Multiple platform build/check report for BioC 3.13 - CHECK results for methylKit on tokay2

Package: methylKit

Version: 1.18.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methylKit.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings methylKit_1.18.0.tar.gz

StartedAt: 2021-10-15 01:45:53 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 01:55:14 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 560.9 seconds

RetCode: 0

Status: WARNINGS

CheckDir: methylKit.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:methylKit.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings methylKit_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/methylKit.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'methylKit/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'methylKit' version '1.18.0'
* 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 whether package 'methylKit' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   7.3Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... WARNING
Undocumented arguments in documentation object 'methylRawList-class'
  '...' 'treatment'

Undocumented arguments in documentation object 'methylRawListDB-class'
  '...' 'treatment'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/methylKit/libs/i386/methylKit.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'putchar', possibly from 'putchar' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
  Found 'rand', possibly from 'rand' (C)
File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/methylKit/libs/x64/methylKit.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'putchar', possibly from 'putchar' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
  Found 'rand', possibly from 'rand' (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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
calculateDiffMeth-methods 5.49   0.68    6.17
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
calculateDiffMeth-methods 5.89    0.2    6.09
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 1 WARNING, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/methylKit.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/methylKit_1.18.0.tar.gz && rm -rf methylKit.buildbin-libdir && mkdir methylKit.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methylKit.buildbin-libdir methylKit_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL methylKit_1.18.0.zip && rm methylKit_1.18.0.tar.gz methylKit_1.18.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 14  638k   14 94289    0     0   444k      0  0:00:01 --:--:--  0:00:01  444k
100  638k  100  638k    0     0  1743k      0 --:--:-- --:--:-- --:--:-- 1743k

install for i386

* installing *source* package 'methylKit' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"c:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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, size_t&)':
methCall.cpp:687:39: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:686:39: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:685:39: 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, size_t&)':
methCall.cpp:1014:39: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1013:39: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1042:76: 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&, size_t&)':
methCall.cpp:1244:39: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1243:39: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1242:39: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o methylKit.dll tmp.def RcppExports.o methCall.o C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -Lc:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/methylKit.buildbin-libdir/00LOCK-methylKit/00new/methylKit/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'methylKit'
    finding HTML links ... done
    PCASamples-methods                      html  
    adjustMethylC                           html  
    assocComp-methods                       html  
    bedgraph-methods                        html  
    calculateDiffMeth-methods               html  
    calculateDiffMethDSS-methods            html  
    clusterSamples-methods                  html  
    dataSim-methods                         html  
    diffMethPerChr-methods                  html  
    extract-methods                         html  
    filterByCoverage-methods                html  
    getAssembly-methods                     html  
    getContext-methods                      html  
    getCorrelation-methods                  html  
    getCoverageStats-methods                html  
    getDBPath-methods                       html  
    getData-methods                         html  
    getMethylDiff-methods                   html  
    getMethylationStats-methods             html  
    getSampleID-methods                     html  
    getTreatment-methods                    html  
    joinSegmentNeighbours                   html  
    makeMethylDB-methods                    html  
    methRead-methods                        html  
    methSeg                                 html  
    finding level-2 HTML links ... done

    methSeg2bed                             html  
    methylBase-class                        html  
    methylBase.obj                          html  
    methylBaseDB-class                      html  
    methylDiff-class                        html  
    methylDiff.obj                          html  
    methylDiffDB-class                      html  
    methylKit-defunct                       html  
    methylRaw-class                         html  
    methylRawDB-class                       html  
    methylRawList-class                     html  
    methylRawList.obj                       html  
    methylRawListDB-class                   html  
    normalizeCoverage-methods               html  
    percMethylation-methods                 html  
    pool-methods                            html  
    processBismarkAln-methods               html  
    readMethylDB-methods                    html  
    reconstruct-methods                     html  
    regionCounts                            html  
    removeComp-methods                      html  
    reorganize-methods                      html  
    select-methods                          html  
    selectByOverlap-methods                 html  
    show-methods                            html  
    tileMethylCounts-methods                html  
    unite-methods                           html  
    updateMethObject                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'methylKit' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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, size_t&)':
methCall.cpp:687:39: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:686:39: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:685:39: 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, size_t&)':
methCall.cpp:1014:39: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1013:39: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1042:76: 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&, size_t&)':
methCall.cpp:1244:39: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1243:39: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1242:39: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o methylKit.dll tmp.def RcppExports.o methCall.o C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/methylKit.buildbin-libdir/methylKit/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methylKit' as methylKit_1.18.0.zip
* DONE (methylKit)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'methylKit' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
> 
> 
> 
> test_check("methylKit")
Using internal DSS code... 
Using internal DSS code... 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 238 ]
> 
> proc.time()
   user  system elapsed 
  81.18    3.89   85.37


