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CHECK report for pqsfinder on tokay1

This page was generated on 2019-04-13 11:26:38 -0400 (Sat, 13 Apr 2019).

Package 1183/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pqsfinder 1.10.1
Jiri Hon
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/pqsfinder
Branch: RELEASE_3_8
Last Commit: 84e32c7
Last Changed Date: 2019-04-04 04:29:22 -0400 (Thu, 04 Apr 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: pqsfinder
Version: 1.10.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pqsfinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings pqsfinder_1.10.1.tar.gz
StartedAt: 2019-04-13 04:38:20 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:43:30 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 310.4 seconds
RetCode: 0
Status:  OK  
CheckDir: pqsfinder.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pqsfinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings pqsfinder_1.10.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/pqsfinder.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pqsfinder/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pqsfinder' version '1.10.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'pqsfinder' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    lib    3.6Mb
    libs   2.8Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for 'BH' is only usable in R >= 3.0.2
* 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 line endings in shell scripts ... 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 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-3.8-bioc/R/library/pqsfinder/libs/i386/pqsfinder.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (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
** running examples for arch 'x64' ... OK
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/pqsfinder.Rcheck/00check.log'
for details.

Installation output

pqsfinder.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/pqsfinder_1.10.1.tar.gz && rm -rf pqsfinder.buildbin-libdir && mkdir pqsfinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pqsfinder.buildbin-libdir pqsfinder_1.10.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL pqsfinder_1.10.1.zip && rm pqsfinder_1.10.1.tar.gz pqsfinder_1.10.1.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  105k  100  105k    0     0  2391k      0 --:--:-- --:--:-- --:--:-- 2646k

install for i386

* installing *source* package 'pqsfinder' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pqsfinder.cpp -o pqsfinder.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/c_regex_traits.cpp -o boost_regex/c_regex_traits.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/cpp_regex_traits.cpp -o boost_regex/cpp_regex_traits.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/cregex.cpp -o boost_regex/cregex.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/fileiter.cpp -o boost_regex/fileiter.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/icu.cpp -o boost_regex/icu.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/instances.cpp -o boost_regex/instances.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/regex.cpp -o boost_regex/regex.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/regex_raw_buffer.cpp -o boost_regex/regex_raw_buffer.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/regex_traits_defaults.cpp -o boost_regex/regex_traits_defaults.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/usinstances.cpp -o boost_regex/usinstances.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/w32_regex_traits.cpp -o boost_regex/w32_regex_traits.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/wc_regex_traits.cpp -o boost_regex/wc_regex_traits.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/winstances.cpp -o boost_regex/winstances.o
mkdir -p "C:/Users/biocbuild/bbs-3.8-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/i386"
C:/Rtools/mingw_32/bin/ar rs "C:/Users/biocbuild/bbs-3.8-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/i386/libboost_regex.a" boost_regex/c_regex_traits.o boost_regex/cpp_regex_traits.o boost_regex/cregex.o boost_regex/fileiter.o boost_regex/icu.o boost_regex/instances.o boost_regex/posix_api.o boost_regex/regex.o boost_regex/regex_debug.o boost_regex/regex_raw_buffer.o boost_regex/regex_traits_defaults.o boost_regex/static_mutex.o boost_regex/usinstances.o boost_regex/w32_regex_traits.o boost_regex/wc_regex_traits.o boost_regex/wide_posix_api.o boost_regex/winstances.o
C:\Rtools\mingw_32\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.8-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/i386/libboost_regex.a
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o pqsfinder.dll tmp.def RcppExports.o pqsfinder.o C:/Users/biocbuild/bbs-3.8-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/i386/libboost_regex.a -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pqsfinder'
    finding HTML links ... done
    PQSViews-class                          html  
    finding level-2 HTML links ... done

    PQSViews                                html  
    as.character-PQSViews-method            html  
    density-PQSViews-method                 html  
    maxScores-PQSViews-method               html  
    maxScores                               html  
    pqsfinder                               html  
    score-PQSViews-method                   html  
    show-PQSViews-method                    html  
    strand-PQSViews-method                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'pqsfinder' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pqsfinder.cpp -o pqsfinder.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/c_regex_traits.cpp -o boost_regex/c_regex_traits.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/cpp_regex_traits.cpp -o boost_regex/cpp_regex_traits.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/cregex.cpp -o boost_regex/cregex.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/fileiter.cpp -o boost_regex/fileiter.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/icu.cpp -o boost_regex/icu.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/instances.cpp -o boost_regex/instances.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/regex.cpp -o boost_regex/regex.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/regex_raw_buffer.cpp -o boost_regex/regex_raw_buffer.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/regex_traits_defaults.cpp -o boost_regex/regex_traits_defaults.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/usinstances.cpp -o boost_regex/usinstances.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/w32_regex_traits.cpp -o boost_regex/w32_regex_traits.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/wc_regex_traits.cpp -o boost_regex/wc_regex_traits.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c boost_regex/winstances.cpp -o boost_regex/winstances.o
mkdir -p "C:/Users/biocbuild/bbs-3.8-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/x64"
C:/Rtools/mingw_64/bin/ar rs "C:/Users/biocbuild/bbs-3.8-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/x64/libboost_regex.a" boost_regex/c_regex_traits.o boost_regex/cpp_regex_traits.o boost_regex/cregex.o boost_regex/fileiter.o boost_regex/icu.o boost_regex/instances.o boost_regex/posix_api.o boost_regex/regex.o boost_regex/regex_debug.o boost_regex/regex_raw_buffer.o boost_regex/regex_traits_defaults.o boost_regex/static_mutex.o boost_regex/usinstances.o boost_regex/w32_regex_traits.o boost_regex/wc_regex_traits.o boost_regex/wide_posix_api.o boost_regex/winstances.o
C:\Rtools\mingw_64\bin\ar.exe: creating C:/Users/biocbuild/bbs-3.8-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/x64/libboost_regex.a
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o pqsfinder.dll tmp.def RcppExports.o pqsfinder.o C:/Users/biocbuild/bbs-3.8-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/x64/libboost_regex.a -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pqsfinder' as pqsfinder_1.10.1.zip
* DONE (pqsfinder)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'pqsfinder' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

pqsfinder.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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(pqsfinder)
Loading required package: Biostrings
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, lengths, 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
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: XVector

