Multiple platform build/check report for BioC 3.11 - CHECK report for Repitools on tokay2

Package: Repitools

Version: 1.34.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Repitools.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings Repitools_1.34.0.tar.gz

StartedAt: 2020-10-17 07:26:00 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 07:42:28 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 987.4 seconds

RetCode: 0

Status: WARNINGS

CheckDir: Repitools.Rcheck

Warnings: 1

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Repitools.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings Repitools_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/Repitools.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Repitools/DESCRIPTION' ... OK
* this is package 'Repitools' version '1.34.0'
* 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 'Repitools' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMRgj8R/R.INSTALL16402f765802/Repitools/man/BAM2GRanges.Rd:27: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/Repitools.Rcheck/00install.out' for details.
* 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
* 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 ... OK
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* 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
methylEst         76.57   3.18   80.14
empBayes          44.96   6.60   51.56
BayMethList-class 11.72   1.50   13.22
cpgDensityCalc    12.57   0.51   13.11
sequenceCalc      10.20   0.47   10.67
determineOffset    8.29   0.52    8.82
maskOut            5.76   0.38    6.14
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
methylEst         63.10   0.17   63.28
empBayes          34.30   2.06   36.37
cpgDensityCalc    11.64   0.65   12.32
sequenceCalc      11.64   0.39   12.03
BayMethList-class  9.19   0.45    9.64
determineOffset    6.65   0.55    7.21
maskOut            5.36   0.11    5.47
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'tests.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
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/Repitools.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/Repitools_1.34.0.tar.gz && rm -rf Repitools.buildbin-libdir && mkdir Repitools.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Repitools.buildbin-libdir Repitools_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL Repitools_1.34.0.zip && rm Repitools_1.34.0.tar.gz Repitools_1.34.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1421k  100 1421k    0     0  17.2M      0 --:--:-- --:--:-- --:--:-- 18.7M

install for i386

* installing *source* package 'Repitools' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D R_NO_REMAP -I.    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c const.c -o const.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D R_NO_REMAP -I.    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hyp2f1.c -o hyp2f1.o
In file included from hyp2f1.c:81:
./mconf.h:100: warning: "DOMAIN" redefined
 #define DOMAIN  1 /* argument domain error */
 
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/Rmath.h:45,
                 from hyp2f1.c:80:
C:/rtools40/mingw32/i686-w64-mingw32/include/math.h:29: note: this is the location of the previous definition
 #define DOMAIN  _DOMAIN
 
In file included from hyp2f1.c:81:
./mconf.h:101: warning: "SING" redefined
 #define SING  2 /* argument singularity */
 
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/Rmath.h:45,
                 from hyp2f1.c:80:
C:/rtools40/mingw32/i686-w64-mingw32/include/math.h:30: note: this is the location of the previous definition
 #define SING  _SING
 
In file included from hyp2f1.c:81:
./mconf.h:102: warning: "OVERFLOW" redefined
 #define OVERFLOW 3 /* overflow range error */
 
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/Rmath.h:45,
                 from hyp2f1.c:80:
C:/rtools40/mingw32/i686-w64-mingw32/include/math.h:31: note: this is the location of the previous definition
 #define OVERFLOW _OVERFLOW
 
In file included from hyp2f1.c:81:
./mconf.h:103: warning: "UNDERFLOW" redefined
 #define UNDERFLOW 4 /* underflow range error */
 
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/Rmath.h:45,
                 from hyp2f1.c:80:
C:/rtools40/mingw32/i686-w64-mingw32/include/math.h:32: note: this is the location of the previous definition
 #define UNDERFLOW _UNDERFLOW
 
In file included from hyp2f1.c:81:
./mconf.h:104: warning: "TLOSS" redefined
 #define TLOSS  5 /* total loss of precision */
 
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/Rmath.h:45,
                 from hyp2f1.c:80:
C:/rtools40/mingw32/i686-w64-mingw32/include/math.h:33: note: this is the location of the previous definition
 #define TLOSS  _TLOSS
 
