BioC 3.5: CHECK report for methylKit on malbec2

Package: methylKit

Version: 1.2.4

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings methylKit_1.2.4.tar.gz

StartedAt: 2017-10-18 00:45:33 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:49:48 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 255.3 seconds

RetCode: 0

Status:  OK

CheckDir: methylKit.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings methylKit_1.2.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/methylKit.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘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 ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   1.7Mb
* 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 7.024  0.012   7.044
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/methylKit.Rcheck/00check.log’
for details.

* installing *source* package ‘methylKit’ ...
** libs
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -c methCall.cpp -o methCall.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o methylKit.so RcppExports.o methCall.o -L/home/biocbuild/bbs-3.5-bioc/R/library/Rhtslib/lib -Wl,-rpath,/home/biocbuild/bbs-3.5-bioc/R/library/Rhtslib/lib -lhts -lz -pthread -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/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	0.496	0.000	0.495
adjustMethylC	0.400	0.016	0.391
assocComp-methods	0.012	0.004	0.013
bedgraph-methods	0.024	0.000	0.024
calculateDiffMeth-methods	7.024	0.012	7.044
calculateDiffMethDSS-methods	0.568	0.000	0.568
clusterSamples-methods	0.028	0.000	0.026
dataSim-methods	0.088	0.000	0.090
diffMethPerChr-methods	0.016	0.000	0.015
extract-methods	0.020	0.000	0.018
filterByCoverage-methods	0.076	0.000	0.075
getAssembly-methods	0.004	0.000	0.004
getContext-methods	0.004	0.000	0.004
getCorrelation-methods	0.280	0.004	0.197
getCoverageStats-methods	0.016	0.000	0.016
getDBPath-methods	0.140	0.004	0.059
getData-methods	0.012	0.000	0.011
getMethylDiff-methods	0.012	0.000	0.012
getMethylationStats-methods	0.012	0.000	0.014
getSampleID-methods	0.004	0.000	0.004
getTreatment-methods	0.004	0.000	0.005
makeMethylDB-methods	0	0	0
methRead-methods	0.216	0.004	0.222
methSeg	0.000	0.000	0.001
methylBase-class	0.120	0.000	0.121
methylBaseDB-class	0.148	0.000	0.065
methylDiff-class	0.012	0.000	0.013
methylDiffDB-class	2.264	0.008	2.274
methylRaw-class	0.044	0.004	0.047
methylRawDB-class	0.068	0.000	0.065
methylRawList-class	0.004	0.000	0.005
methylRawListDB-class	0.108	0.000	0.108
normalizeCoverage-methods	0.168	0.000	0.171
percMethylation-methods	0.016	0.000	0.016
pool-methods	0.044	0.000	0.043
processBismarkAln-methods	0.052	0.004	0.057
reconstruct-methods	0.016	0.000	0.013
regionCounts	1.008	0.004	0.996
removeComp-methods	0.06	0.00	0.06
reorganize-methods	0.584	0.004	0.341
select-methods	0.140	0.000	0.088
selectByOverlap-methods	2.864	0.020	2.885
show-methods	0.024	0.004	0.027
tileMethylCounts-methods	0.716	0.004	0.706
unite-methods	0.432	0.008	0.148