Attaching package: 'Biostrings'

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

    strsplit

> 
> test_check("pqsfinder")
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: 40% ETTC 00:00:01
Search status: 46% ETTC 00:00:03
Search status: 47% ETTC 00:00:04
Search status: 48% ETTC 00:00:06
Search status: 49% ETTC 00:00:08
Search status: 56% ETTC 00:00:07
Search status: 88% ETTC 00:00:01
Search status: finished              
Searching on sense strand...
Search status: 1% ETTC 00:00:00
Search status: 1% ETTC 00:01:39
Search status: 14% ETTC 00:00:12
Search status: 23% ETTC 00:00:10
Search status: 30% ETTC 00:00:07
Search status: 30% ETTC 00:00:09
Search status: 36% ETTC 00:00:08
Search status: 36% ETTC 00:00:08
Search status: 38% ETTC 00:00:09
Search status: 40% ETTC 00:00:10
Search status: 42% ETTC 00:00:11
Search status: 43% ETTC 00:00:10
Search status: 45% ETTC 00:00:11
Search status: 45% ETTC 00:00:12
Search status: 46% ETTC 00:00:11
Search status: 46% ETTC 00:00:12
Search status: 46% ETTC 00:00:12
Search status: 46% ETTC 00:00:14
Search status: 46% ETTC 00:00:14
Search status: 46% ETTC 00:00:15
Search status: 46% ETTC 00:00:16
Search status: 46% ETTC 00:00:16
Search status: 47% ETTC 00:00:16
Search status: 47% ETTC 00:00:16
Search status: 47% ETTC 00:00:18
Search status: 47% ETTC 00:00:19
Search status: 47% ETTC 00:00:19
Search status: 47% ETTC 00:00:20
Search status: 47% ETTC 00:00:20
Search status: 47% ETTC 00:00:21
Search status: 47% ETTC 00:00:21
Search status: 47% ETTC 00:00:22
Search status: 47% ETTC 00:00:22
Search status: 47% ETTC 00:00:23
Search status: 47% ETTC 00:00:24
Search status: 48% ETTC 00:00:23
Search status: 48% ETTC 00:00:24
Search status: 48% ETTC 00:00:26
Search status: 48% ETTC 00:00:26
Search status: 48% ETTC 00:00:27
Search status: 48% ETTC 00:00:27
Search status: 48% ETTC 00:00:28
Search status: 48% ETTC 00:00:29
Search status: 48% ETTC 00:00:29
Search status: 48% ETTC 00:00:30
Search status: 48% ETTC 00:00:30
Search status: 48% ETTC 00:00:31
Search status: 48% ETTC 00:00:31
Search status: 49% ETTC 00:00:31
Search status: 49% ETTC 00:00:32
Search status: 50% ETTC 00:00:31
Search status: 52% ETTC 00:00:29
Search status: 53% ETTC 00:00:29
Search status: 54% ETTC 00:00:28
Search status: 54% ETTC 00:00:28
Search status: 55% ETTC 00:00:28
Search status: 55% ETTC 00:00:29
Search status: 55% ETTC 00:00:29
Search status: 56% ETTC 00:00:29
Search status: 56% ETTC 00:00:29
Search status: 56% ETTC 00:00:29
Search status: 57% ETTC 00:00:29
Search status: 59% ETTC 00:00:27
Search status: 66% ETTC 00:00:20
Search status: 77% ETTC 00:00:12
Search status: 78% ETTC 00:00:11
Search status: 78% ETTC 00:00:12
Search status: 86% ETTC 00:00:07
Search status: 87% ETTC 00:00:06
Search status: 88% ETTC 00:00:06
Search status: 92% ETTC 00:00:04
Search status: finished              
  50000-letter "DNAString" instance
seq: GGAACACTTTTACACTGTTGGTGGGACTGTAAACTA...TATGAGTCATGTTGCAGATCTAAAGTGAGGTAGTTG
##gff-version 3
##source-version rtracklayer 1.42.2
##date 2019-04-13
chr1	pqsfinder	G_quartet	433	447	27	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=5;ll2=2;ll3=0
chr1	pqsfinder	G_quartet	461	489	99	+	.	nt=4;nb=0;nm=0;rl1=4;rl2=4;rl3=4;ll1=8;ll2=3;ll3=2
chr1	pqsfinder	G_quartet	990	1005	26	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=2;ll2=6;ll3=0
chr1	pqsfinder	G_quartet	4522	4536	27	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=0;ll2=6;ll3=1
chr1	pqsfinder	G_quartet	6645	6663	49	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=3;rl3=3;ll1=1;ll2=4;ll3=1
chr1	pqsfinder	G_quartet	9421	9447	55	+	.	nt=4;nb=1;nm=1;rl1=4;rl2=4;rl3=4;ll1=3;ll2=6;ll3=1
chr1	pqsfinder	G_quartet	10511	10535	31	+	.	nt=3;nb=0;nm=1;rl1=3;rl2=3;rl3=3;ll1=6;ll2=6;ll3=1
chr1	pqsfinder	G_quartet	10961	10972	32	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=1;ll2=3;ll3=0
chr1	pqsfinder	G_quartet	11318	11331	29	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=1;ll2=4;ll3=1
chr1	pqsfinder	G_quartet	11481	11490	35	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=0;ll2=1;ll3=1
chr1	pqsfinder	G_quartet	11772	11787	26	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=2;ll2=1;ll3=5
chr1	pqsfinder	G_quartet	14139	14150	32	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=2;ll2=2;ll3=0
chr1	pqsfinder	G_quartet	14923	14937	27	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=5;ll2=2;ll3=0
chr1	pqsfinder	G_quartet	14951	14980	109	+	.	nt=5;nb=2;nm=0;rl1=8;rl2=5;rl3=7;ll1=3;ll2=2;ll3=0