In file included from hyp2f1.c:81:
./mconf.h:105: warning: "PLOSS" redefined
 #define PLOSS  6 /* partial loss of precision */
 
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/Rmath.h:45,
                 from hyp2f1.c:80:
C:/rtools40/mingw32/i686-w64-mingw32/include/math.h:34: note: this is the location of the previous definition
 #define PLOSS  _PLOSS
 
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D R_NO_REMAP -I.    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mtherr.c -o mtherr.o
In file included from mtherr.c:58:
./mconf.h:100: warning: "DOMAIN" redefined
 #define DOMAIN  1 /* argument domain error */
 
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/R.h:58,
                 from mtherr.c:56:
C:/rtools40/mingw32/i686-w64-mingw32/include/math.h:29: note: this is the location of the previous definition
 #define DOMAIN  _DOMAIN
 
In file included from mtherr.c:58:
./mconf.h:101: warning: "SING" redefined
 #define SING  2 /* argument singularity */
 
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/R.h:58,
                 from mtherr.c:56:
C:/rtools40/mingw32/i686-w64-mingw32/include/math.h:30: note: this is the location of the previous definition
 #define SING  _SING
 
In file included from mtherr.c:58:
./mconf.h:102: warning: "OVERFLOW" redefined
 #define OVERFLOW 3 /* overflow range error */
 
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/R.h:58,
                 from mtherr.c:56:
C:/rtools40/mingw32/i686-w64-mingw32/include/math.h:31: note: this is the location of the previous definition
 #define OVERFLOW _OVERFLOW
 
In file included from mtherr.c:58:
./mconf.h:103: warning: "UNDERFLOW" redefined
 #define UNDERFLOW 4 /* underflow range error */
 
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/R.h:58,
                 from mtherr.c:56:
C:/rtools40/mingw32/i686-w64-mingw32/include/math.h:32: note: this is the location of the previous definition
 #define UNDERFLOW _UNDERFLOW
 
In file included from mtherr.c:58:
./mconf.h:104: warning: "TLOSS" redefined
 #define TLOSS  5 /* total loss of precision */
 
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/R.h:58,
                 from mtherr.c:56:
C:/rtools40/mingw32/i686-w64-mingw32/include/math.h:33: note: this is the location of the previous definition
 #define TLOSS  _TLOSS
 
In file included from mtherr.c:58:
./mconf.h:105: warning: "PLOSS" redefined
 #define PLOSS  6 /* partial loss of precision */
 
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/R.h:58,
                 from mtherr.c:56:
C:/rtools40/mingw32/i686-w64-mingw32/include/math.h:34: note: this is the location of the previous definition
 #define PLOSS  _PLOSS
 
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o Repitools.dll tmp.def const.o hyp2f1.o mtherr.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/Repitools.buildbin-libdir/00LOCK-Repitools/00new/Repitools/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Repitools'
    finding HTML links ... done
    AdjustedCopyEstimate-class              html  
    finding level-2 HTML links ... done

