Jiri Hon
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/pqsfinder |
| git_branch: RELEASE_3_16 |
| git_last_commit: 2ef4735 |
| git_last_commit_date: 2023-01-01 11:24:45 -0400 (Sun, 01 Jan 2023) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:14 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
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. |
| Package 1512/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pqsfinder 2.14.1 (landing page) Jiri Hon
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: pqsfinder |
| Version: 2.14.1 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:pqsfinder.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings pqsfinder_2.14.1.tar.gz |
| StartedAt: 2023-04-10 23:02:07 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 23:06:18 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 251.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: pqsfinder.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:pqsfinder.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings pqsfinder_2.14.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/pqsfinder.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘pqsfinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pqsfinder’ version ‘2.14.1’
* 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
* checking installed package size ... NOTE
installed size is 15.4Mb
sub-directories of 1Mb or more:
lib 10.1Mb
libs 4.9Mb
* 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 ... 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 ...
‘pqsfinder.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.16-bioc/meat/pqsfinder.Rcheck/00check.log’
for details.
pqsfinder.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL pqsfinder
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘pqsfinder’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/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:584:53: warning: ‘loop_len’ may be used uninitialized in this function [-Wmaybe-uninitialized]
584 | pqs_storage, int_cnt, res, (loop_len == 0 ? true : zero_loop),
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/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
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/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/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o
mkdir -p "/home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-pqsfinder/00new/pqsfinder/lib"
ar rs "/home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a" boost_regex/regex.o boost_regex/posix_api.o boost_regex/wide_posix_api.o boost_regex/regex_debug.o boost_regex/static_mutex.o
ar: creating /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o pqsfinder.so RcppExports.o pqsfinder.o /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-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)
pqsfinder.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 00:00:00
Search status: 46% ETTC 00:00:01
Search status: 47% ETTC 00:00:01
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: 52% ETTC 00:00:00
Search status: 83% ETTC 00:00:00
Search status: finished
Searching on antisense strand...
Search status: 38% ETTC 00:00:00
Search status: 89% ETTC 00:00:00
Search status: finished
Searching on sense strand...
Search status: 52% ETTC 00:00:00
Search status: 83% ETTC 00:00:00
Search status: finished
Searching on antisense strand...
Search status: 38% ETTC 00:00:00
Search status: 89% ETTC 00:00:00
Search status: finished
Searching on sense strand...
Search status: 40% ETTC 00:00:00
Search status: 94% ETTC 00:00:00
Search status: finished
Searching on antisense strand...
Search status: 47% ETTC 00:00:00
Search status: 87% ETTC 00:00:00
Search status: finished
Searching on sense strand...
Search status: 40% ETTC 00:00:00
Search status: 94% ETTC 00:00:00
Search status: finished
Searching on antisense strand...
Search status: 47% ETTC 00:00:00
Search status: 87% 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: 5% ETTC 00:00:19
Search status: 9% ETTC 00:00:20
Search status: 11% ETTC 00:00:24
Search status: 13% ETTC 00:00:26
Search status: 16% ETTC 00:00:26
Search status: 17% ETTC 00:00:29
Search status: 19% ETTC 00:00:25
Search status: 22% ETTC 00:00:24
Search status: 23% ETTC 00:00:26
Search status: 24% ETTC 00:00:28
Search status: 26% ETTC 00:00:28
Search status: 27% ETTC 00:00:32
Search status: 29% ETTC 00:00:31
Search status: 31% ETTC 00:00:31
Search status: 33% ETTC 00:00:30
Search status: 36% ETTC 00:00:28
Search status: 38% ETTC 00:00:27
Search status: 41% ETTC 00:00:25
Search status: 44% ETTC 00:00:24
Search status: 45% ETTC 00:00:24
Search status: 48% ETTC 00:00:22
Search status: 51% ETTC 00:00:20
Search status: 53% ETTC 00:00:19
Search status: 55% ETTC 00:00:18
Search status: 57% ETTC 00:00:18
Search status: 59% ETTC 00:00:16
Search status: 62% ETTC 00:00:15
Search status: 64% ETTC 00:00:14
Search status: 67% ETTC 00:00:13
Search status: 68% ETTC 00:00:13
Search status: 70% ETTC 00:00:12
Search status: 71% ETTC 00:00:12
Search status: 74% ETTC 00:00:11
Search status: 76% ETTC 00:00:10
Search status: 77% ETTC 00:00:10
Search status: 79% ETTC 00:00:09
Search status: 81% ETTC 00:00:08
Search status: 84% ETTC 00:00:07
Search status: 85% ETTC 00:00:07
Search status: 87% ETTC 00:00:06
Search status: 89% ETTC 00:00:05
Search status: 91% ETTC 00:00:04
Search status: 92% ETTC 00:00:04
Search status: 93% ETTC 00:00:03
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
83.161 0.428 83.699
pqsfinder.Rcheck/pqsfinder-Ex.timings
| name | user | system | elapsed | |
| PQSViews | 0.065 | 0.000 | 0.065 | |
| density-PQSViews-method | 0.03 | 0.00 | 0.03 | |
| maxScores-PQSViews-method | 0.018 | 0.000 | 0.019 | |
| maxScores | 0.002 | 0.000 | 0.002 | |
| pqsfinder | 0.047 | 0.000 | 0.047 | |
| score-PQSViews-method | 0.020 | 0.000 | 0.019 | |
| strand-PQSViews-method | 0.018 | 0.000 | 0.018 | |