chr1	pqsfinder	G_quartet	15518	15530	30	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=0;ll2=1;ll3=4
chr1	pqsfinder	G_quartet	17552	17565	29	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=4;ll2=2;ll3=0
chr1	pqsfinder	G_quartet	17695	17729	44	+	.	nt=4;nb=3;nm=0;rl1=5;rl2=11;rl3=7;ll1=2;ll2=3;ll3=3
chr1	pqsfinder	G_quartet	18706	18730	78	+	.	nt=5;nb=1;nm=2;rl1=5;rl2=5;rl3=8;ll1=1;ll2=0;ll3=1
chr1	pqsfinder	G_quartet	19169	19204	32	+	.	nt=4;nb=2;nm=1;rl1=11;rl2=6;rl3=4;ll1=2;ll2=9;ll3=0
chr1	pqsfinder	G_quartet	20011	20047	30	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=9;rl3=3;ll1=1;ll2=11;ll3=7
chr1	pqsfinder	G_quartet	20191	20220	35	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=6;rl3=3;ll1=3;ll2=4;ll3=8
chr1	pqsfinder	G_quartet	20455	20483	27	+	.	nt=3;nb=2;nm=0;rl1=3;rl2=3;rl3=8;ll1=3;ll2=2;ll3=1
chr1	pqsfinder	G_quartet	20817	20828	32	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=1;ll2=3;ll3=0
chr1	pqsfinder	G_quartet	21070	21095	46	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=10;rl3=3;ll1=3;ll2=2;ll3=2
chr1	pqsfinder	G_quartet	21193	21221	30	+	.	nt=3;nb=2;nm=0;rl1=3;rl2=9;rl3=10;ll1=0;ll2=3;ll3=1
chr1	pqsfinder	G_quartet	21465	21477	30	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=0;ll2=4;ll3=1
chr1	pqsfinder	G_quartet	21529	21542	29	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=4;ll2=1;ll3=1
chr1	pqsfinder	G_quartet	22410	22433	87	+	.	nt=4;nb=1;nm=0;rl1=4;rl2=5;rl3=4;ll1=1;ll2=3;ll3=3
chr1	pqsfinder	G_quartet	22569	22595	56	+	.	nt=3;nb=0;nm=0;rl1=3;rl2=3;rl3=3;ll1=3;ll2=10;ll3=2
chr1	pqsfinder	G_quartet	22703	22737	30	+	.	nt=4;nb=2;nm=1;rl1=4;rl2=4;rl3=9;ll1=10;ll2=2;ll3=1
chr1	pqsfinder	G_quartet	22806	22841	44	+	.	nt=4;nb=3;nm=0;rl1=10;rl2=9;rl3=5;ll1=3;ll2=2;ll3=3
chr1	pqsfinder	G_quartet	22978	23019	54	+	.	nt=4;nb=2;nm=0;rl1=4;rl2=10;rl3=9;ll1=1;ll2=2;ll3=12
chr1	pqsfinder	G_quartet	23182	23204	61	+	.	nt=3;nb=0;nm=0;rl1=3;rl2=3;rl3=3;ll1=6;ll2=5;ll3=0
chr1	pqsfinder	G_quartet	23266	23292	71	+	.	nt=4;nb=2;nm=0;rl1=4;rl2=4;rl3=10;ll1=1;ll2=3;ll3=0
chr1	pqsfinder	G_quartet	23328	23365	43	+	.	nt=3;nb=0;nm=0;rl1=3;rl2=3;rl3=3;ll1=1;ll2=24;ll3=1
chr1	pqsfinder	G_quartet	23399	23439	84	+	.	nt=5;nb=3;nm=0;rl1=5;rl2=9;rl3=10;ll1=3;ll2=4;ll3=0
chr1	pqsfinder	G_quartet	23469	23500	64	+	.	nt=4;nb=2;nm=0;rl1=4;rl2=8;rl3=8;ll1=3;ll2=1;ll3=4
chr1	pqsfinder	G_quartet	23599	23641	41	+	.	nt=4;nb=3;nm=0;rl1=4;rl2=9;rl3=11;ll1=3;ll2=4;ll3=2
chr1	pqsfinder	G_quartet	23655	23690	82	+	.	nt=5;nb=3;nm=0;rl1=8;rl2=6;rl3=8;ll1=7;ll2=1;ll3=1
chr1	pqsfinder	G_quartet	23706	23737	38	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=11;rl3=3;ll1=5;ll2=6;ll3=1
chr1	pqsfinder	G_quartet	23762	23794	50	+	.	nt=4;nb=1;nm=1;rl1=4;rl2=8;rl3=4;ll1=3;ll2=8;ll3=2
chr1	pqsfinder	G_quartet	23804	23839	45	+	.	nt=3;nb=0;nm=0;rl1=3;rl2=3;rl3=3;ll1=10;ll2=11;ll3=3
chr1	pqsfinder	G_quartet	23929	23963	34	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=3;rl3=11;ll1=5;ll2=9;ll3=1
chr1	pqsfinder	G_quartet	23994	24015	63	+	.	nt=3;nb=0;nm=0;rl1=3;rl2=3;rl3=3;ll1=4;ll2=1;ll3=5
chr1	pqsfinder	G_quartet	24039	24076	57	+	.	nt=4;nb=2;nm=0;rl1=4;rl2=10;rl3=4;ll1=4;ll2=8;ll3=1
chr1	pqsfinder	G_quartet	24336	24360	31	+	.	nt=3;nb=0;nm=1;rl1=3;rl2=3;rl3=3;ll1=0;ll2=2;ll3=11
chr1	pqsfinder	G_quartet	24479	24511	45	+	.	nt=4;nb=3;nm=0;rl1=4;rl2=9;rl3=8;ll1=6;ll2=0;ll3=1
chr1	pqsfinder	G_quartet	24572	24620	31	+	.	nt=3;nb=0;nm=0;rl1=3;rl2=3;rl3=3;ll1=7;ll2=27;ll3=3
chr1	pqsfinder	G_quartet	25186	25222	40	+	.	nt=4;nb=3;nm=0;rl1=7;rl2=9;rl3=4;ll1=1;ll2=8;ll3=1
chr1	pqsfinder	G_quartet	25698	25710	30	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=1;ll2=3;ll3=1
chr1	pqsfinder	G_quartet	26086	26101	26	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=4;ll2=2;ll3=2
chr1	pqsfinder	G_quartet	26184	26232	59	+	.	nt=5;nb=2;nm=1;rl1=5;rl2=9;rl3=5;ll1=9;ll2=7;ll3=5
chr1	pqsfinder	G_quartet	26326	26340	27	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=1;ll2=4;ll3=2
chr1	pqsfinder	G_quartet	26543	26558	26	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=1;ll2=5;ll3=2
chr1	pqsfinder	G_quartet	26576	26586	33	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=1;ll2=2;ll3=0
chr1	pqsfinder	G_quartet	26671	26720	71	+	.	nt=5;nb=3;nm=0;rl1=11;rl2=9;rl3=5;ll1=1;ll2=2;ll3=14
chr1	pqsfinder	G_quartet	26751	26773	26	+	.	nt=3;nb=2;nm=0;rl1=3;rl2=4;rl3=3;ll1=4;ll2=3;ll3=1
chr1	pqsfinder	G_quartet	27061	27079	30	+	.	nt=3;nb=2;nm=0;rl1=4;rl2=4;rl3=3;ll1=2;ll2=2;ll3=1
