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CHECK report for methylKit on malbec1

This page was generated on 2019-04-16 11:52:13 -0400 (Tue, 16 Apr 2019).

Package 939/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylKit 1.8.1
Altuna Akalin , Alexander Gosdschan
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/methylKit
Branch: RELEASE_3_8
Last Commit: a1e00fc
Last Changed Date: 2018-12-11 05:41:18 -0400 (Tue, 11 Dec 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: methylKit
Version: 1.8.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:methylKit.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings methylKit_1.8.1.tar.gz
StartedAt: 2019-04-16 01:20:15 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:26:34 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 379.0 seconds
RetCode: 0
Status:  OK 
CheckDir: methylKit.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:methylKit.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings methylKit_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/methylKit.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.8.1’
* 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 ... 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
calculateDiffMeth-methods 10.712  0.172  10.921
unite-methods             10.784  0.036   2.635
selectByOverlap-methods    9.224  0.024   5.703
reorganize-methods         7.972  0.020   2.378
* 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-3.8-bioc/meat/methylKit.Rcheck/00check.log’
for details.

Installation output

methylKit.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL methylKit
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘methylKit’ ...
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c methCall.cpp -o methCall.o
methCall.cpp: In function ‘int process_sam(std::istream*, std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&, int, int)’:
methCall.cpp:708:84: warning: ‘CHGout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
                                                                                    ^
methCall.cpp:707:84: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
                                                                                    ^
methCall.cpp:706:81: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CpGstatus) { processCGmethHash(CGmethHash,out,mincov);     std::fclose(out); }
                                                                                 ^
methCall.cpp: In function ‘int process_bam(std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&, int)’:
methCall.cpp:1027:84: warning: ‘CHGout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
                                                                                    ^
methCall.cpp:1026:84: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
                                                                                    ^
methCall.cpp:1025:81: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CpGstatus) { processCGmethHash(CGmethHash,out,mincov);     std::fclose(out); }
                                                                                 ^
methCall.cpp: In function ‘int process_single_bismark(std::istream*, std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&)’:
methCall.cpp:1254:84: warning: ‘CHGout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
                                                                                    ^
methCall.cpp:1253:84: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
                                                                                    ^
methCall.cpp:1252:81: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CpGstatus) { processCGmethHash(CGmethHash,out,mincov);     std::fclose(out); }
                                                                                 ^
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o methylKit.so RcppExports.o methCall.o -L/home/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/usrlib -Wl,-rpath,/home/biocbuild/bbs-3.8-bioc/R/library/Rhtslib/usrlib -lhts -lz -lm -lbz2 -llzma -lpthread -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/methylKit/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (methylKit)

Tests output

methylKit.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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-3.8-bioc/R/library/methylKit/extdata/test.fastq_bismark.unsorted.min.sam
 using htslib.

Failed to read header, falling back.

Trying to process: 
/home/biocbuild/bbs-3.8-bioc/R/library/methylKit/extdata/test.fastq_bismark.unsorted.min.sam
 paired sam.

Trying to process:
/home/biocbuild/bbs-3.8-bioc/R/library/methylKit/extdata/test.fastq_bismark.unsorted_chr.min.sam
 using htslib.

Failed to read header, falling back.

Trying to process: 
/home/biocbuild/bbs-3.8-bioc/R/library/methylKit/extdata/test.fastq_bismark.unsorted_chr.min.sam
 paired sam.

Trying to process:
/home/biocbuild/bbs-3.8-bioc/R/library/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-3.8-bioc/R/library/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-3.8-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
 using htslib.

Failed to read header, falling back.

Trying to process: 
/home/biocbuild/bbs-3.8-bioc/R/library/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-3.8-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
 using htslib.

Failed to read header, falling back.

Trying to process: 
/home/biocbuild/bbs-3.8-bioc/R/library/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-3.8-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
 using htslib.

Failed to read header, falling back.

Trying to process: 
/home/biocbuild/bbs-3.8-bioc/R/library/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-3.8-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
 using htslib.

Failed to read header, falling back.

Trying to process: 
/home/biocbuild/bbs-3.8-bioc/R/library/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-3.8-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
 using htslib.

Failed to read header, falling back.

Trying to process: 
/home/biocbuild/bbs-3.8-bioc/R/library/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-3.8-bioc/R/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
 using htslib.

Failed to read header, falling back.

Trying to process: 
/home/biocbuild/bbs-3.8-bioc/R/library/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: 438 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
186.640   1.244  98.314

Example timings

methylKit.Rcheck/methylKit-Ex.timings

nameusersystemelapsed
PCASamples-methods0.7080.0000.705
adjustMethylC1.4760.0040.585
assocComp-methods0.0160.0040.020
bedgraph-methods0.0400.0000.041
calculateDiffMeth-methods10.712 0.17210.921
calculateDiffMethDSS-methods0.7280.0040.735
clusterSamples-methods0.0400.0040.046
dataSim-methods0.0200.0000.023
diffMethPerChr-methods0.0240.0000.025
extract-methods0.0400.0040.045
filterByCoverage-methods0.0480.0040.054
getAssembly-methods0.0040.0000.004
getContext-methods0.0080.0000.005
getCorrelation-methods3.7000.0081.161
getCoverageStats-methods0.0120.0040.011
getDBPath-methods3.4200.0080.955
getData-methods0.0120.0040.017
getMethylDiff-methods0.0160.0000.015
getMethylationStats-methods0.0240.0000.021
getSampleID-methods0.0040.0000.007
getTreatment-methods0.0040.0000.005
makeMethylDB-methods000
methRead-methods0.2920.0080.320
methSeg000
methylBase-class0.0160.0000.017
methylBaseDB-class3.6600.0161.010
methylDiff-class0.0200.0000.022
methylDiffDB-class3.2480.0003.093
methylRaw-class0.0640.0040.070
methylRawDB-class0.7160.0040.257
methylRawList-class0.0080.0000.006
methylRawListDB-class0.1800.0000.179
normalizeCoverage-methods0.1720.0040.175
percMethylation-methods0.0200.0040.022
pool-methods0.0120.0000.012
processBismarkAln-methods0.0920.0000.119
reconstruct-methods0.0200.0000.018
regionCounts1.9120.0080.830
removeComp-methods0.0320.0040.034
reorganize-methods7.9720.0202.378
select-methods4.0000.0161.257
selectByOverlap-methods9.2240.0245.703
show-methods0.0240.0040.029
tileMethylCounts-methods2.2040.0041.050
unite-methods10.784 0.036 2.635