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
> 
> 
> 
> test_check("methylKit")
Using internal DSS code... 
Using internal DSS code... 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 238 ]
> 
> proc.time()
   user  system elapsed 
  84.51    1.64   86.40

name	user	system	elapsed
PCASamples-methods	0.02	0.02	0.04
adjustMethylC	0.15	0.02	0.29
assocComp-methods	0.03	0.01	0.05
bedgraph-methods	0.06	0.02	0.09
calculateDiffMeth-methods	5.49	0.68	6.17
calculateDiffMethDSS-methods	0.47	0.04	0.50
clusterSamples-methods	0.04	0.00	0.05
dataSim-methods	0.03	0.00	0.03
diffMethPerChr-methods	0.05	0.00	0.05
extract-methods	0.03	0.01	0.04
filterByCoverage-methods	0.1	0.0	0.1
getAssembly-methods	0.01	0.00	0.01
getContext-methods	0.02	0.00	0.02
getCorrelation-methods	0.08	0.00	0.08
getCoverageStats-methods	0.01	0.00	0.01
getDBPath-methods	0.08	0.00	0.08
getData-methods	0.01	0.00	0.02
getMethylDiff-methods	0.02	0.00	0.02
getMethylationStats-methods	0.01	0.00	0.01
getSampleID-methods	0.00	0.02	0.02
getTreatment-methods	0.02	0.00	0.01
makeMethylDB-methods	0	0	0
methRead-methods	0.34	0.00	0.35
methSeg	0	0	0
methylBase-class	0.03	0.00	0.03
methylBaseDB-class	0.06	0.01	0.08
methylDiff-class	0.04	0.00	0.03
methylDiffDB-class	1.81	0.02	1.83
methylRaw-class	0.05	0.00	0.04
methylRawDB-class	0.09	0.00	0.09
methylRawList-class	0.02	0.00	0.02
methylRawListDB-class	0.33	0.03	0.36
normalizeCoverage-methods	0.34	0.01	0.36
percMethylation-methods	0.03	0.02	0.04
pool-methods	0.03	0.00	0.03
processBismarkAln-methods	0.08	0.02	0.25
readMethylDB-methods	0	0	0
reconstruct-methods	0.03	0.00	0.04
regionCounts	0.49	0.00	0.48
removeComp-methods	0.05	0.00	0.05
reorganize-methods	0.12	0.03	0.15
select-methods	0.16	0.03	0.27
selectByOverlap-methods	2.79	0.06	2.86
show-methods	0.02	0.00	0.01
tileMethylCounts-methods	0.55	0.02	0.57
unite-methods	0.11	0.00	0.11

name	user	system	elapsed
PCASamples-methods	0.03	0.00	0.04
adjustMethylC	0.08	0.02	0.09
assocComp-methods	0.02	0.00	0.02
bedgraph-methods	0.06	0.00	0.08
calculateDiffMeth-methods	5.89	0.20	6.09
calculateDiffMethDSS-methods	0.44	0.02	0.46
clusterSamples-methods	0.01	0.01	0.03
dataSim-methods	0.01	0.00	0.02
diffMethPerChr-methods	0.04	0.00	0.03
extract-methods	0.03	0.00	0.03
filterByCoverage-methods	0.09	0.00	0.09
getAssembly-methods	0	0	0
getContext-methods	0.02	0.00	0.02
getCorrelation-methods	0.07	0.00	0.08
getCoverageStats-methods	0.02	0.00	0.01
getDBPath-methods	0.03	0.02	0.05
getData-methods	0.02	0.00	0.02
getMethylDiff-methods	0	0	0
getMethylationStats-methods	0.02	0.00	0.01
getSampleID-methods	0.00	0.02	0.02
getTreatment-methods	0	0	0
makeMethylDB-methods	0	0	0
methRead-methods	0.26	0.02	0.28
methSeg	0	0	0
methylBase-class	0.02	0.01	0.03
methylBaseDB-class	0.08	0.02	0.09
methylDiff-class	0.01	0.00	0.02
methylDiffDB-class	1.88	0.00	1.88
methylRaw-class	0.05	0.00	0.04
methylRawDB-class	0.09	0.00	0.10
methylRawList-class	0.01	0.00	0.01
methylRawListDB-class	0.19	0.01	0.20
normalizeCoverage-methods	0.3	0.0	0.3
percMethylation-methods	0.03	0.00	0.03
pool-methods	0.03	0.00	0.03
processBismarkAln-methods	0.10	0.02	0.24
readMethylDB-methods	0	0	0
reconstruct-methods	0.04	0.00	0.05
regionCounts	0.50	0.01	0.51
removeComp-methods	0.03	0.00	0.03
reorganize-methods	0.18	0.00	0.17
select-methods	0.17	0.00	0.18
selectByOverlap-methods	2.85	0.02	2.86
show-methods	0.03	0.00	0.03
tileMethylCounts-methods	0.62	0.00	0.63
unite-methods	0.14	0.02	0.15

CHECK results for methylKit on tokay2

Summary

Command output

Installation output

Tests output

Example timings