chr1	pqsfinder	G_quartet	27365	27398	45	+	.	nt=4;nb=3;nm=0;rl1=11;rl2=7;rl3=4;ll1=1;ll2=4;ll3=2
chr1	pqsfinder	G_quartet	27427	27446	54	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=9;rl3=3;ll1=1;ll2=0;ll3=1
chr1	pqsfinder	G_quartet	27560	27575	26	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=0;ll2=7;ll3=1
chr1	pqsfinder	G_quartet	27690	27732	86	+	.	nt=5;nb=3;nm=0;rl1=5;rl2=10;rl3=11;ll1=2;ll2=2;ll3=2
chr1	pqsfinder	G_quartet	27773	27810	44	+	.	nt=4;nb=3;nm=0;rl1=9;rl2=8;rl3=10;ll1=3;ll2=4;ll3=0
chr1	pqsfinder	G_quartet	28003	28016	29	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=1;ll2=1;ll3=4
chr1	pqsfinder	G_quartet	28176	28204	31	+	.	nt=3;nb=2;nm=0;rl1=3;rl2=10;rl3=10;ll1=1;ll2=1;ll3=1
chr1	pqsfinder	G_quartet	28542	28556	27	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=2;ll2=3;ll3=2
chr1	pqsfinder	G_quartet	28637	28672	28	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=3;rl3=3;ll1=15;ll2=1;ll3=5
chr1	pqsfinder	G_quartet	29060	29097	42	+	.	nt=4;nb=1;nm=1;rl1=4;rl2=4;rl3=6;ll1=18;ll2=1;ll3=1
chr1	pqsfinder	G_quartet	29175	29188	29	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=0;ll2=4;ll3=2
chr1	pqsfinder	G_quartet	29242	29276	29	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=6;rl3=3;ll1=0;ll2=19;ll3=1
chr1	pqsfinder	G_quartet	29361	29375	27	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=4;ll2=2;ll3=1
chr1	pqsfinder	G_quartet	29632	29643	32	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=0;ll2=1;ll3=3
chr1	pqsfinder	G_quartet	29762	29773	32	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=2;ll2=2;ll3=0
chr1	pqsfinder	G_quartet	29818	29833	26	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=2;ll2=6;ll3=0
chr1	pqsfinder	G_quartet	29972	29987	26	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=0;ll2=7;ll3=1
chr1	pqsfinder	G_quartet	31092	31106	27	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=5;ll2=2;ll3=0
chr1	pqsfinder	G_quartet	35419	35456	30	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=10;rl3=3;ll1=16;ll2=0;ll3=3
chr1	pqsfinder	G_quartet	36912	36927	26	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=2;ll2=2;ll3=4
chr1	pqsfinder	G_quartet	37586	37595	35	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=1;ll2=1;ll3=0
chr1	pqsfinder	G_quartet	38366	38377	32	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=1;ll2=1;ll3=2
chr1	pqsfinder	G_quartet	38495	38519	54	+	.	nt=4;nb=3;nm=0;rl1=4;rl2=8;rl3=5;ll1=1;ll2=1;ll3=0
chr1	pqsfinder	G_quartet	38564	38588	59	+	.	nt=3;nb=0;nm=0;rl1=3;rl2=3;rl3=3;ll1=1;ll2=2;ll3=10
chr1	pqsfinder	G_quartet	38629	38663	46	+	.	nt=3;nb=0;nm=0;rl1=3;rl2=3;rl3=3;ll1=1;ll2=20;ll3=2
chr1	pqsfinder	G_quartet	38972	38987	26	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=4;ll2=3;ll3=1
chr1	pqsfinder	G_quartet	39234	39257	43	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=3;rl3=3;ll1=0;ll2=9;ll3=1
chr1	pqsfinder	G_quartet	42399	42425	30	+	.	nt=3;nb=2;nm=0;rl1=3;rl2=7;rl3=3;ll1=1;ll2=2;ll3=1
chr1	pqsfinder	G_quartet	42499	42511	30	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=3;ll2=1;ll3=1
chr1	pqsfinder	G_quartet	42535	42549	27	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=1;ll2=4;ll3=2
chr1	pqsfinder	G_quartet	43058	43095	30	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=10;rl3=3;ll1=13;ll2=5;ll3=1
chr1	pqsfinder	G_quartet	43121	43144	69	+	.	nt=4;nb=2;nm=0;rl1=4;rl2=5;rl3=4;ll1=2;ll2=3;ll3=1
chr1	pqsfinder	G_quartet	43370	43384	27	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=1;ll2=4;ll3=2
chr1	pqsfinder	G_quartet	43876	43898	90	+	.	nt=4;nb=1;nm=0;rl1=6;rl2=4;rl3=4;ll1=2;ll2=2;ll3=1
chr1	pqsfinder	G_quartet	44165	44191	31	+	.	nt=3;nb=2;nm=0;rl1=3;rl2=8;rl3=3;ll1=1;ll2=1;ll3=1
chr1	pqsfinder	G_quartet	44513	44539	31	+	.	nt=3;nb=2;nm=0;rl1=3;rl2=8;rl3=3;ll1=1;ll2=1;ll3=1
chr1	pqsfinder	G_quartet	45555	45580	31	+	.	nt=3;nb=2;nm=0;rl1=3;rl2=8;rl3=3;ll1=1;ll2=1;ll3=1
chr1	pqsfinder	G_quartet	46333	46360	36	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=3;rl3=3;ll1=1;ll2=12;ll3=2
chr1	pqsfinder	G_quartet	49197	49213	42	+	.	nt=3;nb=0;nm=1;rl1=3;rl2=3;rl3=3;ll1=3;ll2=1;ll3=1
chr1	pqsfinder	G_quartet	49606	49627	29	+	.	nt=3;nb=2;nm=0;rl1=3;rl2=7;rl3=3;ll1=2;ll2=2;ll3=1
pv_d, pv_r
pqsfinder_1_4_4_d, pqsfinder_1_4_4_r
pv_d, pqsfinder_1_4_4_d
Searching on sense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
== testthat results  ===========================================================
OK: 25 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  66.51    0.62   67.12

