BioC 3.5: CHECK report for methylKit on veracruz2

Package: methylKit

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings methylKit_1.2.0.tar.gz

StartedAt: 2017-08-16 05:13:48 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 05:19:09 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 320.7 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_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/methylKit.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.2.0’
* 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 7.865  0.073   8.115
* 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	0.025	0.003	0.028
adjustMethylC	0.916	0.050	0.953
assocComp-methods	0.032	0.008	0.020
bedgraph-methods	0.062	0.013	0.038
calculateDiffMeth-methods	7.865	0.073	8.115
calculateDiffMethDSS-methods	0.700	0.006	0.743
clusterSamples-methods	0.032	0.002	0.033
dataSim-methods	0.113	0.002	0.117
diffMethPerChr-methods	0.017	0.001	0.018
extract-methods	0.017	0.002	0.018
filterByCoverage-methods	0.080	0.003	0.086
getAssembly-methods	0.005	0.001	0.006
getContext-methods	0.004	0.002	0.006
getCorrelation-methods	0.298	0.032	0.223
getCoverageStats-methods	0.032	0.005	0.018
getDBPath-methods	0.082	0.012	0.047
getData-methods	0.028	0.006	0.017
getMethylDiff-methods	0.027	0.004	0.016
getMethylationStats-methods	0.028	0.005	0.017
getSampleID-methods	0.011	0.003	0.006
getTreatment-methods	0.011	0.002	0.007
makeMethylDB-methods	0.002	0.000	0.001
methRead-methods	0.337	0.037	0.286
methSeg	0.001	0.000	0.000
methylBase-class	0.152	0.001	0.165
methylBaseDB-class	0.108	0.019	0.068
methylDiff-class	0.025	0.004	0.015
methylDiffDB-class	2.826	0.042	2.861
methylRaw-class	0.051	0.002	0.056
methylRawDB-class	0.076	0.003	0.079
methylRawList-class	0.005	0.001	0.006
methylRawListDB-class	0.118	0.008	0.125
normalizeCoverage-methods	0.181	0.007	0.195
percMethylation-methods	0.016	0.001	0.016
pool-methods	0.049	0.001	0.050
processBismarkAln-methods	0.078	0.004	0.084
reconstruct-methods	0.013	0.001	0.016
regionCounts	1.849	0.089	1.688
removeComp-methods	0.151	0.023	0.088
reorganize-methods	0.640	0.105	0.352
select-methods	0.152	0.035	0.086
selectByOverlap-methods	3.048	0.094	3.067
show-methods	0.022	0.002	0.024
tileMethylCounts-methods	1.050	0.120	0.737
unite-methods	0.158	0.026	0.093