BioC 3.5: CHECK report for methylKit on veracruz2

Package: methylKit

Version: 1.2.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings methylKit_1.2.4.tar.gz

StartedAt: 2017-10-18 06:00:25 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 06:05:53 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 327.3 seconds

RetCode: 0

Status:  OK

CheckDir: methylKit.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 methylKit_1.2.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/methylKit.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.2.4’
* 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 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 ... 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’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
calculateDiffMeth-methods 8.157  0.112   8.388
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/methylKit.Rcheck/00check.log’
for details.

* installing *source* package ‘methylKit’ ...
** 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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -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"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c methCall.cpp -o methCall.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 methylKit.so RcppExports.o methCall.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-4.0: warning: argument unused during compilation: '-pthread' [-Wunused-command-line-argument]
installing to /Users/biocbuild/bbs-3.5-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	0.099	0.005	0.105
adjustMethylC	0.939	0.034	0.974
assocComp-methods	0.034	0.008	0.021
bedgraph-methods	0.056	0.012	0.034
calculateDiffMeth-methods	8.157	0.112	8.388
calculateDiffMethDSS-methods	0.767	0.007	0.798
clusterSamples-methods	0.028	0.002	0.032
dataSim-methods	0.114	0.003	0.119
diffMethPerChr-methods	0.017	0.002	0.019
extract-methods	0.021	0.001	0.023
filterByCoverage-methods	0.093	0.004	0.100
getAssembly-methods	0.004	0.001	0.006
getContext-methods	0.003	0.001	0.004
getCorrelation-methods	0.348	0.038	0.253
getCoverageStats-methods	0.017	0.003	0.011
getDBPath-methods	0.129	0.021	0.077
getData-methods	0.028	0.006	0.018
getMethylDiff-methods	0.029	0.006	0.017
getMethylationStats-methods	0.034	0.007	0.019
getSampleID-methods	0.009	0.003	0.006
getTreatment-methods	0.009	0.003	0.006
makeMethylDB-methods	0.002	0.001	0.001
methRead-methods	0.322	0.027	0.295
methSeg	0.001	0.000	0.000
methylBase-class	0.162	0.002	0.173
methylBaseDB-class	0.107	0.015	0.072
methylDiff-class	0.040	0.010	0.019
methylDiffDB-class	2.927	0.076	2.874
methylRaw-class	0.045	0.003	0.048
methylRawDB-class	0.082	0.004	0.088
methylRawList-class	0.004	0.001	0.005
methylRawListDB-class	0.111	0.006	0.119
normalizeCoverage-methods	0.158	0.007	0.167
percMethylation-methods	0.018	0.001	0.020
pool-methods	0.054	0.001	0.056
processBismarkAln-methods	0.073	0.004	0.080
reconstruct-methods	0.017	0.001	0.018
regionCounts	1.478	0.077	1.268
removeComp-methods	0.154	0.020	0.094
reorganize-methods	1.031	0.079	0.800
select-methods	0.124	0.022	0.081
selectByOverlap-methods	3.128	0.117	3.175
show-methods	0.020	0.002	0.030
tileMethylCounts-methods	1.053	0.107	0.741
unite-methods	0.173	0.026	0.101