pqsfinder.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(testthat)
> library(pqsfinder)
Loading required package: Biostrings
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, lengths, 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
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: XVector

Attaching package: 'Biostrings'

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

    strsplit

> 
> test_check("pqsfinder")
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: 40% ETTC 00:00:01
Search status: 46% ETTC 00:00:02
Search status: 47% ETTC 00:00:03
Search status: 48% ETTC 00:00:05
Search status: 49% ETTC 00:00:06
Search status: 56% ETTC 00:00:06
Search status: 88% ETTC 00:00:01
Search status: finished              
Searching on sense strand...
Search status: 1% ETTC 00:00:00
Search status: 1% ETTC 00:01:39
Search status: 14% ETTC 00:00:12
Search status: 23% ETTC 00:00:10
Search status: 30% ETTC 00:00:07
Search status: 30% ETTC 00:00:09
Search status: 36% ETTC 00:00:08
Search status: 36% ETTC 00:00:08
Search status: 38% ETTC 00:00:09
Search status: 40% ETTC 00:00:10
Search status: 42% ETTC 00:00:11
Search status: 43% ETTC 00:00:10
Search status: 45% ETTC 00:00:11
Search status: 45% ETTC 00:00:12
Search status: 46% ETTC 00:00:11
Search status: 46% ETTC 00:00:12
Search status: 46% ETTC 00:00:12
Search status: 46% ETTC 00:00:14
Search status: 46% ETTC 00:00:15
Search status: 46% ETTC 00:00:15
Search status: 46% ETTC 00:00:16
Search status: 46% ETTC 00:00:16
Search status: 47% ETTC 00:00:16
Search status: 47% ETTC 00:00:16
Search status: 47% ETTC 00:00:18
Search status: 47% ETTC 00:00:19
Search status: 47% ETTC 00:00:19
Search status: 47% ETTC 00:00:20
Search status: 47% ETTC 00:00:21
Search status: 47% ETTC 00:00:22
Search status: 47% ETTC 00:00:22
Search status: 47% ETTC 00:00:23
Search status: 47% ETTC 00:00:24
Search status: 47% ETTC 00:00:25
Search status: 47% ETTC 00:00:27
Search status: 48% ETTC 00:00:27
Search status: 48% ETTC 00:00:27
Search status: 48% ETTC 00:00:28
Search status: 48% ETTC 00:00:29
Search status: 48% ETTC 00:00:29
Search status: 48% ETTC 00:00:30
Search status: 48% ETTC 00:00:30
Search status: 48% ETTC 00:00:31
Search status: 48% ETTC 00:00:32
Search status: 48% ETTC 00:00:33
Search status: 48% ETTC 00:00:34
Search status: 48% ETTC 00:00:34
Search status: 48% ETTC 00:00:35
Search status: 49% ETTC 00:00:34
Search status: 49% ETTC 00:00:35
Search status: 50% ETTC 00:00:35
Search status: 52% ETTC 00:00:32
Search status: 53% ETTC 00:00:31
Search status: 54% ETTC 00:00:31
Search status: 54% ETTC 00:00:31
Search status: 55% ETTC 00:00:31
Search status: 55% ETTC 00:00:31
Search status: 55% ETTC 00:00:32
Search status: 56% ETTC 00:00:31
Search status: 56% ETTC 00:00:32
Search status: 56% ETTC 00:00:33
Search status: 57% ETTC 00:00:32
Search status: 59% ETTC 00:00:29
Search status: 66% ETTC 00:00:22
Search status: 77% ETTC 00:00:13
Search status: 78% ETTC 00:00:12
Search status: 78% ETTC 00:00:12
Search status: 86% ETTC 00:00:07
Search status: 87% ETTC 00:00:07
Search status: 88% ETTC 00:00:06
Search status: 92% ETTC 00:00:04
Search status: finished              
  50000-letter "DNAString" instance
seq: GGAACACTTTTACACTGTTGGTGGGACTGTAAACTA...TATGAGTCATGTTGCAGATCTAAAGTGAGGTAGTTG
##gff-version 3
##source-version rtracklayer 1.42.2
##date 2019-04-13
chr1	pqsfinder	G_quartet	433	447	27	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=5;ll2=2;ll3=0
chr1	pqsfinder	G_quartet	461	489	99	+	.	nt=4;nb=0;nm=0;rl1=4;rl2=4;rl3=4;ll1=8;ll2=3;ll3=2
