BioC 3.4: CHECK report for methylKit on morelia

Package: methylKit

Version: 0.99.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings methylKit_0.99.2.tar.gz

StartedAt: 2016-09-20 09:10:33 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 09:15:07 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 273.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: methylKit.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings methylKit_0.99.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/methylKit.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 ‘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 10.765  0.072  10.842
* 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
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/methylKit.Rcheck/00check.log’
for details.

* installing *source* package ‘methylKit’ ...
** 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" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/zlibbioc/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" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/zlibbioc/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c methCall.cpp -o methCall.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 methylKit.so RcppExports.o methCall.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/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	0.016	0.002	0.018
adjustMethylC	0.052	0.001	0.053
annotateWithFeature-methods	0.094	0.004	0.097
annotateWithFeatureFlank-methods	0.495	0.003	0.498
annotateWithGenicParts-methods	0.719	0.011	0.731
annotationByFeature-class	0.178	0.006	0.183
annotationByGenicParts-class	0.676	0.009	0.685
annotationByGenicParts-methods	0.417	0.005	0.422
assocComp-methods	0.012	0.002	0.013
bedgraph-methods	0.016	0.002	0.178
calculateDiffMeth-methods	10.765	0.072	10.842
calculateDiffMethDSS-methods	0.575	0.016	0.590
clusterSamples-methods	0.028	0.002	0.030
dataSim-methods	0.033	0.003	0.037
diffMethPerChr-methods	0.024	0.002	0.025
extract-methods	0.032	0.002	0.034
filterByCoverage-methods	0.064	0.004	0.069
getAssembly-methods	0.004	0.000	0.004
getContext-methods	0.003	0.000	0.004
getCorrelation-methods	0.083	0.005	0.087
getCoverageStats-methods	0.020	0.002	0.022
getDBPath-methods	0.054	0.005	0.059
getData-methods	0.016	0.002	0.018
getFeatsWithTargetsStats-methods	0.264	0.003	0.267
getFlanks-methods	0.165	0.001	0.165
getMembers-methods	0.243	0.001	0.245
getMethylDiff-methods	0.019	0.001	0.020
getMethylationStats-methods	0.020	0.001	0.022
getSampleID-methods	0.006	0.001	0.007
getTargetAnnotationStats-methods	0.288	0.019	0.307
getTreatment-methods	0.005	0.001	0.006
makeMethylDB-methods	0.001	0.001	0.001
methRead-methods	0.258	0.015	0.366
methSeg	0.000	0.000	0.001
methylBase-class	0.016	0.002	0.017
methylBaseDB-class	0.085	0.003	0.088
methylDiff-class	0.023	0.001	0.025
methylDiffDB-class	2.725	0.014	2.745
methylRaw-class	0.047	0.002	0.049
methylRawDB-class	0.106	0.004	0.109
methylRawList-class	0.007	0.001	0.007
methylRawListDB-class	0.152	0.010	0.164
normalizeCoverage-methods	0.132	0.008	0.140
percMethylation-methods	0.008	0.001	0.010
plotTargetAnnotation-methods	1.149	0.021	1.173
pool-methods	0.009	0.001	0.011
processBismarkAln-methods	0.036	0.003	0.039
readBed-methods	0.012	0.000	0.013
readFeatureFlank-methods	0.136	0.000	0.137
readTranscriptFeatures-methods	0.742	0.007	0.751
reconstruct-methods	0.029	0.002	0.031
regionCounts	0.263	0.002	0.266
removeComp-methods	0.032	0.002	0.034
reorganize-methods	0.148	0.003	0.152
select-methods	0.070	0.005	0.075
selectByOverlap-methods	2.969	0.034	3.003
show-methods	0.025	0.002	0.027
tileMethylCounts-methods	0.449	0.003	0.453
unite-methods	0.087	0.001	0.087