Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:06:20 -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: /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_2.14.1.tar.gz |
StartedAt: 2023-04-10 21:55:07 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 21:57:42 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 154.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: pqsfinder.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_2.14.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/pqsfinder.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘pqsfinder/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pqsfinder’ version ‘2.14.1’ * 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 ... 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 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 ... 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.16-bioc/meat/pqsfinder.Rcheck/00check.log’ for details.
pqsfinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL pqsfinder ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘pqsfinder’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c pqsfinder.cpp -o pqsfinder.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c boost_regex/regex.cpp -o boost_regex/regex.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I/usr/local/include -fPIC -Wall -g -O2 -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o mkdir -p "/Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-pqsfinder/00new/pqsfinder/lib" ar rs "/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a /Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Library/Frameworks/R.framework/Versions/4.2/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/4.2/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/4.2/Resources/library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a(static_mutex.o) has no symbols clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o pqsfinder.so RcppExports.o pqsfinder.o /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.2/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)
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-apple-darwin17.0 (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 00:00:02 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: 55% ETTC 00:00:00 Search status: 97% ETTC 00:00:00 Search status: finished Searching on antisense strand... Search status: 56% ETTC 00:00:00 Search status: finished Searching on sense strand... Search status: 55% ETTC 00:00:00 Search status: 97% ETTC 00:00:00 Search status: finished Searching on antisense strand... Search status: 56% ETTC 00:00:00 Search status: finished Searching on sense strand... Search status: 58% ETTC 00:00:00 Search status: finished Searching on antisense strand... Search status: 58% ETTC 00:00:00 Search status: finished Searching on sense strand... Search status: 58% ETTC 00:00:00 Search status: finished Searching on antisense strand... Search status: 58% 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: 2% ETTC 00:00:00 Search status: 4% ETTC 00:00:24 Search status: 7% ETTC 00:00:26 Search status: 10% ETTC 00:00:27 Search status: 11% ETTC 00:00:32 Search status: 14% ETTC 00:00:30 Search status: 17% ETTC 00:00:29 Search status: 19% ETTC 00:00:29 Search status: 21% ETTC 00:00:30 Search status: 23% ETTC 00:00:30 Search status: 25% ETTC 00:00:27 Search status: 26% ETTC 00:00:31 Search status: 29% ETTC 00:00:26 Search status: 31% ETTC 00:00:26 Search status: 34% ETTC 00:00:25 Search status: 37% ETTC 00:00:23 Search status: 39% ETTC 00:00:21 Search status: 43% ETTC 00:00:19 Search status: 47% ETTC 00:00:18 Search status: 49% ETTC 00:00:17 Search status: 50% ETTC 00:00:18 Search status: 52% ETTC 00:00:16 Search status: 54% ETTC 00:00:16 Search status: 57% ETTC 00:00:15 Search status: 59% ETTC 00:00:14 Search status: 61% ETTC 00:00:14 Search status: 62% ETTC 00:00:14 Search status: 65% ETTC 00:00:12 Search status: 66% ETTC 00:00:12 Search status: 69% ETTC 00:00:11 Search status: 71% ETTC 00:00:10 Search status: 75% ETTC 00:00:09 Search status: 77% ETTC 00:00:08 Search status: 79% ETTC 00:00:07 Search status: 80% ETTC 00:00:07 Search status: 83% ETTC 00:00:06 Search status: 85% ETTC 00:00:05 Search status: 87% ETTC 00:00:04 Search status: 90% ETTC 00:00:03 Search status: 91% ETTC 00:00:03 Search status: 94% ETTC 00:00:02 Search status: 97% ETTC 00:00:01 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 66.642 0.510 67.270
pqsfinder.Rcheck/pqsfinder-Ex.timings
name | user | system | elapsed | |
PQSViews | 0.052 | 0.005 | 0.056 | |
density-PQSViews-method | 0.042 | 0.005 | 0.046 | |
maxScores-PQSViews-method | 0.015 | 0.000 | 0.015 | |
maxScores | 0.001 | 0.000 | 0.002 | |
pqsfinder | 0.030 | 0.001 | 0.030 | |
score-PQSViews-method | 0.016 | 0.001 | 0.016 | |
strand-PQSViews-method | 0.016 | 0.000 | 0.016 | |