chr1	pqsfinder	G_quartet	990	1005	26	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=2;ll2=6;ll3=0
chr1	pqsfinder	G_quartet	4522	4536	27	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=0;ll2=6;ll3=1
chr1	pqsfinder	G_quartet	6645	6663	49	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=3;rl3=3;ll1=1;ll2=4;ll3=1
chr1	pqsfinder	G_quartet	9421	9447	55	+	.	nt=4;nb=1;nm=1;rl1=4;rl2=4;rl3=4;ll1=3;ll2=6;ll3=1
chr1	pqsfinder	G_quartet	10511	10535	31	+	.	nt=3;nb=0;nm=1;rl1=3;rl2=3;rl3=3;ll1=6;ll2=6;ll3=1
chr1	pqsfinder	G_quartet	10961	10972	32	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=1;ll2=3;ll3=0
chr1	pqsfinder	G_quartet	11318	11331	29	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=1;ll2=4;ll3=1
chr1	pqsfinder	G_quartet	11481	11490	35	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=0;ll2=1;ll3=1
chr1	pqsfinder	G_quartet	11772	11787	26	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=2;ll2=1;ll3=5
chr1	pqsfinder	G_quartet	14139	14150	32	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=2;ll2=2;ll3=0
chr1	pqsfinder	G_quartet	14923	14937	27	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=5;ll2=2;ll3=0
chr1	pqsfinder	G_quartet	14951	14980	109	+	.	nt=5;nb=2;nm=0;rl1=8;rl2=5;rl3=7;ll1=3;ll2=2;ll3=0
chr1	pqsfinder	G_quartet	15518	15530	30	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=0;ll2=1;ll3=4
chr1	pqsfinder	G_quartet	17552	17565	29	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=4;ll2=2;ll3=0
chr1	pqsfinder	G_quartet	17695	17729	44	+	.	nt=4;nb=3;nm=0;rl1=5;rl2=11;rl3=7;ll1=2;ll2=3;ll3=3
chr1	pqsfinder	G_quartet	18706	18730	78	+	.	nt=5;nb=1;nm=2;rl1=5;rl2=5;rl3=8;ll1=1;ll2=0;ll3=1
chr1	pqsfinder	G_quartet	19169	19204	32	+	.	nt=4;nb=2;nm=1;rl1=11;rl2=6;rl3=4;ll1=2;ll2=9;ll3=0
chr1	pqsfinder	G_quartet	20011	20047	30	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=9;rl3=3;ll1=1;ll2=11;ll3=7
chr1	pqsfinder	G_quartet	20191	20220	35	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=6;rl3=3;ll1=3;ll2=4;ll3=8
chr1	pqsfinder	G_quartet	20455	20483	27	+	.	nt=3;nb=2;nm=0;rl1=3;rl2=3;rl3=8;ll1=3;ll2=2;ll3=1
chr1	pqsfinder	G_quartet	20817	20828	32	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=1;ll2=3;ll3=0
chr1	pqsfinder	G_quartet	21070	21095	46	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=10;rl3=3;ll1=3;ll2=2;ll3=2
chr1	pqsfinder	G_quartet	21193	21221	30	+	.	nt=3;nb=2;nm=0;rl1=3;rl2=9;rl3=10;ll1=0;ll2=3;ll3=1
chr1	pqsfinder	G_quartet	21465	21477	30	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=0;ll2=4;ll3=1
chr1	pqsfinder	G_quartet	21529	21542	29	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=4;ll2=1;ll3=1
chr1	pqsfinder	G_quartet	22410	22433	87	+	.	nt=4;nb=1;nm=0;rl1=4;rl2=5;rl3=4;ll1=1;ll2=3;ll3=3
chr1	pqsfinder	G_quartet	22569	22595	56	+	.	nt=3;nb=0;nm=0;rl1=3;rl2=3;rl3=3;ll1=3;ll2=10;ll3=2
chr1	pqsfinder	G_quartet	22703	22737	30	+	.	nt=4;nb=2;nm=1;rl1=4;rl2=4;rl3=9;ll1=10;ll2=2;ll3=1
chr1	pqsfinder	G_quartet	22806	22841	44	+	.	nt=4;nb=3;nm=0;rl1=10;rl2=9;rl3=5;ll1=3;ll2=2;ll3=3
chr1	pqsfinder	G_quartet	22978	23019	54	+	.	nt=4;nb=2;nm=0;rl1=4;rl2=10;rl3=9;ll1=1;ll2=2;ll3=12
chr1	pqsfinder	G_quartet	23182	23204	61	+	.	nt=3;nb=0;nm=0;rl1=3;rl2=3;rl3=3;ll1=6;ll2=5;ll3=0
chr1	pqsfinder	G_quartet	23266	23292	71	+	.	nt=4;nb=2;nm=0;rl1=4;rl2=4;rl3=10;ll1=1;ll2=3;ll3=0
chr1	pqsfinder	G_quartet	23328	23365	43	+	.	nt=3;nb=0;nm=0;rl1=3;rl2=3;rl3=3;ll1=1;ll2=24;ll3=1
chr1	pqsfinder	G_quartet	23399	23439	84	+	.	nt=5;nb=3;nm=0;rl1=5;rl2=9;rl3=10;ll1=3;ll2=4;ll3=0
chr1	pqsfinder	G_quartet	23469	23500	64	+	.	nt=4;nb=2;nm=0;rl1=4;rl2=8;rl3=8;ll1=3;ll2=1;ll3=4
