Jiri Hon
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/pqsfinder |
| Branch: RELEASE_3_7 |
| Last Commit: e2ce343 |
| Last Changed Date: 2018-04-30 10:35:41 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:56:26 -0400 (Wed, 17 Oct 2018).
| Package 1119/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| pqsfinder 1.8.0 Jiri Hon
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: pqsfinder |
| Version: 1.8.0 |
| 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_1.8.0.tar.gz |
| StartedAt: 2018-10-16 23:19:34 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 23:22:32 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 178.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pqsfinder.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/pqsfinder.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.8.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘pqsfinder’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 12.0Mb
sub-directories of 1Mb or more:
lib 11.0Mb
* 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 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-3.7-bioc/meat/pqsfinder.Rcheck/00check.log’
for details.
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(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 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)
pqsfinder.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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 00:00:06
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 00:00:13
Search status: 30% ETTC 00:00:11
Search status: 30% ETTC 00:00:11
Search status: 36% ETTC 00:00:12
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 00:00:15
Search status: 46% ETTC 00:00:16
Search status: 46% ETTC 00:00:17
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 00:00:22
Search status: 47% ETTC 00:00:21
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 00:00:24
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: 48% ETTC 00:00:31
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 00:00:34
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 00:00:37
Search status: 48% ETTC 00:00:39
Search status: 48% ETTC 00:00:40
Search status: 48% ETTC 00:00:40
Search status: 49% ETTC 00:00:39
Search status: 49% ETTC 00:00:40
Search status: 50% ETTC 00:00:40
Search status: 52% ETTC 00:00:37
Search status: 53% ETTC 00:00:37
Search status: 54% ETTC 00:00:35
Search status: 54% ETTC 00:00:36
Search status: 55% ETTC 00:00:36
Search status: 55% ETTC 00:00:36
Search status: 55% ETTC 00:00:36
Search status: 56% ETTC 00:00:36
Search status: 56% ETTC 00:00:36
Search status: 56% ETTC 00:00:37
Search status: 57% ETTC 00:00:36
Search status: 59% ETTC 00:00:34
Search status: 66% ETTC 00:00:26
Search status: 77% ETTC 00:00:15
Search status: 78% ETTC 00:00:14
Search status: 78% ETTC 00:00:15
