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This page was generated on 2023-02-08 01:15:21 -0000 (Wed, 08 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" 4164
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CHECK results for pqsfinder on kunpeng1


To the developers/maintainers of the pqsfinder package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pqsfinder.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1501/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pqsfinder 2.15.1  (landing page)
Jiri Hon
Snapshot Date: 2023-02-06 00:12:45 -0000 (Mon, 06 Feb 2023)
git_url: https://git.bioconductor.org/packages/pqsfinder
git_branch: master
git_last_commit: c95179a
git_last_commit_date: 2023-01-01 16:14:35 -0000 (Sun, 01 Jan 2023)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    WARNINGS  

Summary

Package: pqsfinder
Version: 2.15.1
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:pqsfinder.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings pqsfinder_2.15.1.tar.gz
StartedAt: 2023-02-07 11:42:31 -0000 (Tue, 07 Feb 2023)
EndedAt: 2023-02-07 11:48:46 -0000 (Tue, 07 Feb 2023)
EllapsedTime: 375.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: pqsfinder.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:pqsfinder.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings pqsfinder_2.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/pqsfinder.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘pqsfinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pqsfinder’ version ‘2.15.1’
* package encoding: UTF-8
* 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
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
  installed size is 12.2Mb
  sub-directories of 1Mb or more:
    lib    7.5Mb
    libs   4.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.17-bioc/R/library/pqsfinder/libs/pqsfinder.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (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 nor [v]sprintf. 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 ... 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 ...
  ‘pqsfinder.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/pqsfinder.Rcheck/00check.log’
for details.

Installation output

pqsfinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL pqsfinder
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘pqsfinder’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c pqsfinder.cpp -o pqsfinder.o
pqsfinder.cpp: In function ‘void find_all_runs(SEXP, int, std::__cxx11::basic_string<char>::const_iterator, std::__cxx11::basic_string<char>::const_iterator, run_match*, const regex&, const opts_t&, const scoring&, const const_iterator&, size_t, storage&, int&, results&, bool, std::chrono::_V2::system_clock::time_point, int, int, int, int&, bool)’:
pqsfinder.cpp:582:22: warning: ‘loop_len’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  582 |         find_all_runs(
      |         ~~~~~~~~~~~~~^
  583 |           subject, i+1, e, end, m, run_re_c, opts, sc, ref, len,
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  584 |           pqs_storage, int_cnt, res, (loop_len == 0 ? true : zero_loop),
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  585 |           s_time, next_tetrad_count, next_defect_count, next_loop_sum, fn_call_count, show_progress
      |           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  586 |         );
      |         ~             
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c boost_regex/regex.cpp -o boost_regex/regex.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o
mkdir -p "/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-pqsfinder/00new/pqsfinder/lib"
ar rs "/home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a" boost_regex/posix_api.o boost_regex/regex.o boost_regex/regex_debug.o boost_regex/static_mutex.o boost_regex/wide_posix_api.o
ar: creating /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o pqsfinder.so RcppExports.o pqsfinder.o /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-pqsfinder/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pqsfinder)

Tests output

pqsfinder.Rcheck/tests/testthat.Rout


R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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

Attaching package: 'BiocGenerics'

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, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb

