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CHECK report for methylKit on merida2

This page was generated on 2019-04-09 13:33:37 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:methylKit.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings methylKit_1.9.3.tar.gz
StartedAt: 2019-04-09 02:09:13 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:15:41 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 388.5 seconds
RetCode: 0
Status:  OK 
CheckDir: methylKit.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:methylKit.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings methylKit_1.9.3.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/methylKit.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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
File ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/methylKit/libs/methylKit.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_printf’, possibly from ‘printf’ (C)
  Found ‘_putchar’, possibly from ‘putchar’ (C)
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘_srand48’, possibly from ‘srand48’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
calculateDiffMeth-methods 11.267  0.400  11.591
selectByOverlap-methods    7.103  1.319   5.602
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/methylKit.Rcheck/00check.log’
for details.



Installation output

methylKit.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL methylKit
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘methylKit’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/zlibbioc/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c methCall.cpp -o methCall.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o methylKit.so RcppExports.o methCall.o /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/usrlib/libhts.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/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 Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/methylKit/extdata/test.fastq_bismark.unsorted.min.sam
 using htslib.

Failed to read header, falling back.

Trying to process: 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/methylKit/extdata/test.fastq_bismark.unsorted.min.sam
 paired sam.

Trying to process:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/methylKit/extdata/test.fastq_bismark.unsorted_chr.min.sam
 using htslib.

Failed to read header, falling back.

Trying to process: 
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/methylKit/extdata/test.fastq_bismark.unsorted_chr.min.sam
 paired sam.

Trying to process:
/Library/Frameworks/R.framework/Versions/3.6/Resources/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:
/Library/Frameworks/R.framework/Versions/3.6/Resources/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:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
 using htslib.

Failed to read header, falling back.

Trying to process: 
/Library/Frameworks/R.framework/Versions/3.6/Resources/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:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
 using htslib.

Failed to read header, falling back.

Trying to process: 
/Library/Frameworks/R.framework/Versions/3.6/Resources/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:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
 using htslib.

Failed to read header, falling back.

Trying to process: 
/Library/Frameworks/R.framework/Versions/3.6/Resources/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:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
 using htslib.

Failed to read header, falling back.

Trying to process: 
/Library/Frameworks/R.framework/Versions/3.6/Resources/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:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
 using htslib.

Failed to read header, falling back.

Trying to process: 
/Library/Frameworks/R.framework/Versions/3.6/Resources/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:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/methylKit/extdata/test.fastq_bismark.sorted.min.sam
 using htslib.

Failed to read header, falling back.

Trying to process: 
/Library/Frameworks/R.framework/Versions/3.6/Resources/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 
 96.993  24.111  76.050 

Example timings

methylKit.Rcheck/methylKit-Ex.timings

nameusersystemelapsed
PCASamples-methods0.0330.0080.042
adjustMethylC0.2470.0660.209
assocComp-methods0.0600.0250.024
bedgraph-methods0.0920.0490.041
calculateDiffMeth-methods11.267 0.40011.591
calculateDiffMethDSS-methods0.7800.0070.812
clusterSamples-methods0.0470.0020.053
dataSim-methods0.0200.0030.023
diffMethPerChr-methods0.0240.0020.025
extract-methods0.0310.0020.033
filterByCoverage-methods0.2040.0330.176
getAssembly-methods0.0160.0110.008
getContext-methods0.0150.0110.007
getCorrelation-methods0.2960.1240.124
getCoverageStats-methods0.0280.0180.014
getDBPath-methods0.2540.1100.104
getData-methods0.0490.0280.023
getMethylDiff-methods0.0460.0220.020
getMethylationStats-methods0.1030.0440.040
getSampleID-methods0.0180.0080.007
getTreatment-methods0.0180.0080.008
makeMethylDB-methods0.0010.0010.001
methRead-methods1.0920.4540.519
methSeg0.0010.0010.001
methylBase-class0.0380.0230.019
methylBaseDB-class0.3200.1480.125
methylDiff-class0.0540.0250.022
methylDiffDB-class4.2440.2864.189
methylRaw-class0.1840.0910.081
methylRawDB-class0.3590.1440.148
methylRawList-class0.0210.0110.008
methylRawListDB-class0.7890.3620.322
normalizeCoverage-methods0.7890.3730.322
percMethylation-methods0.0650.0350.029
pool-methods0.0350.0180.016
processBismarkAln-methods0.3120.1460.133
reconstruct-methods0.0540.0230.026
regionCounts0.8280.2810.451
removeComp-methods0.1140.0480.044
reorganize-methods1.3240.5860.539
select-methods0.4170.1910.168
selectByOverlap-methods7.1031.3195.602
show-methods0.0290.0030.032
tileMethylCounts-methods1.3890.5070.682
unite-methods0.5230.2280.213