BioC 3.4: CHECK report for genomation on zin1

Package: genomation

Version: 1.5.5

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings genomation_1.5.5.tar.gz

StartedAt: 2016-09-20 06:59:56 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 07:03:20 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 203.5 seconds

RetCode: 0

Status:  OK

CheckDir: genomation.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings genomation_1.5.5.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/genomation.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genomation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genomation’ version ‘1.5.5’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘genomation’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.3Mb
  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
* 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 ... NOTE
plotGeneAnnotation,list: no visible binding for global variable
  ‘SampleName’
plotGeneAnnotation,list: no visible binding for global variable ‘value’
Undefined global functions or variables:
  SampleName value
* 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 C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/genomation.Rcheck/00check.log’
for details.

* installing *source* package ‘genomation’ ...
** libs
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include"   -fpic  -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/include"   -fpic  -g -O2 -c idxstats.cpp -o idxstats.o
g++ -std=c++11 -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o genomation.so RcppExports.o idxstats.o -L/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/lib -Wl,-rpath,/home/biocbuild/bbs-3.4-bioc/R/library/Rhtslib/lib -lhts -lz -pthread -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/genomation.Rcheck/genomation/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (genomation)

name	user	system	elapsed
AnnotationByGeneParts-methods	0.480	0.008	0.517
ScoreMatrix-methods	3.704	0.108	3.813
ScoreMatrixBin-methods	0.524	0.016	0.542
ScoreMatrixList-methods	0.728	0.000	0.725
annotateWithFeature-methods	0.036	0.000	0.034
annotateWithFeatureFlank-methods	0.176	0.000	0.175
annotateWithGeneParts-methods	0.332	0.004	0.336
binMatrix-methods	0.160	0.004	0.164
convertBed2Exons-methods	0.072	0.000	0.072
convertBed2Introns-methods	0.068	0.000	0.068
findFeatureComb-methods	0.272	0.004	0.275
getFeatsWithTargetsStats-methods	0.348	0.000	0.347
getFlanks-methods	0.108	0.000	0.110
getRandomEnrichment-methods	0.000	0.000	0.003
getTargetAnnotationStats-methods	0.352	0.004	0.356
gffToGRanges	0.076	0.000	0.075
heatMatrix	0.648	0.080	0.729
heatMeta	0.42	0.00	0.42
intersectScoreMatrixList-methods	0.236	0.004	0.249
multiHeatMatrix	0.760	0.004	0.764
orderBy-methods	0.772	0.004	0.775
patternMatrix-methods	0.104	0.004	0.111
plotGeneAnnotation-methods	0.664	0.008	0.671
plotMeta	0.792	0.008	0.797
plotTargetAnnotation-methods	0.312	0.008	0.320
readBed	0.052	0.008	0.058
readBroadPeak	0.032	0.004	0.035
readFeatureFlank-methods	0.108	0.004	0.113
readGeneric	0.036	0.004	0.039
readNarrowPeak	0.040	0.004	0.041
readTranscriptFeatures-methods	0.168	0.000	0.169
scaleScoreMatrix-methods	0.176	0.000	0.173
scaleScoreMatrixList	0.800	0.004	0.804