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              
 compare pqsfinder_1_4_4_d, pqsfinder_1_4_4_r
 run default pqsfinder
Searching on sense strand...
Search status: finished              
 run pqsfinder using boost regex engine
Searching on sense strand...
Search status: finished              
 compare pv_d, pv_r
 compare 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: 30% ETTC 00:00:00
Search status: 43% ETTC 00:00:01
Search status: 46% ETTC 00:00:02
Search status: 47% ETTC 00:00:03
Search status: 48% ETTC 00:00:04
Search status: 49% ETTC 00:00:05
Search status: 55% ETTC 00:00:04
Search status: 59% ETTC 00:00:04
Search status: 78% ETTC 00:00:01
Search status: 99% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 23% ETTC 00:00:00
Search status: 42% ETTC 00:00:01
Search status: 46% ETTC 00:00:01
Search status: 51% ETTC 00:00:01
Search status: 57% ETTC 00:00:01
Search status: 83% ETTC 00:00:00
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: 57% ETTC 00:00:00
Search status: 97% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 41% ETTC 00:00:01
Search status: 95% ETTC 00:00:00
Search status: finished              
Searching on sense strand...
Search status: 57% ETTC 00:00:00
Search status: 97% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 41% ETTC 00:00:01
Search status: 95% ETTC 00:00:00
Search status: finished              
Searching on sense strand...
Search status: 47% ETTC 00:00:00
Search status: 100% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 32% ETTC 00:00:02
Search status: 72% ETTC 00:00:00
Search status: finished              
Searching on sense strand...
Search status: 47% ETTC 00:00:00
Search status: 100% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 32% ETTC 00:00:00
Search status: 72% ETTC 00:00:00
Search status: finished              
Searching on sense strand...
Search status: finished              
Searching on antisense strand...
Search status: finished              
Searching on sense strand...
Search status: 5% ETTC 00:00:19
Search status: 7% ETTC 00:00:39
Search status: 10% ETTC 00:00:45
Search status: 12% ETTC 00:00:51
Search status: 12% ETTC 00:01:06
Search status: 14% ETTC 00:01:01
Search status: 18% ETTC 00:00:50
Search status: 20% ETTC 00:00:48
Search status: 21% ETTC 00:00:52
Search status: 22% ETTC 00:01:00
Search status: 23% ETTC 00:01:03
Search status: 25% ETTC 00:01:03
Search status: 26% ETTC 00:01:05
Search status: 30% ETTC 00:00:58
Search status: 33% ETTC 00:00:52
Search status: 33% ETTC 00:01:02
Search status: 33% ETTC 00:01:11
Search status: 36% ETTC 00:01:04
Search status: 39% ETTC 00:00:57
Search status: 40% ETTC 00:00:58
Search status: 42% ETTC 00:00:56
Search status: 43% ETTC 00:00:55
Search status: 46% ETTC 00:00:51
Search status: 48% ETTC 00:00:49
Search status: 49% ETTC 00:00:49
Search status: 52% ETTC 00:00:45
Search status: 53% ETTC 00:00:45
Search status: 53% ETTC 00:00:47
Search status: 56% ETTC 00:00:42
Search status: 60% ETTC 00:00:37
Search status: 64% ETTC 00:00:32
Search status: 66% ETTC 00:00:30
Search status: 67% ETTC 00:00:30
Search status: 68% ETTC 00:00:29
Search status: 69% ETTC 00:00:29
Search status: 72% ETTC 00:00:25
Search status: 75% ETTC 00:00:22
Search status: 76% ETTC 00:00:22
Search status: 79% ETTC 00:00:18
Search status: 80% ETTC 00:00:18
Search status: 81% ETTC 00:00:17
Search status: 82% ETTC 00:00:16
Search status: 86% ETTC 00:00:12
Search status: 88% ETTC 00:00:10
Search status: 90% ETTC 00:00:09
Search status: 92% ETTC 00:00:07
Search status: 95% ETTC 00:00:04
Search status: 99% ETTC 00:00:00
Search status: 100% ETTC 00:00:00
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              
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: 92% ETTC 00:00:00
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: 49% ETTC 00:00:01
Search status: 93% ETTC 00:00:00
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: 74% ETTC 00:00:00
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              
Searching on sense strand...
Search status: 98% ETTC 00:00:00
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 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              
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 83 ]
> 
> proc.time()
   user  system elapsed 
 90.748   0.585 136.743

Example timings

pqsfinder.Rcheck/pqsfinder-Ex.timings

nameusersystemelapsed
PQSViews0.0800.0040.168
density-PQSViews-method0.0420.0000.081
maxScores-PQSViews-method0.0230.0000.055
maxScores0.0020.0000.002
pqsfinder0.0500.0000.097
score-PQSViews-method0.0260.0000.055
strand-PQSViews-method0.0260.0000.050