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This page was generated on 2025-10-23 12:05 -0400 (Thu, 23 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4894
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4684
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4629
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4642
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1627/2355HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pqsfinder 2.25.0  (landing page)
Jiri Hon
Snapshot Date: 2025-10-22 13:45 -0400 (Wed, 22 Oct 2025)
git_url: https://git.bioconductor.org/packages/pqsfinder
git_branch: devel
git_last_commit: 969f685
git_last_commit_date: 2025-04-15 11:01:10 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  ERROR    ERROR  skipped

CHECK results for pqsfinder on lconway

To the developers/maintainers of the pqsfinder package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: pqsfinder
Version: 2.25.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pqsfinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pqsfinder_2.25.0.tar.gz
StartedAt: 2025-10-22 23:16:39 -0400 (Wed, 22 Oct 2025)
EndedAt: 2025-10-22 23:19:43 -0400 (Wed, 22 Oct 2025)
EllapsedTime: 183.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: pqsfinder.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pqsfinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pqsfinder_2.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/pqsfinder.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pqsfinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pqsfinder’ version ‘2.25.0’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  PQSViews-class.Rd: XStringViews-class
  PQSViews.Rd: XStringViews, elementMetadata
  pqsfinder.Rd: elementMetadata
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... INFO
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 ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/pqsfinder/libs/pqsfinder.so’:
  Found ‘_sprintf’, 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/pqsfinder.Rcheck/00check.log’
for details.

Installation output

pqsfinder.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘pqsfinder’ ...
** this is package ‘pqsfinder’ version ‘2.25.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c pqsfinder.cpp -o pqsfinder.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c boost_regex/regex.cpp -o boost_regex/regex.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o
mkdir -p "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-pqsfinder/00new/pqsfinder/lib"
ar rs "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 archive /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a(regex.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a(regex_debug.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a(static_mutex.o) has no symbols
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o pqsfinder.so RcppExports.o pqsfinder.o /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: XVector
Loading required package: Seqinfo

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 00:00:00
Search status: 46% ETTC 00:00:01
Search status: 47% ETTC 00:00:02
Search status: 48% ETTC 00:00:02
Search status: 49% ETTC 00:00:03
Search status: 55% ETTC 00:00:02
Search status: 59% ETTC 00:00:02
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 00:00:00
Search status: 46% ETTC 00:00:01
Search status: 51% ETTC 00:00:00
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: 56% ETTC 00:00:00
Search status: 99% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 47% ETTC 00:00:00
Search status: 99% ETTC 00:00:00
Search status: finished              
Searching on sense strand...
Search status: 56% ETTC 00:00:00
Search status: 99% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 47% ETTC 00:00:00
Search status: 99% ETTC 00:00:00
Search status: finished              
Searching on sense strand...
Search status: 43% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 50% ETTC 00:00:00
Search status: 98% ETTC 00:00:00
Search status: finished              
Searching on sense strand...
Search status: 43% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 50% ETTC 00:00:00
Search status: 98% 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: 4% ETTC 00:00:24
Search status: 6% ETTC 00:00:31
Search status: 8% ETTC 00:00:34
Search status: 10% ETTC 00:00:36
Search status: 11% ETTC 00:00:40
Search status: 14% ETTC 00:00:36
Search status: 15% ETTC 00:00:45
Search status: 18% ETTC 00:00:36
Search status: 21% ETTC 00:00:33
Search status: 23% ETTC 00:00:33
Search status: 25% ETTC 00:00:36
Search status: 27% ETTC 00:00:35
Search status: 30% ETTC 00:00:32
Search status: 31% ETTC 00:00:33
Search status: 32% ETTC 00:00:34
Search status: 33% ETTC 00:00:36
Search status: 35% ETTC 00:00:35
Search status: 37% ETTC 00:00:34
Search status: 38% ETTC 00:00:34
Search status: 40% ETTC 00:00:33
Search status: 43% ETTC 00:00:30
Search status: 45% ETTC 00:00:29
Search status: 49% ETTC 00:00:26
Search status: 51% ETTC 00:00:24
Search status: 52% ETTC 00:00:24
Search status: 53% ETTC 00:00:24
Search status: 55% ETTC 00:00:23
Search status: 56% ETTC 00:00:24
Search status: 58% ETTC 00:00:23
Search status: 60% ETTC 00:00:22
Search status: 60% ETTC 00:00:23
Search status: 62% ETTC 00:00:22
Search status: 66% ETTC 00:00:19
Search status: 69% ETTC 00:00:17
Search status: 72% ETTC 00:00:15
Search status: 73% ETTC 00:00:14
Search status: 74% ETTC 00:00:14
Search status: 74% ETTC 00:00:15
Search status: 75% ETTC 00:00:15
Search status: 77% ETTC 00:00:13
Search status: 80% ETTC 00:00:11
Search status: 83% ETTC 00:00:09
Search status: 86% ETTC 00:00:07
Search status: 87% ETTC 00:00:07
Search status: 89% ETTC 00:00:06
Search status: 92% ETTC 00:00:04
Search status: 95% ETTC 00:00:02
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 
 86.743   0.915  88.211

Example timings

pqsfinder.Rcheck/pqsfinder-Ex.timings

nameusersystemelapsed
PQSViews0.0810.0040.085
density-PQSViews-method0.0290.0010.032
maxScores-PQSViews-method0.0200.0010.020
maxScores0.0030.0000.003
pqsfinder0.0360.0040.040
score-PQSViews-method0.0200.0020.022
strand-PQSViews-method0.0170.0020.019