    AffymetrixCdfFile-class                 html  
    AffymetrixCelSet-class                  html  
    BAM2GRanges                             html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpMRgj8R/R.INSTALL16402f765802/Repitools/man/BAM2GRanges.Rd:27: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
    BayMethList-class                       html  
    ChromaBlocks                            html  
    ChromaResults-class                     html  
    ClusteredScoresList-class               html  
    CopyEstimate-class                      html  
    FastQC-class                            html  
    GCAdjustParams-class                    html  
    GCadjustCopy                            html  
    GCbiasPlots                             html  
    MappabilitySource-class                 html  
    QdnaData                                html  
    ScoresList-class                        html  
    abcdDNA                                 html  
    absoluteCN                              html  
    annoDF2GR                               html  
    annoGR2DF                               html  
    annotationBlocksCounts                  html  
    annotationBlocksLookup                  html  
    annotationCounts                        html  
    annotationLookup                        html  
    binPlots                                html  
    blocksStats                             html  
    checkProbes                             html  
    chr21genes                              html  
    chromosomeCNplots                       html  
    clusterPlots                            html  
    cpgBoxPlots                             html  
    cpgDensityCalc                          html  
    cpgDensityPlot                          html  
    determineOffset                         html  
    empBayes                                html  
    enrichmentCalc                          html  
    enrichmentPlot                          html  
    expr                                    html  
    featureBlocks                           html  
    featureScores                           html  
    findClusters                            html  
    gcContentCalc                           html  
    genQC                                   html  
    genomeBlocks                            html  
    getProbePositionsDf                     html  
    getSampleOffsets                        html  
    hcRegions                               html  
    hyper                                   html  
    loadPairFile                            html  
    loadSampleDirectory                     html  
    makeWindowLookupTable                   html  
    mappabilityCalc                         html  
    maskOut                                 html  
    mergeReplicates                         html  
    methylEst                               html  
    multiHeatmap                            html  
    plotClusters                            html  
    plotQdnaByCN                            html  
    processNDF                              html  
    profilePlots                            html  
    regionStats                             html  
    relativeCN                              html  
    samplesList                             html  
    sequenceCalc                            html  
    setCNVOffsets                           html  
    summarizeScores                         html  
    writeWig                                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 'Repitools' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D R_NO_REMAP -I.    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c const.c -o const.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D R_NO_REMAP -I.    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hyp2f1.c -o hyp2f1.o
In file included from hyp2f1.c:81:
./mconf.h:100: warning: "DOMAIN" redefined
 #define DOMAIN  1 /* argument domain error */
 
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/Rmath.h:45,
                 from hyp2f1.c:80:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/math.h:29: note: this is the location of the previous definition
 #define DOMAIN  _DOMAIN
 
In file included from hyp2f1.c:81:
./mconf.h:101: warning: "SING" redefined
 #define SING  2 /* argument singularity */
 
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/Rmath.h:45,
                 from hyp2f1.c:80:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/math.h:30: note: this is the location of the previous definition
 #define SING  _SING
 
In file included from hyp2f1.c:81:
./mconf.h:102: warning: "OVERFLOW" redefined
 #define OVERFLOW 3 /* overflow range error */
 
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/Rmath.h:45,
                 from hyp2f1.c:80:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/math.h:31: note: this is the location of the previous definition
 #define OVERFLOW _OVERFLOW
 
In file included from hyp2f1.c:81:
./mconf.h:103: warning: "UNDERFLOW" redefined
 #define UNDERFLOW 4 /* underflow range error */
 
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/Rmath.h:45,
                 from hyp2f1.c:80:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/math.h:32: note: this is the location of the previous definition
 #define UNDERFLOW _UNDERFLOW
 
In file included from hyp2f1.c:81:
./mconf.h:104: warning: "TLOSS" redefined
 #define TLOSS  5 /* total loss of precision */
 
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/Rmath.h:45,
                 from hyp2f1.c:80:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/math.h:33: note: this is the location of the previous definition
 #define TLOSS  _TLOSS
 
In file included from hyp2f1.c:81:
./mconf.h:105: warning: "PLOSS" redefined
 #define PLOSS  6 /* partial loss of precision */
 
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/Rmath.h:45,
                 from hyp2f1.c:80:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/math.h:34: note: this is the location of the previous definition
 #define PLOSS  _PLOSS
 
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -D R_NO_REMAP -I.    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mtherr.c -o mtherr.o
In file included from mtherr.c:58:
./mconf.h:100: warning: "DOMAIN" redefined
 #define DOMAIN  1 /* argument domain error */
 
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/R.h:58,
                 from mtherr.c:56:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/math.h:29: note: this is the location of the previous definition
 #define DOMAIN  _DOMAIN
 
In file included from mtherr.c:58:
./mconf.h:101: warning: "SING" redefined
 #define SING  2 /* argument singularity */
 
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/R.h:58,
                 from mtherr.c:56:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/math.h:30: note: this is the location of the previous definition
 #define SING  _SING
 
In file included from mtherr.c:58:
./mconf.h:102: warning: "OVERFLOW" redefined
 #define OVERFLOW 3 /* overflow range error */
 
