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BioC 3.5: CHECK report for methylKit on malbec2

This page was generated on 2017-10-18 14:17:53 -0400 (Wed, 18 Oct 2017).

Package 805/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylKit 1.2.4
Altuna Akalin
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/methylKit
Branch: RELEASE_3_5
Last Commit: 066892b
Last Changed Date: 2017-08-24 09:55:33 -0400 (Thu, 24 Aug 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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


* 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.


methylKit.Rcheck/00install.out:

* 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)

methylKit.Rcheck/methylKit-Ex.timings:

nameusersystemelapsed
PCASamples-methods0.4960.0000.495
adjustMethylC0.4000.0160.391
assocComp-methods0.0120.0040.013
bedgraph-methods0.0240.0000.024
calculateDiffMeth-methods7.0240.0127.044
calculateDiffMethDSS-methods0.5680.0000.568
clusterSamples-methods0.0280.0000.026
dataSim-methods0.0880.0000.090
diffMethPerChr-methods0.0160.0000.015
extract-methods0.0200.0000.018
filterByCoverage-methods0.0760.0000.075
getAssembly-methods0.0040.0000.004
getContext-methods0.0040.0000.004
getCorrelation-methods0.2800.0040.197
getCoverageStats-methods0.0160.0000.016
getDBPath-methods0.1400.0040.059
getData-methods0.0120.0000.011
getMethylDiff-methods0.0120.0000.012
getMethylationStats-methods0.0120.0000.014
getSampleID-methods0.0040.0000.004
getTreatment-methods0.0040.0000.005
makeMethylDB-methods000
methRead-methods0.2160.0040.222
methSeg0.0000.0000.001
methylBase-class0.1200.0000.121
methylBaseDB-class0.1480.0000.065
methylDiff-class0.0120.0000.013
methylDiffDB-class2.2640.0082.274
methylRaw-class0.0440.0040.047
methylRawDB-class0.0680.0000.065
methylRawList-class0.0040.0000.005
methylRawListDB-class0.1080.0000.108
normalizeCoverage-methods0.1680.0000.171
percMethylation-methods0.0160.0000.016
pool-methods0.0440.0000.043
processBismarkAln-methods0.0520.0040.057
reconstruct-methods0.0160.0000.013
regionCounts1.0080.0040.996
removeComp-methods0.060.000.06
reorganize-methods0.5840.0040.341
select-methods0.1400.0000.088
selectByOverlap-methods2.8640.0202.885
show-methods0.0240.0040.027
tileMethylCounts-methods0.7160.0040.706
unite-methods0.4320.0080.148