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CHECK report for pqsfinder on merida1

This page was generated on 2019-04-16 11:59:33 -0400 (Tue, 16 Apr 2019).

Package 1183/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pqsfinder 1.10.1
Jiri Hon
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 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
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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pqsfinder.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pqsfinder_1.10.1.tar.gz
StartedAt: 2019-04-16 01:59:17 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:02:20 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 182.1 seconds
RetCode: 0
Status:  OK 
CheckDir: pqsfinder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pqsfinder.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pqsfinder_1.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/pqsfinder.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* 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 ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘pqsfinder’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.8Mb
  sub-directories of 1Mb or more:
    lib   7.9Mb
* 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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/pqsfinder.Rcheck/00check.log’
for details.

Installation output

pqsfinder.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘pqsfinder’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c pqsfinder.cpp -o pqsfinder.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/c_regex_traits.cpp -o boost_regex/c_regex_traits.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/cpp_regex_traits.cpp -o boost_regex/cpp_regex_traits.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/cregex.cpp -o boost_regex/cregex.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/fileiter.cpp -o boost_regex/fileiter.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/icu.cpp -o boost_regex/icu.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/instances.cpp -o boost_regex/instances.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/regex.cpp -o boost_regex/regex.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/regex_raw_buffer.cpp -o boost_regex/regex_raw_buffer.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/regex_traits_defaults.cpp -o boost_regex/regex_traits_defaults.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/usinstances.cpp -o boost_regex/usinstances.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/w32_regex_traits.cpp -o boost_regex/w32_regex_traits.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/wc_regex_traits.cpp -o boost_regex/wc_regex_traits.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/winstances.cpp -o boost_regex/winstances.o
mkdir -p "/Library/Frameworks/R.framework/Versions/3.5/Resources/library/pqsfinder/lib"
ar rs "/Library/Frameworks/R.framework/Versions/3.5/Resources/library/pqsfinder/lib/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
ar: creating archive /Library/Frameworks/R.framework/Versions/3.5/Resources/library/pqsfinder/lib/libboost_regex.a
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/pqsfinder/lib/libboost_regex.a(icu.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/pqsfinder/lib/libboost_regex.a(instances.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/pqsfinder/lib/libboost_regex.a(regex_debug.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/pqsfinder/lib/libboost_regex.a(usinstances.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/pqsfinder/lib/libboost_regex.a(w32_regex_traits.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/pqsfinder/lib/libboost_regex.a(winstances.o) has no symbols
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o pqsfinder.so RcppExports.o pqsfinder.o /Library/Frameworks/R.framework/Versions/3.5/Resources/library/pqsfinder/lib/libboost_regex.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/pqsfinder/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pqsfinder)

Tests output

pqsfinder.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(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
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 00:00:05
Search status: 48% ETTC 00:00:07
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 00:00:13
Search status: 30% ETTC 00:00:11
Search status: 30% ETTC 00:00:11
Search status: 36% ETTC 00:00:10
Search status: 36% ETTC 00:00:12
Search status: 38% ETTC 00:00:13
Search status: 40% ETTC 00:00:13
Search status: 42% ETTC 00:00:13
Search status: 43% ETTC 00:00:14
Search status: 45% ETTC 00:00:14
Search status: 45% ETTC 00:00:15
Search status: 46% ETTC 00:00:16
Search status: 46% ETTC 00:00:16
Search status: 46% ETTC 00:00:17
Search status: 46% ETTC 00:00:18
Search status: 46% ETTC 00:00:19
Search status: 46% ETTC 00:00:21
Search status: 46% ETTC 00:00:21
Search status: 46% ETTC 00:00:22
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: 47% ETTC 00:00:27
Search status: 47% ETTC 00:00:28
Search status: 47% ETTC 00:00:29
Search status: 47% ETTC 00:00:29
Search status: 47% ETTC 00:00:30
Search status: 47% ETTC 00:00:31
Search status: 47% ETTC 00:00:32
Search status: 48% ETTC 00:00:32
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 00:00:35
Search status: 48% ETTC 00:00:35
Search status: 48% ETTC 00:00:36
Search status: 48% ETTC 00:00:37
Search status: 48% ETTC 00:00:39
Search status: 48% ETTC 00:00:39
Search status: 48% ETTC 00:00:40
Search status: 48% ETTC 00:00:41
Search status: 48% ETTC 00:00:41
Search status: 49% ETTC 00:00:40
Search status: 49% ETTC 00:00:41
Search status: 50% ETTC 00:00:41
Search status: 52% ETTC 00:00:38
Search status: 53% ETTC 00:00:38
Search status: 54% ETTC 00:00:37
Search status: 54% ETTC 00:00:37
Search status: 55% ETTC 00:00:37
Search status: 55% ETTC 00:00:37
Search status: 55% ETTC 00:00:38
Search status: 56% ETTC 00:00:37
Search status: 56% ETTC 00:00:38
Search status: 56% ETTC 00:00:39
Search status: 57% ETTC 00:00:38
Search status: 59% ETTC 00:00:36
Search status: 66% ETTC 00:00:27
Search status: 77% ETTC 00:00:16
Search status: 78% ETTC 00:00:15
Search status: 78% ETTC 00:00:15
Search status: 86% ETTC 00:00:09
Search status: 87% ETTC 00:00:08
Search status: 88% ETTC 00:00:08
Search status: 92% ETTC 00:00:05
Search status: finished              
  50000-letter "DNAString" instance
seq: GGAACACTTTTACACTGTTGGTGGGACTGTAAACTA...TATGAGTCATGTTGCAGATCTAAAGTGAGGTAGTTG
##gff-version 3
##source-version rtracklayer 1.42.2
##date 2019-04-16
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 
 83.960   0.711  85.051

Example timings

pqsfinder.Rcheck/pqsfinder-Ex.timings

nameusersystemelapsed
PQSViews0.0870.0050.093
density-PQSViews-method0.0440.0050.051
maxScores-PQSViews-method0.0210.0010.021
maxScores0.0020.0000.002
pqsfinder0.0450.0010.046
score-PQSViews-method0.0230.0000.023
strand-PQSViews-method0.0260.0000.026