Search status: 86% ETTC 00:00:08
Search status: 87% ETTC 00:00:08
Search status: 88% ETTC 00:00:07
Search status: 92% ETTC 00:00:04
Search status: finished
50000-letter "DNAString" instance
seq: GGAACACTTTTACACTGTTGGTGGGACTGTAAACTA...TATGAGTCATGTTGCAGATCTAAAGTGAGGTAGTTG
##gff-version 3
##source-version rtracklayer 1.40.6
##date 2018-10-16
chr1 pqsfinder G_quartet 433 447 27 + . nt=2;nb=0;nm=0;ll1=5;ll2=2;ll3=0
chr1 pqsfinder G_quartet 461 489 99 + . nt=4;nb=0;nm=0;ll1=8;ll2=3;ll3=2
chr1 pqsfinder G_quartet 990 1005 26 + . nt=2;nb=0;nm=0;ll1=2;ll2=6;ll3=0
chr1 pqsfinder G_quartet 4522 4536 27 + . nt=2;nb=0;nm=0;ll1=0;ll2=6;ll3=1
chr1 pqsfinder G_quartet 6645 6663 49 + . nt=3;nb=1;nm=0;ll1=1;ll2=4;ll3=1
chr1 pqsfinder G_quartet 9421 9447 55 + . nt=4;nb=1;nm=1;ll1=3;ll2=6;ll3=1
chr1 pqsfinder G_quartet 10511 10535 31 + . nt=3;nb=0;nm=1;ll1=6;ll2=6;ll3=1
chr1 pqsfinder G_quartet 10961 10972 32 + . nt=2;nb=0;nm=0;ll1=1;ll2=3;ll3=0
chr1 pqsfinder G_quartet 11318 11331 29 + . nt=2;nb=0;nm=0;ll1=1;ll2=4;ll3=1
chr1 pqsfinder G_quartet 11481 11490 35 + . nt=2;nb=0;nm=0;ll1=0;ll2=1;ll3=1
chr1 pqsfinder G_quartet 11772 11787 26 + . nt=2;nb=0;nm=0;ll1=2;ll2=1;ll3=5
chr1 pqsfinder G_quartet 14139 14150 32 + . nt=2;nb=0;nm=0;ll1=2;ll2=2;ll3=0
chr1 pqsfinder G_quartet 14923 14937 27 + . nt=2;nb=0;nm=0;ll1=5;ll2=2;ll3=0
chr1 pqsfinder G_quartet 14951 14980 109 + . nt=5;nb=2;nm=0;ll1=3;ll2=2;ll3=0
chr1 pqsfinder G_quartet 15518 15530 30 + . nt=2;nb=0;nm=0;ll1=0;ll2=1;ll3=4
chr1 pqsfinder G_quartet 17552 17565 29 + . nt=2;nb=0;nm=0;ll1=4;ll2=2;ll3=0
chr1 pqsfinder G_quartet 17695 17729 44 + . nt=4;nb=3;nm=0;ll1=2;ll2=3;ll3=3
chr1 pqsfinder G_quartet 18706 18730 78 + . nt=5;nb=1;nm=2;ll1=1;ll2=0;ll3=1
chr1 pqsfinder G_quartet 19169 19204 32 + . nt=4;nb=2;nm=1;ll1=2;ll2=9;ll3=0
chr1 pqsfinder G_quartet 20011 20047 30 + . nt=3;nb=1;nm=0;ll1=1;ll2=11;ll3=7
chr1 pqsfinder G_quartet 20191 20220 35 + . nt=3;nb=1;nm=0;ll1=3;ll2=4;ll3=8
chr1 pqsfinder G_quartet 20455 20483 27 + . nt=3;nb=2;nm=0;ll1=3;ll2=2;ll3=1
chr1 pqsfinder G_quartet 20817 20828 32 + . nt=2;nb=0;nm=0;ll1=1;ll2=3;ll3=0
chr1 pqsfinder G_quartet 21070 21095 46 + . nt=3;nb=1;nm=0;ll1=3;ll2=2;ll3=2
chr1 pqsfinder G_quartet 21193 21221 30 + . nt=3;nb=2;nm=0;ll1=0;ll2=3;ll3=1
chr1 pqsfinder G_quartet 21465 21477 30 + . nt=2;nb=0;nm=0;ll1=0;ll2=4;ll3=1
chr1 pqsfinder G_quartet 21529 21542 29 + . nt=2;nb=0;nm=0;ll1=4;ll2=1;ll3=1
chr1 pqsfinder G_quartet 22410 22433 87 + . nt=4;nb=1;nm=0;ll1=1;ll2=3;ll3=3
chr1 pqsfinder G_quartet 22569 22595 56 + . nt=3;nb=0;nm=0;ll1=3;ll2=10;ll3=2
chr1 pqsfinder G_quartet 22703 22737 30 + . nt=4;nb=2;nm=1;ll1=10;ll2=2;ll3=1
chr1 pqsfinder G_quartet 22806 22841 44 + . nt=4;nb=3;nm=0;ll1=3;ll2=2;ll3=3
chr1 pqsfinder G_quartet 22978 23019 54 + . nt=4;nb=2;nm=0;ll1=1;ll2=2;ll3=12