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/R.h:58,
                 from mtherr.c:56:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/math.h:31: note: this is the location of the previous definition
 #define OVERFLOW _OVERFLOW
 
In file included from mtherr.c:58:
./mconf.h:103: warning: "UNDERFLOW" redefined
 #define UNDERFLOW 4 /* underflow range error */
 
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/R.h:58,
                 from mtherr.c:56:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/math.h:32: note: this is the location of the previous definition
 #define UNDERFLOW _UNDERFLOW
 
In file included from mtherr.c:58:
./mconf.h:104: warning: "TLOSS" redefined
 #define TLOSS  5 /* total loss of precision */
 
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/R.h:58,
                 from mtherr.c:56:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/math.h:33: note: this is the location of the previous definition
 #define TLOSS  _TLOSS
 
In file included from mtherr.c:58:
./mconf.h:105: warning: "PLOSS" redefined
 #define PLOSS  6 /* partial loss of precision */
 
In file included from C:/Users/BIOCBU~1/BBS-3~1.11-/R/include/R.h:58,
                 from mtherr.c:56:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/math.h:34: note: this is the location of the previous definition
 #define PLOSS  _PLOSS
 
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o Repitools.dll tmp.def const.o hyp2f1.o mtherr.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/Repitools.buildbin-libdir/Repitools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Repitools' as Repitools_1.34.0.zip
* DONE (Repitools)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'Repitools' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.

> require("Repitools")
Loading required package: Repitools
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

> require("BSgenome.Hsapiens.UCSC.hg18")
Loading required package: BSgenome.Hsapiens.UCSC.hg18
Loading required package: BSgenome
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: rtracklayer

Attaching package: 'rtracklayer'