chr1	pqsfinder	G_quartet	23599	23641	41	+	.	nt=4;nb=3;nm=0;rl1=4;rl2=9;rl3=11;ll1=3;ll2=4;ll3=2
chr1	pqsfinder	G_quartet	23655	23690	82	+	.	nt=5;nb=3;nm=0;rl1=8;rl2=6;rl3=8;ll1=7;ll2=1;ll3=1
chr1	pqsfinder	G_quartet	23706	23737	38	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=11;rl3=3;ll1=5;ll2=6;ll3=1
chr1	pqsfinder	G_quartet	23762	23794	50	+	.	nt=4;nb=1;nm=1;rl1=4;rl2=8;rl3=4;ll1=3;ll2=8;ll3=2
chr1	pqsfinder	G_quartet	23804	23839	45	+	.	nt=3;nb=0;nm=0;rl1=3;rl2=3;rl3=3;ll1=10;ll2=11;ll3=3
chr1	pqsfinder	G_quartet	23929	23963	34	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=3;rl3=11;ll1=5;ll2=9;ll3=1
chr1	pqsfinder	G_quartet	23994	24015	63	+	.	nt=3;nb=0;nm=0;rl1=3;rl2=3;rl3=3;ll1=4;ll2=1;ll3=5
chr1	pqsfinder	G_quartet	24039	24076	57	+	.	nt=4;nb=2;nm=0;rl1=4;rl2=10;rl3=4;ll1=4;ll2=8;ll3=1
chr1	pqsfinder	G_quartet	24336	24360	31	+	.	nt=3;nb=0;nm=1;rl1=3;rl2=3;rl3=3;ll1=0;ll2=2;ll3=11
chr1	pqsfinder	G_quartet	24479	24511	45	+	.	nt=4;nb=3;nm=0;rl1=4;rl2=9;rl3=8;ll1=6;ll2=0;ll3=1
chr1	pqsfinder	G_quartet	24572	24620	31	+	.	nt=3;nb=0;nm=0;rl1=3;rl2=3;rl3=3;ll1=7;ll2=27;ll3=3
chr1	pqsfinder	G_quartet	25186	25222	40	+	.	nt=4;nb=3;nm=0;rl1=7;rl2=9;rl3=4;ll1=1;ll2=8;ll3=1
chr1	pqsfinder	G_quartet	25698	25710	30	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=1;ll2=3;ll3=1
chr1	pqsfinder	G_quartet	26086	26101	26	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=4;ll2=2;ll3=2
chr1	pqsfinder	G_quartet	26184	26232	59	+	.	nt=5;nb=2;nm=1;rl1=5;rl2=9;rl3=5;ll1=9;ll2=7;ll3=5
chr1	pqsfinder	G_quartet	26326	26340	27	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=1;ll2=4;ll3=2
chr1	pqsfinder	G_quartet	26543	26558	26	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=1;ll2=5;ll3=2
chr1	pqsfinder	G_quartet	26576	26586	33	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=1;ll2=2;ll3=0
chr1	pqsfinder	G_quartet	26671	26720	71	+	.	nt=5;nb=3;nm=0;rl1=11;rl2=9;rl3=5;ll1=1;ll2=2;ll3=14
chr1	pqsfinder	G_quartet	26751	26773	26	+	.	nt=3;nb=2;nm=0;rl1=3;rl2=4;rl3=3;ll1=4;ll2=3;ll3=1
chr1	pqsfinder	G_quartet	27061	27079	30	+	.	nt=3;nb=2;nm=0;rl1=4;rl2=4;rl3=3;ll1=2;ll2=2;ll3=1
chr1	pqsfinder	G_quartet	27365	27398	45	+	.	nt=4;nb=3;nm=0;rl1=11;rl2=7;rl3=4;ll1=1;ll2=4;ll3=2
chr1	pqsfinder	G_quartet	27427	27446	54	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=9;rl3=3;ll1=1;ll2=0;ll3=1
chr1	pqsfinder	G_quartet	27560	27575	26	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=0;ll2=7;ll3=1
chr1	pqsfinder	G_quartet	27690	27732	86	+	.	nt=5;nb=3;nm=0;rl1=5;rl2=10;rl3=11;ll1=2;ll2=2;ll3=2
chr1	pqsfinder	G_quartet	27773	27810	44	+	.	nt=4;nb=3;nm=0;rl1=9;rl2=8;rl3=10;ll1=3;ll2=4;ll3=0
chr1	pqsfinder	G_quartet	28003	28016	29	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=1;ll2=1;ll3=4
chr1	pqsfinder	G_quartet	28176	28204	31	+	.	nt=3;nb=2;nm=0;rl1=3;rl2=10;rl3=10;ll1=1;ll2=1;ll3=1
chr1	pqsfinder	G_quartet	28542	28556	27	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=2;ll2=3;ll3=2
chr1	pqsfinder	G_quartet	28637	28672	28	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=3;rl3=3;ll1=15;ll2=1;ll3=5
chr1	pqsfinder	G_quartet	29060	29097	42	+	.	nt=4;nb=1;nm=1;rl1=4;rl2=4;rl3=6;ll1=18;ll2=1;ll3=1
chr1	pqsfinder	G_quartet	29175	29188	29	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=0;ll2=4;ll3=2
chr1	pqsfinder	G_quartet	29242	29276	29	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=6;rl3=3;ll1=0;ll2=19;ll3=1
chr1	pqsfinder	G_quartet	29361	29375	27	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=4;ll2=2;ll3=1
chr1	pqsfinder	G_quartet	29632	29643	32	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=0;ll2=1;ll3=3