chr1 pqsfinder G_quartet 23182 23204 61 + . nt=3;nb=0;nm=0;ll1=6;ll2=5;ll3=0
chr1 pqsfinder G_quartet 23266 23292 71 + . nt=4;nb=2;nm=0;ll1=1;ll2=3;ll3=0
chr1 pqsfinder G_quartet 23328 23365 43 + . nt=3;nb=0;nm=0;ll1=1;ll2=24;ll3=1
chr1 pqsfinder G_quartet 23399 23439 84 + . nt=5;nb=3;nm=0;ll1=3;ll2=4;ll3=0
chr1 pqsfinder G_quartet 23469 23500 64 + . nt=4;nb=2;nm=0;ll1=3;ll2=1;ll3=4
chr1 pqsfinder G_quartet 23599 23641 41 + . nt=4;nb=3;nm=0;ll1=3;ll2=4;ll3=2
chr1 pqsfinder G_quartet 23655 23690 82 + . nt=5;nb=3;nm=0;ll1=7;ll2=1;ll3=1
chr1 pqsfinder G_quartet 23706 23737 38 + . nt=3;nb=1;nm=0;ll1=5;ll2=6;ll3=1
chr1 pqsfinder G_quartet 23762 23794 50 + . nt=4;nb=1;nm=1;ll1=3;ll2=8;ll3=2
chr1 pqsfinder G_quartet 23804 23839 45 + . nt=3;nb=0;nm=0;ll1=10;ll2=11;ll3=3
chr1 pqsfinder G_quartet 23929 23963 34 + . nt=3;nb=1;nm=0;ll1=5;ll2=9;ll3=1
chr1 pqsfinder G_quartet 23994 24015 63 + . nt=3;nb=0;nm=0;ll1=4;ll2=1;ll3=5
chr1 pqsfinder G_quartet 24039 24076 57 + . nt=4;nb=2;nm=0;ll1=4;ll2=8;ll3=1
chr1 pqsfinder G_quartet 24336 24360 31 + . nt=3;nb=0;nm=1;ll1=0;ll2=2;ll3=11
chr1 pqsfinder G_quartet 24479 24511 45 + . nt=4;nb=3;nm=0;ll1=6;ll2=0;ll3=1
chr1 pqsfinder G_quartet 24572 24620 31 + . nt=3;nb=0;nm=0;ll1=7;ll2=27;ll3=3
chr1 pqsfinder G_quartet 25186 25222 40 + . nt=4;nb=3;nm=0;ll1=1;ll2=8;ll3=1
chr1 pqsfinder G_quartet 25698 25710 30 + . nt=2;nb=0;nm=0;ll1=1;ll2=3;ll3=1
chr1 pqsfinder G_quartet 26086 26101 26 + . nt=2;nb=0;nm=0;ll1=4;ll2=2;ll3=2
chr1 pqsfinder G_quartet 26184 26232 59 + . nt=5;nb=2;nm=1;ll1=9;ll2=7;ll3=5
chr1 pqsfinder G_quartet 26326 26340 27 + . nt=2;nb=0;nm=0;ll1=1;ll2=4;ll3=2
chr1 pqsfinder G_quartet 26543 26558 26 + . nt=2;nb=0;nm=0;ll1=1;ll2=5;ll3=2
chr1 pqsfinder G_quartet 26576 26586 33 + . nt=2;nb=0;nm=0;ll1=1;ll2=2;ll3=0
chr1 pqsfinder G_quartet 26671 26720 71 + . nt=5;nb=3;nm=0;ll1=1;ll2=2;ll3=14
chr1 pqsfinder G_quartet 26751 26773 26 + . nt=3;nb=2;nm=0;ll1=4;ll2=3;ll3=1
chr1 pqsfinder G_quartet 27061 27079 30 + . nt=3;nb=2;nm=0;ll1=2;ll2=2;ll3=1
chr1 pqsfinder G_quartet 27365 27398 45 + . nt=4;nb=3;nm=0;ll1=1;ll2=4;ll3=2
chr1 pqsfinder G_quartet 27427 27446 54 + . nt=3;nb=1;nm=0;ll1=1;ll2=0;ll3=1
chr1 pqsfinder G_quartet 27560 27575 26 + . nt=2;nb=0;nm=0;ll1=0;ll2=7;ll3=1
chr1 pqsfinder G_quartet 27690 27732 86 + . nt=5;nb=3;nm=0;ll1=2;ll2=2;ll3=2
chr1 pqsfinder G_quartet 27773 27810 44 + . nt=4;nb=3;nm=0;ll1=3;ll2=4;ll3=0
chr1 pqsfinder G_quartet 28003 28016 29 + . nt=2;nb=0;nm=0;ll1=1;ll2=1;ll3=4
chr1 pqsfinder G_quartet 28176 28204 31 + . nt=3;nb=2;nm=0;ll1=1;ll2=1;ll3=1
chr1 pqsfinder G_quartet 28542 28556 27 + . nt=2;nb=0;nm=0;ll1=2;ll2=3;ll3=2
chr1 pqsfinder G_quartet 28637 28672 28 + . nt=3;nb=1;nm=0;ll1=15;ll2=1;ll3=5
chr1 pqsfinder G_quartet 29060 29097 42 + . nt=4;nb=1;nm=1;ll1=18;ll2=1;ll3=1
chr1 pqsfinder G_quartet 29175 29188 29 + . nt=2;nb=0;nm=0;ll1=0;ll2=4;ll3=2
