Package: methylKit

Version: 1.4.1

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings methylKit_1.4.1.tar.gz

StartedAt: 2018-04-12 01:00:49 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:05:02 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 252.8 seconds

RetCode: 0

Status:  OK

CheckDir: methylKit.Rcheck

Warnings: 0

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings methylKit_1.4.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.4.1’
* 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  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    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 6.428  0.028   6.462
* 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-3.6-bioc/meat/methylKit.Rcheck/00check.log’
for details.

* installing *source* package ‘methylKit’ ...
** libs
g++ -std=gnu++11 -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.6-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-3.6-bioc/R/lib -L/usr/local/lib -o methylKit.so RcppExports.o methCall.o -L/home/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/lib -Wl,-rpath,/home/biocbuild/bbs-3.6-bioc/R/library/Rhtslib/lib -lhts -lz -pthread -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-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)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(methylKit)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 
> 
> 
> test_check("methylKit")
Trying to process:
/home/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.unsorted.min.sam
 using htslib.

Failed to read header, falling back.

Trying to process: 
/home/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.unsorted.min.sam
 paired sam.

Trying to process:
/home/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.unsorted_chr.min.sam
 using htslib.

Failed to read header, falling back.

Trying to process: 
/home/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.unsorted_chr.min.sam
 paired sam.

Trying to process:
/home/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.bismark_single_end.sorted.bam
 using htslib.

Conversion Statistics:

total otherC considered (>95% C+T): 20
average conversion rate = 95.184207585947
total otherC considered (Forward) (>95% C+T): 8
average conversion rate (Forward) = 97.528594771242
total otherC considered (Reverse) (>95% C+T): 12
average conversion rate (Reverse) = 93.62128279575

Done.

Reading methylation percentage per base for sample: test1 

Trying to process:
/home/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/ctrl.bismark_paired_end.sorted.bam
 using htslib.

Conversion Statistics:

total otherC considered (>95% C+T): 4
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 4
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0

Done.

Reading methylation percentage per base for sample: ctrl1 

Trying to process:
/home/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.sorted.min.sam
 using htslib.

Failed to read header, falling back.

Trying to process: 
/home/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.sorted.min.sam
 paired sam.

Conversion Statistics:

total otherC considered (>95% C+T): 10
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 10
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0

Done.

Reading methylation percentage per base for sample: test1 

Trying to process:
/home/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.sorted.min.sam
 using htslib.

Failed to read header, falling back.

Trying to process: 
/home/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.sorted.min.sam
 paired sam.

Conversion Statistics:

total otherC considered (>95% C+T): 10
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 10
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0

Done.

Reading methylation percentage per base for sample: test1 

Trying to process:
/home/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.sorted.min.sam
 using htslib.

Failed to read header, falling back.

Trying to process: 
/home/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.sorted.min.sam
 paired sam.

Conversion Statistics:

total otherC considered (>95% C+T): 10
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 10
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0

Done.

Reading methylation percentage per base for sample: test1 

Trying to process:
/home/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.sorted.min.sam
 using htslib.

Failed to read header, falling back.

Trying to process: 
/home/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.sorted.min.sam
 paired sam.

Conversion Statistics:

total otherC considered (>95% C+T): 10
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 10
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0

Done.

Reading methylation percentage per base for sample: test1 

Trying to process:
/home/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.sorted.min.sam
 using htslib.

Failed to read header, falling back.

Trying to process: 
/home/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.sorted.min.sam
 paired sam.

Conversion Statistics:

total otherC considered (>95% C+T): 10
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 10
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0

Done.

Reading methylation percentage per base for sample: test1 

Trying to process:
/home/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.sorted.min.sam
 using htslib.

Failed to read header, falling back.

Trying to process: 
/home/biocbuild/bbs-3.6-bioc/meat/methylKit.Rcheck/methylKit/extdata/test.fastq_bismark.sorted.min.sam
 paired sam.

Conversion Statistics:

total otherC considered (>95% C+T): 10
average conversion rate = 100
total otherC considered (Forward) (>95% C+T): 10
average conversion rate (Forward) = 100
total otherC considered (Reverse) (>95% C+T): 0
average conversion rate (Reverse) = 0

Done.

Reading methylation percentage per base for sample: test1 

Using internal DSS code... 
Using internal DSS code... 
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 423 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 39.960   0.284  38.210 

name	user	system	elapsed
PCASamples-methods	0.02	0.00	0.02
adjustMethylC	0.420	0.012	0.367
assocComp-methods	0.012	0.000	0.013
bedgraph-methods	0.024	0.000	0.023
calculateDiffMeth-methods	6.428	0.028	6.462
calculateDiffMethDSS-methods	0.584	0.000	0.585
clusterSamples-methods	0.024	0.000	0.027
dataSim-methods	0.080	0.000	0.081
diffMethPerChr-methods	0.016	0.000	0.015
extract-methods	0.020	0.000	0.018
filterByCoverage-methods	0.068	0.000	0.070
getAssembly-methods	0.004	0.000	0.004
getContext-methods	0.004	0.000	0.004
getCorrelation-methods	0.268	0.000	0.191
getCoverageStats-methods	0.008	0.000	0.008
getDBPath-methods	0.168	0.000	0.083
getData-methods	0.016	0.000	0.015
getMethylDiff-methods	0.016	0.000	0.014
getMethylationStats-methods	0.020	0.000	0.019
getSampleID-methods	0.012	0.000	0.013
getTreatment-methods	0.004	0.004	0.007
makeMethylDB-methods	0.004	0.000	0.001
methRead-methods	0.288	0.004	0.298
methSeg	0	0	0
methylBase-class	0.120	0.000	0.119
methylBaseDB-class	0.152	0.000	0.069
methylDiff-class	0.008	0.004	0.012
methylDiffDB-class	2.064	0.008	2.073
methylRaw-class	0.040	0.000	0.039
methylRawDB-class	0.072	0.000	0.072
methylRawList-class	0.004	0.000	0.005
methylRawListDB-class	0.104	0.000	0.104
normalizeCoverage-methods	0.140	0.000	0.138
percMethylation-methods	0.012	0.004	0.015
pool-methods	0.040	0.004	0.042
processBismarkAln-methods	0.056	0.000	0.055
reconstruct-methods	0.012	0.000	0.013
regionCounts	0.884	0.004	0.868
removeComp-methods	0.060	0.000	0.059
reorganize-methods	0.632	0.000	0.362
select-methods	0.168	0.000	0.102
selectByOverlap-methods	2.340	0.000	2.341
show-methods	0.016	0.004	0.019
tileMethylCounts-methods	1.060	0.000	1.045
unite-methods	0.496	0.000	0.148