BioC 3.5: CHECK report for genomation on tokay2

Package: genomation

Version: 1.8.0

Command: rm -rf genomation.buildbin-libdir genomation.Rcheck && mkdir genomation.buildbin-libdir genomation.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genomation.buildbin-libdir genomation_1.8.0.tar.gz >genomation.Rcheck\00install.out 2>&1 && cp genomation.Rcheck\00install.out genomation-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=genomation.buildbin-libdir --install="check:genomation-install.out" --force-multiarch --no-vignettes --timings genomation_1.8.0.tar.gz

StartedAt: 2017-08-16 00:00:29 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:07:48 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 439.1 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:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genomation.buildbin-libdir genomation_1.8.0.tar.gz >genomation.Rcheck\00install.out 2>&1 && cp genomation.Rcheck\00install.out genomation-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=genomation.buildbin-libdir --install="check:genomation-install.out" --force-multiarch --no-vignettes --timings genomation_1.8.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/genomation.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.8.0'
* 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 ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.2Mb
* 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
Namespace in Imports field not imported from: 'RUnit'
  All declared Imports should be used.
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 ... OK
* 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 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' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'genomation_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'genomation_unit_tests.R'
 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:/Users/biocbuild/bbs-3.5-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_1.8.0.zip
* DONE (genomation)

name	user	system	elapsed
AnnotationByGeneParts-methods	0.99	0.08	1.06
ScoreMatrix-methods	3.90	0.22	4.12
ScoreMatrixBin-methods	2.73	0.09	2.83
ScoreMatrixList-methods	1.05	0.02	1.07
annotateWithFeature-methods	0.07	0.00	0.06
annotateWithFeatureFlank-methods	0.48	0.01	0.50
annotateWithFeatures-methods	0.75	0.08	0.83
annotateWithGeneParts-methods	0.92	0.10	1.02
binMatrix-methods	0.19	0.01	0.20
convertBed2Exons-methods	0.08	0.00	0.08
convertBed2Introns-methods	0.12	0.00	0.12
findFeatureComb-methods	0.31	0.02	0.33
getFeatsWithTargetsStats-methods	0.33	0.03	0.36
getFlanks-methods	0.11	0.00	0.11
getRandomEnrichment-methods	0.01	0.00	0.01
getTargetAnnotationStats-methods	0.30	0.01	0.31
gffToGRanges	0.25	0.00	0.25
heatMatrix	1.14	0.08	1.22
heatMeta	1.41	0.08	1.49
heatTargetAnnotation-methods	0.89	0.03	0.92
intersectScoreMatrixList-methods	0.54	0.00	0.55
multiHeatMatrix	1.57	0.06	1.62
orderBy-methods	0.79	0.04	0.83
patternMatrix-methods	0.32	0.03	0.34
plotMeta	1.65	0.07	1.74
plotTargetAnnotation-methods	0.27	0.04	0.29
readBed	0.25	0.03	0.28
readBroadPeak	0.03	0.03	0.06
readFeatureFlank-methods	0.14	0.04	0.18
readGeneric	0.03	0.03	0.06
readNarrowPeak	0.05	0.01	0.06
readTranscriptFeatures-methods	0.22	0.03	0.25
scaleScoreMatrix-methods	0.29	0.05	0.34
scaleScoreMatrixList	1.14	0.03	1.18

name	user	system	elapsed
AnnotationByGeneParts-methods	1.59	0.01	1.61
ScoreMatrix-methods	4.20	0.22	4.42
ScoreMatrixBin-methods	2.94	0.03	2.97
ScoreMatrixList-methods	0.87	0.02	0.89
annotateWithFeature-methods	0.05	0.00	0.05
annotateWithFeatureFlank-methods	0.30	0.00	0.29
annotateWithFeatures-methods	0.56	0.03	0.60
annotateWithGeneParts-methods	0.70	0.01	0.72
binMatrix-methods	0.17	0.02	0.18
convertBed2Exons-methods	0.07	0.00	0.07
convertBed2Introns-methods	0.14	0.00	0.14
findFeatureComb-methods	0.28	0.00	0.28
getFeatsWithTargetsStats-methods	0.31	0.00	0.31
getFlanks-methods	0.09	0.00	0.09
getRandomEnrichment-methods	0	0	0
getTargetAnnotationStats-methods	0.31	0.00	0.31
gffToGRanges	0.24	0.02	0.25
heatMatrix	0.78	0.12	0.91
heatMeta	0.95	0.05	1.00
heatTargetAnnotation-methods	0.49	0.01	0.50
intersectScoreMatrixList-methods	0.24	0.00	0.24
multiHeatMatrix	0.46	0.07	0.53
orderBy-methods	0.75	0.04	0.80
patternMatrix-methods	0.16	0.00	0.15
plotMeta	0.97	0.13	1.10
plotTargetAnnotation-methods	0.31	0.01	0.32
readBed	0.30	0.02	0.32
readBroadPeak	0.07	0.00	0.06
readFeatureFlank-methods	0.11	0.01	0.13
readGeneric	0.03	0.02	0.05
readNarrowPeak	0.01	0.02	0.03
readTranscriptFeatures-methods	0.17	0.00	0.18
scaleScoreMatrix-methods	0.2	0.0	0.2
scaleScoreMatrixList	0.88	0.00	0.87