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

    blocks

> options(warn = -1)
> 
> probes <- data.frame(chr = c("chr1", "chr9", "chrY", "chr1", "chr21", "chr6", "chr6", "chr2", "chrX", "chr11"), position = c(10000, 5500, 100000, 11000, 20000000, 500100, 499900, 700000, 9900, 90000), strand = c('+', '+', '+', '+', '-', '-', '-', '+', '-', '+'), stringsAsFactors = FALSE)
> genes <- data.frame(chr = c("chr1", "chr9", "chr11", "chr1", "chr11", "chr6", "chr6", "chr22", "chrY", "chr21"), start = c(10000, 7900, 950000, 10500, 74000000, 450000, 5000000, 44000000, 1500, 9800000), end = c(12500, 9500, 1000000, 14500, 75000000, 500000, 9000000, 45000000, 3000, 10000000), strand = c('+', '-', '-', '+', '-', '-', '-', '+', '+', '-'), name = paste("Gene", 1:10), stringsAsFactors = FALSE)
> 
> crossMatch <- annotationLookup(probes, genes, 5000, 5000)
Processing mapping between probes and features.
Mapping done.
> correctCrossMatch <- list(indexes = list(`Gene 1` = as.integer(c(1, 4)), `Gene 2` = as.integer(2), `Gene 3` = integer(), `Gene 4` = as.integer(c(1, 4)), `Gene 5` = integer(), `Gene 6` = as.integer(c(6, 7)), `Gene 7` = integer(), `Gene 8` = integer(), `Gene 9` = integer(), `Gene 10` = integer()), offsets = list(`Gene 1` = as.integer(c(0, 1000)), `Gene 2` = as.integer(4000), `Gene 3` = numeric(), `Gene 4` = as.integer(c(-500, 500)), `Gene 5` = numeric(), `Gene 6` = as.integer(c(-100, 100)), `Gene 7` = numeric(), `Gene 8` = numeric(), `Gene 9` = numeric(), `Gene 10` = numeric()))
> names(correctCrossMatch$offsets$`Gene 1`) <- c(1, 4)
> names(correctCrossMatch$offsets$`Gene 2`) <- c(2)
> names(correctCrossMatch$offsets$`Gene 4`) <- c(1, 4)
> names(correctCrossMatch$offsets$`Gene 6`) <- c(6, 7)
> names(correctCrossMatch$offsets$`Gene 8`) <- character()
> names(correctCrossMatch$offsets$`Gene 9`) <- character()
> 
> if(!isTRUE(all.equal(crossMatch, correctCrossMatch))) 
+ 	stop("Error in annotationLookup function.")
> cat("anontationLookup tested fine.\n")
anontationLookup tested fine.
> 
> lookupTable <- makeWindowLookupTable(crossMatch$indexes, crossMatch$offsets, starts = seq(-5000, 4900, 100), ends = seq(-4900, 5000, 100))
> correctLookupTable <- matrix(NA, nrow = 10, ncol = 100, dimnames = list(genes$names, seq(-4950, 4950, 100)))
> correctLookupTable[1, c(50, 51)] <- 1
> correctLookupTable[1, c(60, 61)] <- 4
> correctLookupTable[2, c(90, 91)] <- 2
> correctLookupTable[4, c(45, 46)] <- 1
> correctLookupTable[4, c(55, 56)] <- 4
> correctLookupTable[6, c(49, 50)] <- 6
> correctLookupTable[6, c(51, 52)] <- 7
> 
> if(!all(lookupTable == correctLookupTable, na.rm = TRUE))
+     stop("Error in makeWindowLookupTable function")
> cat("makeWindowLookupTable tested fine.\n")
makeWindowLookupTable tested fine.
> 
> cpgDensity <- cpgDensityCalc(genes, organism = Hsapiens, window = 500, w.function="linear")
CpG density calculated for a sample.
> if(!isTRUE(all.equal(cpgDensity, c(5.784, 7.620, 5.828, 2.928, 2.080, 1.252, 0.000, 7.404, 3.928, 0.000))))
+     stop("cpgDensityCalc not working for window = 500, scaling = linear")
> cpgDensity <- cpgDensityCalc(genes, window = 100, w.function = "log", organism = Hsapiens)
CpG density calculated for a sample.
> if(!isTRUE(all.equal(round(cpgDensity, 3), c(2.424, 1.882, 1.436, 0.084, 0.379, 0.000, 0.000, 0.263, 1.392, 0.000))))
+     stop("cpgDensityCalc not working for window = 100, scaling = log")
> cpgDensity <- cpgDensityCalc(genes, window = 1000, w.function = "exp", organism = Hsapiens)
CpG density calculated for a sample.
> if(!isTRUE(all.equal(round(cpgDensity, 3), c(4.874, 5.835, 4.999, 2.239, 1.567, 0.851, 0.054, 5.589, 3.229,0.062))))
+     stop("cpgDensityCalc not working for window = 1000, scaling = exp")
> cpgDensity <- cpgDensityCalc(genes, window = 500, w.function = "none", organism = Hsapiens)
CpG density calculated for a sample.
> if(!isTRUE(all.equal(cpgDensity, c(11, 14, 16, 6, 4, 2, 0, 15, 9, 0))))
+     stop("cpgDensityCalc not working for window = 500, scaling = none")
> cat("cpgDensityCalc tested fine.\n")
cpgDensityCalc tested fine.
> 
> GCpercent <- gcContentCalc(genes, Hsapiens, 500)
Calculating GC content.
> if(!isTRUE(all.equal(GCpercent, c(0.504, 0.586, 0.560, 0.470, 0.540, 0.304, 0.356, 0.638, 0.444, 0.388))))
+     stop("Error in gcContentCalc function")
> cat("gcContentCalc tested fine.\n")
gcContentCalc tested fine.
> 
> findsCount <- sequenceCalc(genes, Hsapiens, 500, pattern = "AATT")
> if(!isTRUE(all.equal(findsCount, c(1, 1, 0, 2, 1, 8, 2, 0, 4, 10))))
+     stop("Error in sequenceCalc function counting task")
> 
> findsPlaces <- sequenceCalc(genes, Hsapiens, 500, pattern = "AATT", positions = TRUE)
> correctPlaces <- list(-62, 181, NULL, c(-140, -98), 231, c(-219, -146, -88, -12, 12, 182, 209, 214), c(-61, 60), NULL, c(-115, -30, 11, 80), c(-238, -228, -202, -189, -177, -106, -21, 148, 158, 238))
> if(!isTRUE(all.equal(findsPlaces, correctPlaces)))
+     stop("Error in sequenceCalc function positions task")
> cat("sequenceCalc tested fine.\n")
sequenceCalc tested fine.
> cat("All tests passed.\n")
All tests passed.
> 
> proc.time()
   user  system elapsed 
 112.51    8.14  120.70


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.

