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CHECK report for methylKit on machv2

This page was generated on 2020-10-17 11:58:56 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE methylKit PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1060/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylKit 1.14.2
Altuna Akalin , Alexander Gosdschan
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/methylKit
Branch: RELEASE_3_11
Last Commit: a4a2fdf
Last Changed Date: 2020-05-20 12:13:42 -0400 (Wed, 20 May 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: methylKit
Version: 1.14.2
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_1.14.2.tar.gz
StartedAt: 2020-10-17 02:56:16 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:04:51 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 515.0 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_1.14.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/methylKit.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.14.2’
* 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 ... NOTE
.CpG.dinuc.unify: no visible binding for global variable ‘coverage.x’
.CpG.dinuc.unify: no visible binding for global variable ‘coverage.y’
.CpG.dinuc.unify: no visible binding for global variable ‘numCs.x’
.CpG.dinuc.unify: no visible binding for global variable ‘numCs.y’
.CpG.dinuc.unify: no visible binding for global variable ‘numTs.x’
.CpG.dinuc.unify: no visible binding for global variable ‘numTs.y’
.diffMethPerChr: no visible binding for global variable ‘type’
.diffMethPerChr: no visible binding for global variable ‘meth.diff’
.diffMethPerChr: no visible global function definition for ‘.’
.diffMethPerChr: no visible binding for global variable ‘.N’
reconstruct,ANY-methylBaseDB : reconstr: no visible global function
  definition for ‘read.delim’
Undefined global functions or variables:
  . .N coverage.x coverage.y meth.diff numCs.x numCs.y numTs.x numTs.y
  read.delim type
Consider adding
  importFrom("utils", "read.delim")
to your NAMESPACE file.
* 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 ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.0/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 (user + system) or elapsed time > 5s
                            user system elapsed
calculateDiffMeth-methods 12.143  0.272  14.205
selectByOverlap-methods    5.185  0.112   6.245
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-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/4.0/Resources/library’
* installing *source* package ‘methylKit’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c methCall.cpp -o methCall.o
clang++ -mmacosx-version-min=10.13 -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/4.0/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/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 version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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, 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, 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/4.0/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/4.0/Resources/library/methylKit/extdata/test.fastq_bismark.unsorted.min.sam
 paired sam.

Trying to process:
/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/methylKit/extdata/test.fastq_bismark.unsorted_chr.min.sam
 paired sam.

Trying to process:
/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/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/4.0/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/4.0/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/4.0/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/4.0/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/4.0/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/4.0/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/4.0/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/4.0/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/4.0/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/4.0/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/4.0/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 

Using internal DSS code... 
Using internal DSS code... 
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 189 | SKIPPED: 0 | WARNINGS: 344 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
110.719   2.312 122.998 

Example timings

methylKit.Rcheck/methylKit-Ex.timings

nameusersystemelapsed
PCASamples-methods0.0490.0050.069
adjustMethylC0.1820.0080.242
assocComp-methods0.0370.0050.047
bedgraph-methods0.0400.0070.054
calculateDiffMeth-methods12.143 0.27214.205
calculateDiffMethDSS-methods0.9320.0091.115
clusterSamples-methods0.0640.0040.083
dataSim-methods0.0300.0030.040
diffMethPerChr-methods0.0500.0030.061
extract-methods0.0470.0030.062
filterByCoverage-methods0.1490.0080.183
getAssembly-methods0.0180.0030.020
getContext-methods0.0170.0030.023
getCorrelation-methods0.0960.0080.119
getCoverageStats-methods0.0230.0030.034
getDBPath-methods0.0760.0070.094
getData-methods0.0320.0050.042
getMethylDiff-methods0.0290.0030.040
getMethylationStats-methods0.0350.0040.042
getSampleID-methods0.0180.0030.024
getTreatment-methods0.0180.0020.023
makeMethylDB-methods0.0000.0000.001
methRead-methods0.3860.0320.505
methSeg0.0010.0010.000
methylBase-class0.0360.0030.047
methylBaseDB-class0.1020.0070.120
methylDiff-class0.0420.0030.051
methylDiffDB-class4.3020.0184.997
methylRaw-class0.1050.0070.126
methylRawDB-class0.1250.0090.152
methylRawList-class0.0190.0030.024
methylRawListDB-class0.2040.0190.254
normalizeCoverage-methods0.2160.0180.277
percMethylation-methods0.0440.0040.054
pool-methods0.0260.0030.031
processBismarkAln-methods0.1370.0120.187
readMethylDB-methods0.0000.0010.000
reconstruct-methods0.0340.0030.045
regionCounts0.5910.0040.703
removeComp-methods0.0540.0030.067
reorganize-methods0.2030.0050.252
select-methods0.1360.0110.174
selectByOverlap-methods5.1850.1126.245
show-methods0.0480.0040.057
tileMethylCounts-methods1.0100.0081.072
unite-methods0.1730.0050.188