chr1	pqsfinder	G_quartet	29762	29773	32	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=2;ll2=2;ll3=0
chr1	pqsfinder	G_quartet	29818	29833	26	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=2;ll2=6;ll3=0
chr1	pqsfinder	G_quartet	29972	29987	26	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=0;ll2=7;ll3=1
chr1	pqsfinder	G_quartet	31092	31106	27	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=5;ll2=2;ll3=0
chr1	pqsfinder	G_quartet	35419	35456	30	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=10;rl3=3;ll1=16;ll2=0;ll3=3
chr1	pqsfinder	G_quartet	36912	36927	26	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=2;ll2=2;ll3=4
chr1	pqsfinder	G_quartet	37586	37595	35	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=1;ll2=1;ll3=0
chr1	pqsfinder	G_quartet	38366	38377	32	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=1;ll2=1;ll3=2
chr1	pqsfinder	G_quartet	38495	38519	54	+	.	nt=4;nb=3;nm=0;rl1=4;rl2=8;rl3=5;ll1=1;ll2=1;ll3=0
chr1	pqsfinder	G_quartet	38564	38588	59	+	.	nt=3;nb=0;nm=0;rl1=3;rl2=3;rl3=3;ll1=1;ll2=2;ll3=10
chr1	pqsfinder	G_quartet	38629	38663	46	+	.	nt=3;nb=0;nm=0;rl1=3;rl2=3;rl3=3;ll1=1;ll2=20;ll3=2
chr1	pqsfinder	G_quartet	38972	38987	26	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=4;ll2=3;ll3=1
chr1	pqsfinder	G_quartet	39234	39257	43	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=3;rl3=3;ll1=0;ll2=9;ll3=1
chr1	pqsfinder	G_quartet	42399	42425	30	+	.	nt=3;nb=2;nm=0;rl1=3;rl2=7;rl3=3;ll1=1;ll2=2;ll3=1
chr1	pqsfinder	G_quartet	42499	42511	30	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=3;ll2=1;ll3=1
chr1	pqsfinder	G_quartet	42535	42549	27	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=1;ll2=4;ll3=2
chr1	pqsfinder	G_quartet	43058	43095	30	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=10;rl3=3;ll1=13;ll2=5;ll3=1
chr1	pqsfinder	G_quartet	43121	43144	69	+	.	nt=4;nb=2;nm=0;rl1=4;rl2=5;rl3=4;ll1=2;ll2=3;ll3=1
chr1	pqsfinder	G_quartet	43370	43384	27	+	.	nt=2;nb=0;nm=0;rl1=2;rl2=2;rl3=2;ll1=1;ll2=4;ll3=2
chr1	pqsfinder	G_quartet	43876	43898	90	+	.	nt=4;nb=1;nm=0;rl1=6;rl2=4;rl3=4;ll1=2;ll2=2;ll3=1
chr1	pqsfinder	G_quartet	44165	44191	31	+	.	nt=3;nb=2;nm=0;rl1=3;rl2=8;rl3=3;ll1=1;ll2=1;ll3=1
chr1	pqsfinder	G_quartet	44513	44539	31	+	.	nt=3;nb=2;nm=0;rl1=3;rl2=8;rl3=3;ll1=1;ll2=1;ll3=1
chr1	pqsfinder	G_quartet	45555	45580	31	+	.	nt=3;nb=2;nm=0;rl1=3;rl2=8;rl3=3;ll1=1;ll2=1;ll3=1
chr1	pqsfinder	G_quartet	46333	46360	36	+	.	nt=3;nb=1;nm=0;rl1=3;rl2=3;rl3=3;ll1=1;ll2=12;ll3=2
chr1	pqsfinder	G_quartet	49197	49213	42	+	.	nt=3;nb=0;nm=1;rl1=3;rl2=3;rl3=3;ll1=3;ll2=1;ll3=1
chr1	pqsfinder	G_quartet	49606	49627	29	+	.	nt=3;nb=2;nm=0;rl1=3;rl2=7;rl3=3;ll1=2;ll2=2;ll3=1
pv_d, pv_r
pqsfinder_1_4_4_d, pqsfinder_1_4_4_r
pv_d, pqsfinder_1_4_4_d
Searching on sense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
== testthat results  ===========================================================
OK: 25 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  70.45    0.40   70.98

Example timings

pqsfinder.Rcheck/examples_i386/pqsfinder-Ex.timings

nameusersystemelapsed
PQSViews0.030.030.07
density-PQSViews-method0.030.020.04
maxScores-PQSViews-method0.020.000.02
maxScores000
pqsfinder0.030.000.03
score-PQSViews-method0.010.000.02
strand-PQSViews-method0.020.000.01

pqsfinder.Rcheck/examples_x64/pqsfinder-Ex.timings

nameusersystemelapsed
PQSViews0.060.020.08
density-PQSViews-method0.030.000.09
maxScores-PQSViews-method0.020.000.01
maxScores0.010.000.02
pqsfinder0.020.000.02
score-PQSViews-method0.020.000.02
strand-PQSViews-method0.010.000.01