chr1 pqsfinder G_quartet 29242 29276 29 + . nt=3;nb=1;nm=0;ll1=0;ll2=19;ll3=1
chr1 pqsfinder G_quartet 29361 29375 27 + . nt=2;nb=0;nm=0;ll1=4;ll2=2;ll3=1
chr1 pqsfinder G_quartet 29632 29643 32 + . nt=2;nb=0;nm=0;ll1=0;ll2=1;ll3=3
chr1 pqsfinder G_quartet 29762 29773 32 + . nt=2;nb=0;nm=0;ll1=2;ll2=2;ll3=0
chr1 pqsfinder G_quartet 29818 29833 26 + . nt=2;nb=0;nm=0;ll1=2;ll2=6;ll3=0
chr1 pqsfinder G_quartet 29972 29987 26 + . nt=2;nb=0;nm=0;ll1=0;ll2=7;ll3=1
chr1 pqsfinder G_quartet 31092 31106 27 + . nt=2;nb=0;nm=0;ll1=5;ll2=2;ll3=0
chr1 pqsfinder G_quartet 35419 35456 30 + . nt=3;nb=1;nm=0;ll1=16;ll2=0;ll3=3
chr1 pqsfinder G_quartet 36912 36927 26 + . nt=2;nb=0;nm=0;ll1=2;ll2=2;ll3=4
chr1 pqsfinder G_quartet 37586 37595 35 + . nt=2;nb=0;nm=0;ll1=1;ll2=1;ll3=0
chr1 pqsfinder G_quartet 38366 38377 32 + . nt=2;nb=0;nm=0;ll1=1;ll2=1;ll3=2
chr1 pqsfinder G_quartet 38495 38519 54 + . nt=4;nb=3;nm=0;ll1=1;ll2=1;ll3=0
chr1 pqsfinder G_quartet 38564 38588 59 + . nt=3;nb=0;nm=0;ll1=1;ll2=2;ll3=10
chr1 pqsfinder G_quartet 38629 38663 46 + . nt=3;nb=0;nm=0;ll1=1;ll2=20;ll3=2
chr1 pqsfinder G_quartet 38972 38987 26 + . nt=2;nb=0;nm=0;ll1=4;ll2=3;ll3=1
chr1 pqsfinder G_quartet 39234 39257 43 + . nt=3;nb=1;nm=0;ll1=0;ll2=9;ll3=1
chr1 pqsfinder G_quartet 42399 42425 30 + . nt=3;nb=2;nm=0;ll1=1;ll2=2;ll3=1
chr1 pqsfinder G_quartet 42499 42511 30 + . nt=2;nb=0;nm=0;ll1=3;ll2=1;ll3=1
chr1 pqsfinder G_quartet 42535 42549 27 + . nt=2;nb=0;nm=0;ll1=1;ll2=4;ll3=2
chr1 pqsfinder G_quartet 43058 43095 30 + . nt=3;nb=1;nm=0;ll1=13;ll2=5;ll3=1
chr1 pqsfinder G_quartet 43121 43144 69 + . nt=4;nb=2;nm=0;ll1=2;ll2=3;ll3=1
chr1 pqsfinder G_quartet 43370 43384 27 + . nt=2;nb=0;nm=0;ll1=1;ll2=4;ll3=2
chr1 pqsfinder G_quartet 43876 43898 90 + . nt=4;nb=1;nm=0;ll1=2;ll2=2;ll3=1
chr1 pqsfinder G_quartet 44165 44191 31 + . nt=3;nb=2;nm=0;ll1=1;ll2=1;ll3=1
chr1 pqsfinder G_quartet 44513 44539 31 + . nt=3;nb=2;nm=0;ll1=1;ll2=1;ll3=1
chr1 pqsfinder G_quartet 45555 45580 31 + . nt=3;nb=2;nm=0;ll1=1;ll2=1;ll3=1
chr1 pqsfinder G_quartet 46333 46360 36 + . nt=3;nb=1;nm=0;ll1=1;ll2=12;ll3=2
chr1 pqsfinder G_quartet 49197 49213 42 + . nt=3;nb=0;nm=1;ll1=3;ll2=1;ll3=1
chr1 pqsfinder G_quartet 49606 49627 29 + . nt=3;nb=2;nm=0;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 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: 24 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
81.403 0.709 82.425
pqsfinder.Rcheck/pqsfinder-Ex.timings
| name | user | system | elapsed | |
| PQSViews | 0.074 | 0.002 | 0.075 | |
| density-PQSViews-method | 0.045 | 0.006 | 0.052 | |
| maxScores-PQSViews-method | 0.042 | 0.001 | 0.044 | |
| maxScores | 0.004 | 0.000 | 0.004 | |
| pqsfinder | 0.047 | 0.001 | 0.048 | |
| score-PQSViews-method | 0.018 | 0.000 | 0.019 | |
| strand-PQSViews-method | 0.02 | 0.00 | 0.02 | |