> require("Repitools")
Loading required package: Repitools
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

> require("BSgenome.Hsapiens.UCSC.hg18")
Loading required package: BSgenome.Hsapiens.UCSC.hg18
Loading required package: BSgenome
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: rtracklayer

Attaching package: 'rtracklayer'

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

    blocks

> options(warn = -1)
> 
> probes <- data.frame(chr = c("chr1", "chr9", "chrY", "chr1", "chr21", "chr6", "chr6", "chr2", "chrX", "chr11"), position = c(10000, 5500, 100000, 11000, 20000000, 500100, 499900, 700000, 9900, 90000), strand = c('+', '+', '+', '+', '-', '-', '-', '+', '-', '+'), stringsAsFactors = FALSE)
> genes <- data.frame(chr = c("chr1", "chr9", "chr11", "chr1", "chr11", "chr6", "chr6", "chr22", "chrY", "chr21"), start = c(10000, 7900, 950000, 10500, 74000000, 450000, 5000000, 44000000, 1500, 9800000), end = c(12500, 9500, 1000000, 14500, 75000000, 500000, 9000000, 45000000, 3000, 10000000), strand = c('+', '-', '-', '+', '-', '-', '-', '+', '+', '-'), name = paste("Gene", 1:10), stringsAsFactors = FALSE)
> 
> crossMatch <- annotationLookup(probes, genes, 5000, 5000)
Processing mapping between probes and features.
Mapping done.
> correctCrossMatch <- list(indexes = list(`Gene 1` = as.integer(c(1, 4)), `Gene 2` = as.integer(2), `Gene 3` = integer(), `Gene 4` = as.integer(c(1, 4)), `Gene 5` = integer(), `Gene 6` = as.integer(c(6, 7)), `Gene 7` = integer(), `Gene 8` = integer(), `Gene 9` = integer(), `Gene 10` = integer()), offsets = list(`Gene 1` = as.integer(c(0, 1000)), `Gene 2` = as.integer(4000), `Gene 3` = numeric(), `Gene 4` = as.integer(c(-500, 500)), `Gene 5` = numeric(), `Gene 6` = as.integer(c(-100, 100)), `Gene 7` = numeric(), `Gene 8` = numeric(), `Gene 9` = numeric(), `Gene 10` = numeric()))
> names(correctCrossMatch$offsets$`Gene 1`) <- c(1, 4)
> names(correctCrossMatch$offsets$`Gene 2`) <- c(2)
> names(correctCrossMatch$offsets$`Gene 4`) <- c(1, 4)
> names(correctCrossMatch$offsets$`Gene 6`) <- c(6, 7)
> names(correctCrossMatch$offsets$`Gene 8`) <- character()
> names(correctCrossMatch$offsets$`Gene 9`) <- character()
> 
> if(!isTRUE(all.equal(crossMatch, correctCrossMatch))) 
+ 	stop("Error in annotationLookup function.")
> cat("anontationLookup tested fine.\n")
anontationLookup tested fine.
> 
> lookupTable <- makeWindowLookupTable(crossMatch$indexes, crossMatch$offsets, starts = seq(-5000, 4900, 100), ends = seq(-4900, 5000, 100))
> correctLookupTable <- matrix(NA, nrow = 10, ncol = 100, dimnames = list(genes$names, seq(-4950, 4950, 100)))
> correctLookupTable[1, c(50, 51)] <- 1
> correctLookupTable[1, c(60, 61)] <- 4
> correctLookupTable[2, c(90, 91)] <- 2
