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This page was generated on 2024-12-23 11:40 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4372
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Package 1574/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pqsfinder 2.23.0  (landing page)
Jiri Hon
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
git_url: https://git.bioconductor.org/packages/pqsfinder
git_branch: devel
git_last_commit: acbc114
git_last_commit_date: 2024-10-29 10:10:06 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for pqsfinder on nebbiolo1

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: 2.23.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:pqsfinder.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings pqsfinder_2.23.0.tar.gz
StartedAt: 2024-12-23 01:03:43 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 01:07:44 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 241.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: pqsfinder.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:pqsfinder.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings pqsfinder_2.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/pqsfinder.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘pqsfinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pqsfinder’ version ‘2.23.0’
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    lib    2.6Mb
    libs   2.0Mb
* 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 loading without being on the library search path ... 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 ‘/home/biocbuild/bbs-3.21-bioc/R/site-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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/pqsfinder.Rcheck/00check.log’
for details.

Installation output

pqsfinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL pqsfinder
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘pqsfinder’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -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 boost::regex&, const opts_t&, const scoring&, const std::__cxx11::basic_string<char>::const_iterator&, size_t, storage&, int&, results&, bool, std::chrono::_V2::system_clock::time_point, int, int, int, int&, bool)’:
pqsfinder.cpp:584:53: warning: ‘loop_len’ may be used uninitialized [-Wmaybe-uninitialized]
  584 |           pqs_storage, int_cnt, res, (loop_len == 0 ? true : zero_loop),
      |                                      ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
pqsfinder.cpp:489:14: note: ‘loop_len’ was declared here
  489 |   int score, loop_len;
      |              ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c boost_regex/regex.cpp -o boost_regex/regex.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1  -fpic  -g -O2  -Wall -DR_NO_REMAP -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o
mkdir -p "/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-pqsfinder/00new/pqsfinder/lib"
ar rs "/home/biocbuild/bbs-3.21-bioc/R/site-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-3.21-bioc/R/site-library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o pqsfinder.so RcppExports.o pqsfinder.o /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-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) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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: 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 00:00:00
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: 46% ETTC 00:00:00
Search status: 87% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 48% ETTC 00:00:00
Search status: 87% ETTC 00:00:00
Search status: finished              
Searching on sense strand...
Search status: 46% ETTC 00:00:00
Search status: 87% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 48% ETTC 00:00:00
Search status: 87% ETTC 00:00:00
Search status: finished              
Searching on sense strand...
Search status: 44% ETTC 00:00:00
Search status: 81% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 45% ETTC 00:00:00
Search status: 100% ETTC 00:00:00
Search status: finished              
Searching on sense strand...
Search status: 44% ETTC 00:00:00
Search status: 81% ETTC 00:00:00
Search status: finished              
Searching on antisense strand...
Search status: 45% ETTC 00:00:00
Search status: 100% 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: 3% ETTC 00:00:00
Search status: 6% ETTC 00:00:15
Search status: 8% ETTC 00:00:23
Search status: 9% ETTC 00:00:30
Search status: 11% ETTC 00:00:40
Search status: 14% ETTC 00:00:36
Search status: 15% ETTC 00:00:39
Search status: 17% ETTC 00:00:39
Search status: 19% ETTC 00:00:38
Search status: 21% ETTC 00:00:37
Search status: 24% ETTC 00:00:34
Search status: 27% ETTC 00:00:32
Search status: 28% ETTC 00:00:33
Search status: 30% ETTC 00:00:32
Search status: 31% ETTC 00:00:33
Search status: 32% ETTC 00:00:34
Search status: 36% ETTC 00:00:30
Search status: 38% ETTC 00:00:29
Search status: 40% ETTC 00:00:28
Search status: 42% ETTC 00:00:27
Search status: 46% ETTC 00:00:24
Search status: 49% ETTC 00:00:22
Search status: 51% ETTC 00:00:22
Search status: 52% ETTC 00:00:22
Search status: 54% ETTC 00:00:21
Search status: 58% ETTC 00:00:18
Search status: 60% ETTC 00:00:18
Search status: 62% ETTC 00:00:16
Search status: 64% ETTC 00:00:15
Search status: 66% ETTC 00:00:14
Search status: 67% ETTC 00:00:15
Search status: 69% ETTC 00:00:14
Search status: 71% ETTC 00:00:13
Search status: 72% ETTC 00:00:13
Search status: 72% ETTC 00:00:14
Search status: 74% ETTC 00:00:13
Search status: 78% ETTC 00:00:10
Search status: 81% ETTC 00:00:09
Search status: 83% ETTC 00:00:07
Search status: 86% ETTC 00:00:06
Search status: 88% ETTC 00:00:05
Search status: 90% ETTC 00:00:04
Search status: 92% ETTC 00:00:03
Search status: 93% ETTC 00:00:03
Search status: 94% ETTC 00:00:02
Search status: 95% ETTC 00:00:02
Search status: 96% ETTC 00:00:02
Search status: 98% ETTC 00:00:01
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 
 83.931   0.543  84.470

Example timings

pqsfinder.Rcheck/pqsfinder-Ex.timings

nameusersystemelapsed
PQSViews0.0660.0150.080
density-PQSViews-method0.0260.0010.028
maxScores-PQSViews-method0.0150.0000.015
maxScores0.0020.0000.002
pqsfinder0.0320.0010.033
score-PQSViews-method0.0160.0000.015
strand-PQSViews-method0.0160.0000.015