BioC 3.4: CHECK report for genomation on morelia

Package: genomation

Version: 1.5.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genomation_1.5.5.tar.gz

StartedAt: 2016-09-20 07:03:22 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 07:06:56 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 213.6 seconds

RetCode: 0

Status:  OK

CheckDir: genomation.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genomation_1.5.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/genomation.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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  6.0Mb
  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
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/genomation.Rcheck/00check.log’
for details.

* installing *source* package ‘genomation’ ...
** libs
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c idxstats.cpp -o idxstats.o
clang++ -std=c++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o genomation.so RcppExports.o idxstats.o /Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rhtslib/lib/libhts.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang: warning: argument unused during compilation: '-pthread'
installing to /Users/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	0.440	0.025	0.515
ScoreMatrix-methods	3.549	0.116	3.666
ScoreMatrixBin-methods	0.489	0.039	0.527
ScoreMatrixList-methods	0.762	0.013	0.775
annotateWithFeature-methods	0.056	0.002	0.058
annotateWithFeatureFlank-methods	0.209	0.004	0.212
annotateWithGeneParts-methods	0.357	0.011	0.368
binMatrix-methods	0.226	0.005	0.231
convertBed2Exons-methods	0.111	0.002	0.113
convertBed2Introns-methods	0.090	0.001	0.090
findFeatureComb-methods	0.403	0.005	0.407
getFeatsWithTargetsStats-methods	0.328	0.008	0.335
getFlanks-methods	0.108	0.001	0.109
getRandomEnrichment-methods	0.003	0.001	0.004
getTargetAnnotationStats-methods	0.328	0.006	0.334
gffToGRanges	0.071	0.003	0.073
heatMatrix	0.708	0.066	0.775
heatMeta	0.665	0.087	0.755
intersectScoreMatrixList-methods	0.335	0.004	0.341
multiHeatMatrix	0.843	0.048	0.892
orderBy-methods	0.758	0.029	0.787
patternMatrix-methods	0.120	0.003	0.123
plotGeneAnnotation-methods	0.694	0.014	0.709
plotMeta	0.794	0.049	0.844
plotTargetAnnotation-methods	0.318	0.005	0.323
readBed	0.036	0.006	0.043
readBroadPeak	0.026	0.003	0.029
readFeatureFlank-methods	0.106	0.006	0.112
readGeneric	0.025	0.004	0.029
readNarrowPeak	0.031	0.006	0.037
readTranscriptFeatures-methods	0.154	0.004	0.159
scaleScoreMatrix-methods	0.183	0.003	0.186
scaleScoreMatrixList	0.778	0.009	0.786