BioC 3.5: CHECK report for genomation on oaxaca

Package: genomation

Version: 1.7.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genomation_1.7.1.tar.gz

StartedAt: 2017-03-04 03:25:09 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 03:30:36 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 327.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: genomation.Rcheck

Warnings: 1

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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_1.7.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/genomation.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.7.1’
* 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  6.1Mb
  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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'ScoreMatrix,ANY,ANY,ANY'
  generic '[' and siglist 'ScoreMatrixList,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/genomation.Rcheck/00check.log’
for details.

* installing *source* package ‘genomation’ ...
** libs
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rhtslib/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2 -c idxstats.cpp -o idxstats.o
clang++ -std=gnu++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/3.4/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-3.5-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	1.296	0.052	1.522
ScoreMatrix-methods	3.072	0.121	3.196
ScoreMatrixBin-methods	0.743	0.041	0.786
ScoreMatrixList-methods	1.147	0.018	1.165
annotateWithFeature-methods	0.032	0.001	0.032
annotateWithFeatureFlank-methods	0.430	0.002	0.433
annotateWithFeatures-methods	1.120	0.021	1.141
annotateWithGeneParts-methods	0.978	0.025	1.003
binMatrix-methods	0.267	0.012	0.280
convertBed2Exons-methods	0.104	0.004	0.108
convertBed2Introns-methods	0.199	0.004	0.203
findFeatureComb-methods	0.350	0.006	0.356
getFeatsWithTargetsStats-methods	0.451	0.013	0.465
getFlanks-methods	0.154	0.001	0.155
getRandomEnrichment-methods	0.004	0.001	0.005
getTargetAnnotationStats-methods	0.383	0.007	0.390
gffToGRanges	0.331	0.005	0.335
heatMatrix	0.810	0.062	0.873
heatMeta	1.024	0.085	1.109
heatTargetAnnotation-methods	0.737	0.012	0.749
intersectScoreMatrixList-methods	0.414	0.014	0.428
multiHeatMatrix	0.582	0.046	1.277
orderBy-methods	1.129	0.025	1.154
patternMatrix-methods	0.263	0.006	0.270
plotMeta	0.677	0.067	0.745
plotTargetAnnotation-methods	0.444	0.007	0.488
readBed	0.427	0.010	0.489
readBroadPeak	0.073	0.004	0.078
readFeatureFlank-methods	0.113	0.005	0.117
readGeneric	0.037	0.005	0.041
readNarrowPeak	0.026	0.003	0.030
readTranscriptFeatures-methods	0.155	0.004	0.704
scaleScoreMatrix-methods	0.221	0.004	0.225
scaleScoreMatrixList	1.021	0.011	1.033