Jiri Hon
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/pqsfinder |
| git_branch: RELEASE_3_17 |
| git_last_commit: a798b81 |
| git_last_commit_date: 2023-04-25 10:46:21 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:37:23 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 1547/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pqsfinder 2.16.0 (landing page) Jiri Hon
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: pqsfinder |
| Version: 2.16.0 |
| 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_2.16.0.tar.gz |
| StartedAt: 2023-10-16 05:25:42 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 05:32:56 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 434.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: pqsfinder.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### 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_2.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/pqsfinder.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pqsfinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pqsfinder’ version ‘2.16.0’
* 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.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 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 ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.3-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 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, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.17-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/4.3-x86_64/Resources/library’ * installing *source* package ‘pqsfinder’ ... ** 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.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/00LOCK-pqsfinder/00new/pqsfinder/lib" ar rs "/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a /Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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 -single_module -multiply_defined suppress -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/4.3-x86_64/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/4.3-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)
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: x86_64-apple-darwin20 (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 00:00:02
Search status: 43% ETTC 00:00:02
Search status: 46% ETTC 00:00:03
Search status: 47% ETTC 00:00:05
Search status: 48% ETTC 00:00:07
Search status: 49% ETTC 00:00:08
Search status: 55% ETTC 00:00:07
Search status: 59% ETTC 00:00:07
Search status: 78% ETTC 00:00:03
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 00:00:01
Search status: 46% ETTC 00:00:03
Search status: 51% ETTC 00:00:03
Search status: 57% ETTC 00:00:03
Search status: 83% ETTC 00:00:01
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: 64% ETTC 00:00:00
Search status: 98% ETTC 00:00:00
Search status: finished
Searching on antisense strand...
Search status: 59% ETTC 00:00:00
Search status: 90% ETTC 00:00:00
Search status: finished
Searching on sense strand...
Search status: 64% ETTC 00:00:00
Search status: 98% ETTC 00:00:00
Search status: finished
Searching on antisense strand...
Search status: 59% ETTC 00:00:00
Search status: 90% ETTC 00:00:00
Search status: finished
Searching on sense strand...
Search status: 44% ETTC 00:00:01
Search status: 90% ETTC 00:00:00
Search status: finished
Searching on antisense strand...
Search status: 66% ETTC 00:00:00
Search status: 96% ETTC 00:00:00
Search status: finished
Searching on sense strand...
Search status: 44% ETTC 00:00:01
Search status: 90% ETTC 00:00:00
Search status: finished
Searching on antisense strand...
Search status: 66% ETTC 00:00:00
Search status: 96% 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 00:01:04
Search status: 5% ETTC 00:01:16
Search status: 6% ETTC 00:01:49
Search status: 7% ETTC 00:02:12
Search status: 9% ETTC 00:02:11
Search status: 14% ETTC 00:01:26
Search status: 17% ETTC 00:01:23
Search status: 18% ETTC 00:01:26
Search status: 22% ETTC 00:01:14
Search status: 24% ETTC 00:01:16
Search status: 25% ETTC 00:01:21
Search status: 28% ETTC 00:01:17
Search status: 30% ETTC 00:01:14
Search status: 32% ETTC 00:01:14
Search status: 32% ETTC 00:01:20
Search status: 34% ETTC 00:01:19
Search status: 36% ETTC 00:01:16
Search status: 38% ETTC 00:01:13
Search status: 40% ETTC 00:01:12
Search status: 41% ETTC 00:01:13
Search status: 43% ETTC 00:01:11
Search status: 46% ETTC 00:01:05
Search status: 48% ETTC 00:01:02
Search status: 51% ETTC 00:00:57
Search status: 54% ETTC 00:00:52
Search status: 57% ETTC 00:00:48
Search status: 59% ETTC 00:00:46
Search status: 61% ETTC 00:00:44
Search status: 63% ETTC 00:00:42
Search status: 63% ETTC 00:00:44
Search status: 65% ETTC 00:00:42
Search status: 68% ETTC 00:00:37
Search status: 71% ETTC 00:00:33
Search status: 71% ETTC 00:00:35
Search status: 73% ETTC 00:00:33
Search status: 76% ETTC 00:00:29
Search status: 76% ETTC 00:00:30
Search status: 79% ETTC 00:00:26
Search status: 80% ETTC 00:00:25
Search status: 83% ETTC 00:00:21
Search status: 89% ETTC 00:00:12
Search status: 90% ETTC 00:00:12
Search status: 90% ETTC 00:00:12
Search status: 92% ETTC 00:00:09
Search status: 93% ETTC 00:00:08
Search status: 95% ETTC 00:00:06
Search status: 98% ETTC 00:00:02
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 00:00:02
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
146.859 1.419 205.848
pqsfinder.Rcheck/pqsfinder-Ex.timings
| name | user | system | elapsed | |
| PQSViews | 0.138 | 0.004 | 0.208 | |
| density-PQSViews-method | 0.071 | 0.001 | 0.104 | |
| maxScores-PQSViews-method | 0.042 | 0.001 | 0.064 | |
| maxScores | 0.003 | 0.001 | 0.004 | |
| pqsfinder | 0.088 | 0.002 | 0.135 | |
| score-PQSViews-method | 0.044 | 0.001 | 0.063 | |
| strand-PQSViews-method | 0.043 | 0.000 | 0.066 | |