.00	0.06
findFeatureComb-methods	0.36	0.00	0.36
getFeatsWithTargetsStats-methods	0.41	0.00	0.41
getFlanks-methods	0.11	0.00	0.11
getRandomEnrichment-methods	0	0	0
getTargetAnnotationStats-methods	0.41	0.00	0.41
gffToGRanges	0.09	0.00	0.09
heatMatrix	0.80	0.03	0.83
heatMeta	1.11	0.05	1.16
intersectScoreMatrixList-methods	0.30	0.01	0.31
multiHeatMatrix	1.05	0.10	1.14
orderBy-methods	0.98	0.03	1.01
patternMatrix-methods	0.19	0.01	0.20
plotGeneAnnotation-methods	0.84	0.02	0.86
plotMeta	0.73	0.09	0.83
plotTargetAnnotation-methods	0.41	0.00	0.40
readBed	0.03	0.00	0.04
readBroadPeak	0.03	0.00	0.03
readFeatureFlank-methods	0.11	0.00	0.11
readGeneric	0.03	0.02	0.05
readNarrowPeak	0.03	0.00	0.03
readTranscriptFeatures-methods	0.2	0.0	0.2
scaleScoreMatrix-methods	0.24	0.00	0.24
scaleScoreMatrixList	1.08	0.03	1.11