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: 2017-10-18 00:03:53 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:11:29 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 456.2 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 3.4.2 Patched (2017-10-07 r73498)
* 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	1.11	0.17	1.28
ScoreMatrix-methods	4.15	0.16	4.31
ScoreMatrixBin-methods	2.70	0.14	2.84
ScoreMatrixList-methods	0.72	0.01	0.73
annotateWithFeature-methods	0.03	0.00	0.04
annotateWithFeatureFlank-methods	0.25	0.00	0.25
annotateWithFeatures-methods	0.49	0.08	0.56
annotateWithGeneParts-methods	0.59	0.02	0.61
binMatrix-methods	0.13	0.01	0.14
convertBed2Exons-methods	0.06	0.00	0.07
convertBed2Introns-methods	0.11	0.00	0.11
findFeatureComb-methods	0.24	0.00	0.23
getFeatsWithTargetsStats-methods	0.24	0.02	0.25
getFlanks-methods	0.09	0.00	0.09
getRandomEnrichment-methods	0	0	0
getTargetAnnotationStats-methods	0.27	0.01	0.28
gffToGRanges	0.22	0.00	0.22
heatMatrix	0.73	0.04	0.76
heatMeta	1.30	0.06	1.36
heatTargetAnnotation-methods	0.53	0.00	0.54
intersectScoreMatrixList-methods	0.23	0.01	0.25
multiHeatMatrix	0.94	0.10	1.03
orderBy-methods	1.22	0.01	1.23
patternMatrix-methods	0.2	0.0	0.2
plotMeta	1.00	0.03	1.04
plotTargetAnnotation-methods	0.30	0.02	0.31
readBed	0.26	0.01	0.28
readBroadPeak	0.07	0.00	0.07
readFeatureFlank-methods	0.07	0.02	0.09
readGeneric	0.05	0.00	0.05
readNarrowPeak	0.02	0.01	0.03
readTranscriptFeatures-methods	0.15	0.02	0.17
scaleScoreMatrix-methods	0.14	0.03	0.17
scaleScoreMatrixList	0.74	0.03	0.77

name	user	system	elapsed
AnnotationByGeneParts-methods	1.47	0.02	2.28
ScoreMatrix-methods	4.20	0.10	4.32
ScoreMatrixBin-methods	3.44	0.05	3.49
ScoreMatrixList-methods	1.86	0.02	1.87
annotateWithFeature-methods	0.07	0.00	0.08
annotateWithFeatureFlank-methods	0.57	0.00	0.56
annotateWithFeatures-methods	1.01	0.03	1.04
annotateWithGeneParts-methods	1.30	0.05	1.35
binMatrix-methods	0.30	0.02	0.31
convertBed2Exons-methods	0.11	0.00	0.11
convertBed2Introns-methods	0.21	0.00	0.22
findFeatureComb-methods	0.44	0.01	0.45
getFeatsWithTargetsStats-methods	0.58	0.00	0.57
getFlanks-methods	0.20	0.00	0.21
getRandomEnrichment-methods	0	0	0
getTargetAnnotationStats-methods	0.55	0.03	0.58
gffToGRanges	0.45	0.00	0.45
heatMatrix	1.33	0.14	1.47
heatMeta	1.27	0.08	1.34
heatTargetAnnotation-methods	0.81	0.04	0.86
intersectScoreMatrixList-methods	0.50	0.02	0.52
multiHeatMatrix	0.66	0.13	0.78
orderBy-methods	1.09	0.03	1.12
patternMatrix-methods	0.22	0.00	0.22
plotMeta	1.25	0.04	1.30
plotTargetAnnotation-methods	0.46	0.00	0.45
readBed	0.31	0.02	0.33
readBroadPeak	0.06	0.01	0.07
readFeatureFlank-methods	0.10	0.02	0.11
readGeneric	0.04	0.00	0.05
readNarrowPeak	0.03	0.02	0.05
readTranscriptFeatures-methods	0.16	0.00	0.15
scaleScoreMatrix-methods	0.19	0.00	0.19
scaleScoreMatrixList	1.25	0.01	1.27