> correctLookupTable[4, c(45, 46)] <- 1
> correctLookupTable[4, c(55, 56)] <- 4
> correctLookupTable[6, c(49, 50)] <- 6
> correctLookupTable[6, c(51, 52)] <- 7
> 
> if(!all(lookupTable == correctLookupTable, na.rm = TRUE))
+     stop("Error in makeWindowLookupTable function")
> cat("makeWindowLookupTable tested fine.\n")
makeWindowLookupTable tested fine.
> 
> cpgDensity <- cpgDensityCalc(genes, organism = Hsapiens, window = 500, w.function="linear")
CpG density calculated for a sample.
> if(!isTRUE(all.equal(cpgDensity, c(5.784, 7.620, 5.828, 2.928, 2.080, 1.252, 0.000, 7.404, 3.928, 0.000))))
+     stop("cpgDensityCalc not working for window = 500, scaling = linear")
> cpgDensity <- cpgDensityCalc(genes, window = 100, w.function = "log", organism = Hsapiens)
CpG density calculated for a sample.
> if(!isTRUE(all.equal(round(cpgDensity, 3), c(2.424, 1.882, 1.436, 0.084, 0.379, 0.000, 0.000, 0.263, 1.392, 0.000))))
+     stop("cpgDensityCalc not working for window = 100, scaling = log")
> cpgDensity <- cpgDensityCalc(genes, window = 1000, w.function = "exp", organism = Hsapiens)
CpG density calculated for a sample.
> if(!isTRUE(all.equal(round(cpgDensity, 3), c(4.874, 5.835, 4.999, 2.239, 1.567, 0.851, 0.054, 5.589, 3.229,0.062))))
+     stop("cpgDensityCalc not working for window = 1000, scaling = exp")
> cpgDensity <- cpgDensityCalc(genes, window = 500, w.function = "none", organism = Hsapiens)
CpG density calculated for a sample.
> if(!isTRUE(all.equal(cpgDensity, c(11, 14, 16, 6, 4, 2, 0, 15, 9, 0))))
+     stop("cpgDensityCalc not working for window = 500, scaling = none")
> cat("cpgDensityCalc tested fine.\n")
cpgDensityCalc tested fine.
> 
> GCpercent <- gcContentCalc(genes, Hsapiens, 500)
Calculating GC content.
> if(!isTRUE(all.equal(GCpercent, c(0.504, 0.586, 0.560, 0.470, 0.540, 0.304, 0.356, 0.638, 0.444, 0.388))))
+     stop("Error in gcContentCalc function")
> cat("gcContentCalc tested fine.\n")
gcContentCalc tested fine.
> 
> findsCount <- sequenceCalc(genes, Hsapiens, 500, pattern = "AATT")
> if(!isTRUE(all.equal(findsCount, c(1, 1, 0, 2, 1, 8, 2, 0, 4, 10))))
+     stop("Error in sequenceCalc function counting task")
> 
> findsPlaces <- sequenceCalc(genes, Hsapiens, 500, pattern = "AATT", positions = TRUE)
> correctPlaces <- list(-62, 181, NULL, c(-140, -98), 231, c(-219, -146, -88, -12, 12, 182, 209, 214), c(-61, 60), NULL, c(-115, -30, 11, 80), c(-238, -228, -202, -189, -177, -106, -21, 148, 158, 238))
> if(!isTRUE(all.equal(findsPlaces, correctPlaces)))
+     stop("Error in sequenceCalc function positions task")
> cat("sequenceCalc tested fine.\n")
sequenceCalc tested fine.
> cat("All tests passed.\n")
All tests passed.
> 
> proc.time()
   user  system elapsed 
  91.04    6.65   97.89

