Leandro Roser
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/FastqCleaner |
| Branch: RELEASE_3_9 |
| Last Commit: b6d7db7 |
| Last Changed Date: 2019-05-02 11:54:12 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:14:54 -0400 (Wed, 16 Oct 2019).
| Package 538/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| FastqCleaner 1.2.0 Leandro Roser
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: FastqCleaner |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:FastqCleaner.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings FastqCleaner_1.2.0.tar.gz |
| StartedAt: 2019-10-16 01:36:05 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 01:39:36 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 210.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FastqCleaner.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:FastqCleaner.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings FastqCleaner_1.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/FastqCleaner.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FastqCleaner/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘FastqCleaner’ version ‘1.2.0’ * 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 ‘FastqCleaner’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ A package should be listed in only one of these fields. * 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 C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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 ‘/home/biocbuild/bbs-3.9-bioc/meat/FastqCleaner.Rcheck/00check.log’ for details.
FastqCleaner.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL FastqCleaner ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘FastqCleaner’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I../inst/include/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I../inst/include/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c cpp_GC_content.cpp -o cpp_GC_content.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I../inst/include/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c cpp_base_content.cpp -o cpp_base_content.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I../inst/include/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c cpp_check_quality_threshold.cpp -o cpp_check_quality_threshold.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I../inst/include/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c cpp_create_stringvec.cpp -o cpp_create_stringvec.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I../inst/include/ -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c cpp_which_true.cpp -o cpp_which_true.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o FastqCleaner.so RcppExports.o cpp_GC_content.o cpp_base_content.o cpp_check_quality_threshold.o cpp_create_stringvec.o cpp_which_true.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-FastqCleaner/00new/FastqCleaner/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 (FastqCleaner)
FastqCleaner.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(FastqCleaner)
>
> test_check("FastqCleaner")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 0 | SKIPPED: 10 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
9.713 0.345 10.149
FastqCleaner.Rcheck/FastqCleaner-Ex.timings
| name | user | system | elapsed | |
| adapter_filter | 0.316 | 0.036 | 0.353 | |
| check_encoding | 0.099 | 0.016 | 0.116 | |
| complex_filter | 0.252 | 0.014 | 0.266 | |
| fixed_filter | 0.224 | 0.004 | 0.228 | |
| inject_letter_random | 0.131 | 0.000 | 0.131 | |
| launch_fqc | 0 | 0 | 0 | |
| length_filter | 0.195 | 0.006 | 0.202 | |
| matching | 0 | 0 | 0 | |
| n_filter | 0.376 | 0.012 | 0.389 | |
| qmean_filter | 0.221 | 0.000 | 0.221 | |
| random_length | 0.02 | 0.00 | 0.02 | |
| random_qual | 0.013 | 0.000 | 0.013 | |
| random_seq | 0.028 | 0.000 | 0.027 | |
| seq_filter | 0.313 | 0.000 | 0.314 | |
| seq_names | 0.037 | 0.000 | 0.037 | |
| trim3q_filter | 0.429 | 0.008 | 0.436 | |
| unique_filter | 0.35 | 0.00 | 0.35 | |