BioC 3.4: CHECK report for methylKit on zin1

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings methylKit_0.99.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/methylKit.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 ‘methylKit/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methylKit’ version ‘0.99.2’
* 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 ‘methylKit’ can be installed ... OK
* checking installed package size ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘KernSmooth’
  All declared Imports should be used.
* 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 'methylBase,ANY,ANY,ANY'
  generic '[' and siglist 'methylBaseDB,ANY,ANY,ANY'
  generic '[' and siglist 'methylDiff,ANY,ANY,ANY'
  generic '[' and siglist 'methylDiffDB,ANY,ANY,ANY'
  generic '[' and siglist 'methylRaw,ANY,ANY,ANY'
  generic '[' and siglist 'methylRawDB,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’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
calculateDiffMeth-methods 8.68  0.036   8.716
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/methylKit.Rcheck/00check.log’
for details.

* installing *source* package ‘methylKit’ ...
** 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" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/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" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include"   -fpic  -g -O2 -c methCall.cpp -o methCall.o
g++ -std=c++11 -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o methylKit.so RcppExports.o methCall.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/methylKit.Rcheck/methylKit/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 (methylKit)

name	user	system	elapsed
PCASamples-methods	0.02	0.00	0.02
adjustMethylC	0.060	0.000	0.059
annotateWithFeature-methods	0.100	0.000	0.101
annotateWithFeatureFlank-methods	0.560	0.000	0.559
annotateWithGenicParts-methods	0.832	0.008	0.837
annotationByFeature-class	0.180	0.004	0.184
annotationByGenicParts-class	0.792	0.012	0.805
annotationByGenicParts-methods	0.504	0.000	0.505
assocComp-methods	0.016	0.000	0.014
bedgraph-methods	0.020	0.000	0.021
calculateDiffMeth-methods	8.680	0.036	8.716
calculateDiffMethDSS-methods	0.592	0.012	0.604
clusterSamples-methods	0.016	0.004	0.022
dataSim-methods	0.032	0.000	0.032
diffMethPerChr-methods	0.016	0.000	0.015
extract-methods	0.024	0.000	0.023
filterByCoverage-methods	0.052	0.000	0.052
getAssembly-methods	0.000	0.004	0.004
getContext-methods	0.008	0.000	0.005
getCorrelation-methods	0.056	0.000	0.058
getCoverageStats-methods	0.016	0.000	0.016
getDBPath-methods	0.048	0.000	0.047
getData-methods	0.012	0.000	0.013
getFeatsWithTargetsStats-methods	0.204	0.000	0.202
getFlanks-methods	0.112	0.000	0.112
getMembers-methods	0.204	0.000	0.204
getMethylDiff-methods	0.012	0.000	0.014
getMethylationStats-methods	0.016	0.000	0.014
getSampleID-methods	0.000	0.004	0.005
getTargetAnnotationStats-methods	0.236	0.000	0.236
getTreatment-methods	0.000	0.004	0.005
makeMethylDB-methods	0.004	0.000	0.001
methRead-methods	0.188	0.008	0.196
methSeg	0.000	0.000	0.001
methylBase-class	0.012	0.000	0.011
methylBaseDB-class	0.06	0.00	0.06
methylDiff-class	0.016	0.000	0.017
methylDiffDB-class	2.208	0.000	2.207
methylRaw-class	0.040	0.000	0.038
methylRawDB-class	0.080	0.000	0.078
methylRawList-class	0.004	0.000	0.005
methylRawListDB-class	0.104	0.012	0.116
normalizeCoverage-methods	0.112	0.004	0.116
percMethylation-methods	0.008	0.000	0.008
plotTargetAnnotation-methods	0.884	0.000	0.883
pool-methods	0.012	0.000	0.010
processBismarkAln-methods	0.032	0.000	0.039
readBed-methods	0.008	0.004	0.011
readFeatureFlank-methods	0.1	0.0	0.1
readTranscriptFeatures-methods	0.652	0.000	0.652
reconstruct-methods	0.012	0.000	0.014
regionCounts	0.180	0.000	0.178
removeComp-methods	0.032	0.000	0.029
reorganize-methods	0.100	0.004	0.105
select-methods	0.072	0.000	0.072
selectByOverlap-methods	2.360	0.004	2.363
show-methods	0.016	0.000	0.018
tileMethylCounts-methods	0.424	0.004	0.428
unite-methods	0.096	0.000	0.097

BioC 3.4: CHECK report for methylKit on zin1

Summary

Command output