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CHECK report for methylKit on malbec2

This page was generated on 2019-04-09 11:46:24 -0400 (Tue, 09 Apr 2019).

Package 964/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylKit 1.9.3
Altuna Akalin , Alexander Gosdschan
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/methylKit
Branch: master
Last Commit: 21fb06e
Last Changed Date: 2019-02-05 04:13:38 -0400 (Tue, 05 Feb 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: methylKit
Version: 1.9.3
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:methylKit.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings methylKit_1.9.3.tar.gz
StartedAt: 2019-04-09 01:54:49 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:01:40 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 411.2 seconds
RetCode: 0
Status:  OK 
CheckDir: methylKit.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:methylKit.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings methylKit_1.9.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/methylKit.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.9.3’
* 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
selectByOverlap-methods   12.367  0.042   6.441
unite-methods              9.770  0.062   2.385
calculateDiffMeth-methods  6.738  0.152   6.889
reorganize-methods         5.934  0.025   1.359
* 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-3.9-bioc/meat/methylKit.Rcheck/00check.log’
for details.

Installation output

methylKit.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL methylKit
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘methylKit’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"/home/biocbuild/bbs-3.9-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_single_bismark(std::istream*, std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&)’:
methCall.cpp:1220:39: warning: ‘CHGout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
methCall.cpp:1219:39: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
methCall.cpp:1218:39: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
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:678:39: warning: ‘CHGout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
methCall.cpp:677:39: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
methCall.cpp:676:39: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
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:997:39: warning: ‘CHGout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
methCall.cpp:996:39: warning: ‘CHHout’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
methCall.cpp:995:39: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o methylKit.so RcppExports.o methCall.o -L/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib -Wl,-rpath,/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib -lhts -lz -lm -lbz2 -llzma -lpthread -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-methylKit/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (methylKit)

Tests output

methylKit.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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, 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-3.9-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-3.9-bioc/R/library/methylKit/extdata/test.fastq_bismark.unsorted.min.sam
 paired sam.

Trying to process:
/home/biocbuild/bbs-3.9-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-3.9-bioc/R/library/methylKit/extdata/test.fastq_bismark.unsorted_chr.min.sam
 paired sam.

Trying to process:
/home/biocbuild/bbs-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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-3.9-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 

object has more than one sample id:  
 only one allowed
object has more than one sample id:  
 only one allowed
Using internal DSS code... 
Using internal DSS code... 
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 441 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
225.918   1.913 112.876

Example timings

methylKit.Rcheck/methylKit-Ex.timings

nameusersystemelapsed
PCASamples-methods0.0200.0120.032
adjustMethylC1.2310.0040.338
assocComp-methods0.0190.0000.019
bedgraph-methods0.0370.0000.038
calculateDiffMeth-methods6.7380.1526.889
calculateDiffMethDSS-methods0.4010.0000.401
clusterSamples-methods0.0210.0040.024
dataSim-methods0.0110.0000.011
diffMethPerChr-methods0.0130.0000.013
extract-methods0.020.000.02
filterByCoverage-methods0.7320.0000.185
getAssembly-methods0.0100.0000.006
getContext-methods0.0050.0000.005
getCorrelation-methods3.4370.0080.541
getCoverageStats-methods0.0210.0000.010
getDBPath-methods3.1730.0060.792
getData-methods0.0310.0000.017
getMethylDiff-methods0.0240.0040.028
getMethylationStats-methods0.0180.0000.019
getSampleID-methods0.0060.0000.005
getTreatment-methods0.0010.0040.006
makeMethylDB-methods000
methRead-methods4.2140.0151.368
methSeg0.0050.0000.000
methylBase-class0.0140.0000.014
methylBaseDB-class3.0690.0110.572
methylDiff-class0.0160.0000.017
methylDiffDB-class2.2900.0042.155
methylRaw-class0.0410.0000.041
methylRawDB-class1.1740.0110.258
methylRawList-class0.0020.0040.006
methylRawListDB-class3.0250.0270.625
normalizeCoverage-methods3.0390.0240.614
percMethylation-methods0.0240.0000.024
pool-methods0.0140.0000.014
processBismarkAln-methods0.0980.0040.103
reconstruct-methods0.0200.0000.019
regionCounts1.4230.0040.489
removeComp-methods0.0210.0000.021
reorganize-methods5.9340.0251.359
select-methods4.6590.0091.281
selectByOverlap-methods12.367 0.042 6.441
show-methods0.0280.0000.028
tileMethylCounts-methods1.9530.0050.910
unite-methods9.7700.0622.385