Jiri Hon
| Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023) |
| git_url: https://git.bioconductor.org/packages/pqsfinder |
| git_branch: RELEASE_3_18 |
| git_last_commit: 3f8caa0 |
| git_last_commit_date: 2023-10-24 10:49:36 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:41:05 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 1578/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pqsfinder 2.18.0 (landing page) Jiri Hon
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: pqsfinder |
| Version: 2.18.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:pqsfinder.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings pqsfinder_2.18.0.tar.gz |
| StartedAt: 2023-11-02 13:12:40 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 13:15:46 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 186.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: pqsfinder.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:pqsfinder.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings pqsfinder_2.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/pqsfinder.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pqsfinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pqsfinder’ version ‘2.18.0’
* 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++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 17.0Mb
sub-directories of 1Mb or more:
lib 11.3Mb
libs 5.2Mb
* 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 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 ... 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/R/R-4.3.1/site-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 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: 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/pqsfinder.Rcheck/00check.log’
for details.
pqsfinder.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL pqsfinder
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘pqsfinder’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-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/R/R-4.3.1/site-library/00LOCK-pqsfinder/00new/pqsfinder/lib"
ar rs "/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/site-library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o pqsfinder.so RcppExports.o pqsfinder.o /home/biocbuild/R/R-4.3.1/site-library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/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)
pqsfinder.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
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 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: 57% ETTC 00:00:00
Search status: 96% ETTC 00:00:00
Search status: finished
Searching on antisense strand...
Search status: 64% ETTC 00:00:00
Search status: 98% ETTC 00:00:00
Search status: finished
Searching on sense strand...
Search status: 57% ETTC 00:00:00
Search status: 96% ETTC 00:00:00
Search status: finished
Searching on antisense strand...
Search status: 64% ETTC 00:00:00
Search status: 98% ETTC 00:00:00
Search status: finished
Searching on sense strand...
Search status: 63% ETTC 00:00:00
Search status: 90% ETTC 00:00:00
Search status: finished
Searching on antisense strand...
Search status: 70% ETTC 00:00:00
Search status: 97% ETTC 00:00:00
Search status: finished
Searching on sense strand...
Search status: 63% ETTC 00:00:00
Search status: 90% ETTC 00:00:00
Search status: finished
Searching on antisense strand...
Search status: 70% ETTC 00:00:00
Search status: 97% 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: 6% ETTC 00:00:00
Search status: 9% ETTC 00:00:10
Search status: 12% ETTC 00:00:14
Search status: 15% ETTC 00:00:17
Search status: 17% ETTC 00:00:19
Search status: 18% ETTC 00:00:22
Search status: 20% ETTC 00:00:24
Search status: 22% ETTC 00:00:24
Search status: 24% ETTC 00:00:25
Search status: 26% ETTC 00:00:25
Search status: 26% ETTC 00:00:28
Search status: 29% ETTC 00:00:26
Search status: 32% ETTC 00:00:25
Search status: 34% ETTC 00:00:25
Search status: 37% ETTC 00:00:23
Search status: 39% ETTC 00:00:23
Search status: 41% ETTC 00:00:23
Search status: 46% ETTC 00:00:18
Search status: 49% ETTC 00:00:17
Search status: 50% ETTC 00:00:18
Search status: 51% ETTC 00:00:19
Search status: 52% ETTC 00:00:19
Search status: 54% ETTC 00:00:18
Search status: 57% ETTC 00:00:17
Search status: 59% ETTC 00:00:16
Search status: 59% ETTC 00:00:17
Search status: 59% ETTC 00:00:18
Search status: 61% ETTC 00:00:17
Search status: 62% ETTC 00:00:17
Search status: 65% ETTC 00:00:16
Search status: 67% ETTC 00:00:15
Search status: 68% ETTC 00:00:15
Search status: 70% ETTC 00:00:14
Search status: 72% ETTC 00:00:13
Search status: 74% ETTC 00:00:12
Search status: 76% ETTC 00:00:11
Search status: 78% ETTC 00:00:10
Search status: 80% ETTC 00:00:09
Search status: 81% ETTC 00:00:09
Search status: 84% ETTC 00:00:07
Search status: 85% ETTC 00:00:07
Search status: 87% ETTC 00:00:06
Search status: 91% ETTC 00:00:04
Search status: 93% ETTC 00:00:03
Search status: 95% ETTC 00:00:02
Search status: 97% 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
83.530 0.446 84.101
pqsfinder.Rcheck/pqsfinder-Ex.timings
| name | user | system | elapsed | |
| PQSViews | 0.089 | 0.004 | 0.093 | |
| density-PQSViews-method | 0.066 | 0.000 | 0.066 | |
| maxScores-PQSViews-method | 0.026 | 0.000 | 0.027 | |
| maxScores | 0.003 | 0.000 | 0.002 | |
| pqsfinder | 0.055 | 0.000 | 0.055 | |
| score-PQSViews-method | 0.026 | 0.000 | 0.025 | |
| strand-PQSViews-method | 0.026 | 0.000 | 0.026 | |