name	user	system	elapsed
BAM2GRanges	0.12	0.00	0.13
BayMethList-class	11.72	1.50	13.22
GCadjustCopy	0	0	0
GCbiasPlots	0	0	0
QdnaData	0.08	0.11	0.19
abcdDNA	0	0	0
absoluteCN	0	0	0
annoDF2GR	0.05	0.00	0.05
annoGR2DF	0.18	0.05	0.23
annotationBlocksCounts	0.19	0.09	0.28
annotationBlocksLookup	0.09	0.02	0.11
annotationCounts	0.21	0.03	0.24
annotationLookup	0.11	0.00	0.11
binPlots	1.49	0.11	1.60
blocksStats	0.22	0.00	0.21
checkProbes	0.18	0.00	0.19
chromosomeCNplots	0	0	0
clusterPlots	1.07	0.11	1.17
cpgDensityCalc	12.57	0.51	13.11
cpgDensityPlot	4.14	0.47	4.82
determineOffset	8.29	0.52	8.82
empBayes	44.96	6.60	51.56
enrichmentCalc	1.35	0.02	1.37
enrichmentPlot	3.41	0.27	3.67
featureBlocks	0.02	0.00	0.02
featureScores	0.84	0.14	0.98
findClusters	2.33	0.00	2.33
gcContentCalc	4.34	0.29	4.64
genQC	0	0	0
genomeBlocks	0.14	0.00	0.14
getProbePositionsDf	0	0	0
getSampleOffsets	0	0	0
hyper	0	0	0
loadPairFile	0	0	0
loadSampleDirectory	0.01	0.00	0.02
makeWindowLookupTable	0.10	0.00	0.09
mappabilityCalc	0	0	0
maskOut	5.76	0.38	6.14
mergeReplicates	0.98	0.05	1.03
methylEst	76.57	3.18	80.14
multiHeatmap	0.06	0.00	0.07
plotClusters	0.24	0.00	0.23
plotQdnaByCN	0	0	0
processNDF	0	0	0
profilePlots	0	0	0
regionStats	0	0	0
relativeCN	0.14	0.00	0.14
sequenceCalc	10.20	0.47	10.67
setCNVOffsets	0	0	0
summarizeScores	0.69	0.08	0.77
writeWig	0	0	0

name	user	system	elapsed
BAM2GRanges	0.15	0.00	0.15
BayMethList-class	9.19	0.45	9.64
GCadjustCopy	0	0	0
GCbiasPlots	0	0	0
QdnaData	0.06	0.04	0.09
abcdDNA	0	0	0
absoluteCN	0	0	0
annoDF2GR	0.03	0.00	0.03
annoGR2DF	0.11	0.00	0.11
annotationBlocksCounts	0.21	0.00	0.20
annotationBlocksLookup	0.06	0.00	0.06
annotationCounts	0.14	0.00	0.15
annotationLookup	0.11	0.00	0.10
binPlots	1.39	0.09	1.49
blocksStats	0.20	0.01	0.22
checkProbes	0.21	0.00	0.20
chromosomeCNplots	0	0	0
clusterPlots	1.25	0.10	1.34
cpgDensityCalc	11.64	0.65	12.32
cpgDensityPlot	4.09	0.33	4.42
determineOffset	6.65	0.55	7.21
empBayes	34.30	2.06	36.37
enrichmentCalc	1.39	0.02	1.41
enrichmentPlot	2.39	0.08	2.47
featureBlocks	0.03	0.00	0.03
featureScores	0.60	0.01	0.61
findClusters	2.78	0.02	2.80
gcContentCalc	3.48	0.48	3.96
genQC	0	0	0
genomeBlocks	0.14	0.00	0.14
getProbePositionsDf	0	0	0
getSampleOffsets	0	0	0
hyper	0	0	0
loadPairFile	0	0	0
loadSampleDirectory	0	0	0
makeWindowLookupTable	0.09	0.00	0.09
mappabilityCalc	0	0	0
maskOut	5.36	0.11	5.47
mergeReplicates	1.03	0.02	1.05
methylEst	63.10	0.17	63.28
multiHeatmap	0.07	0.00	0.08
plotClusters	0.29	0.00	0.28
plotQdnaByCN	0	0	0
processNDF	0	0	0
profilePlots	0	0	0
regionStats	0	0	0
relativeCN	0.15	0.00	0.16
sequenceCalc	11.64	0.39	12.03
setCNVOffsets	0	0	0
summarizeScores	0.67	0.01	0.69
writeWig	0	0	0

CHECK report for Repitools on tokay2

Summary

Command output

Installation output

Tests output

Example timings