Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 13:39:24 -0400 (Tue, 09 Apr 2019).
Package 1256/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
qckitfastq 0.99.22 August Guang
| 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 | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
Package: qckitfastq |
Version: 0.99.22 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:qckitfastq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings qckitfastq_0.99.22.tar.gz |
StartedAt: 2019-04-09 03:04:54 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 03:06:40 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 106.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: qckitfastq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:qckitfastq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings qckitfastq_0.99.22.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/qckitfastq.Rcheck’ * using R Under development (unstable) (2018-11-27 r75683) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘qckitfastq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘qckitfastq’ version ‘0.99.22’ * 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 ‘qckitfastq’ 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 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed run_all 17.549 7.622 22.295 * 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 NOTE See ‘/Users/biocbuild/bbs-3.9-bioc/meat/qckitfastq.Rcheck/00check.log’ for details.
qckitfastq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL qckitfastq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘qckitfastq’ ... ** libs clang++ -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RSeqAn/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RSeqAn/include" -I/usr/local/include -fPIC -Wall -g -O2 -c calc_adapter_content.cpp -o calc_adapter_content.o clang++ -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RSeqAn/include" -I/usr/local/include -fPIC -Wall -g -O2 -c gzstream.cpp -o gzstream.o clang++ -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RSeqAn/include" -I/usr/local/include -fPIC -Wall -g -O2 -c read_fastq.cpp -o read_fastq.o clang++ -std=gnu++14 -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 qckitfastq.so RcppExports.o calc_adapter_content.o gzstream.o read_fastq.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/qckitfastq/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 * DONE (qckitfastq)
qckitfastq.Rcheck/tests/testthat.Rout
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (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(qckitfastq) > > test_check("qckitfastq") [fastqq] File ( 1/1) '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done. [fastq_Klocs] File ( 1/1) '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done. [fastqq] File ( 1/1) '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done. [fastqq] File ( 1/1) '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done. [fastq_Klocs] File ( 1/1) '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done. [fastqq] File ( 1/1) '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done. [fastq_Klocs] File ( 1/1) '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done. ══ testthat results ═══════════════════════════════════════════════════════════ OK: 39 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 38.439 15.201 32.858
qckitfastq.Rcheck/qckitfastq-Ex.timings
name | user | system | elapsed | |
GC_content | 0.223 | 0.002 | 0.228 | |
adapter_content | 0.003 | 0.001 | 0.004 | |
calc_adapter_content | 0.003 | 0.001 | 0.004 | |
calc_format_score | 0.001 | 0.000 | 0.000 | |
calc_over_rep_seq | 0.137 | 0.003 | 0.142 | |
dimensions | 0.133 | 0.007 | 0.140 | |
find_format | 0.001 | 0.000 | 0.001 | |
gc_per_read | 0.260 | 0.002 | 0.262 | |
kmer_count | 0.079 | 0.003 | 0.080 | |
overrep_kmer | 1.815 | 0.968 | 1.007 | |
overrep_reads | 0.154 | 0.003 | 0.164 | |
per_base_quality | 0.368 | 0.011 | 0.389 | |
per_read_quality | 0.292 | 0.004 | 0.299 | |
plot_GC_content | 0.557 | 0.013 | 0.571 | |
plot_adapter_content | 0.188 | 0.001 | 0.189 | |
plot_overrep_kmer | 2.007 | 1.140 | 1.080 | |
plot_overrep_reads | 0.355 | 0.005 | 0.370 | |
plot_per_base_quality | 0.533 | 0.009 | 0.545 | |
plot_per_read_quality | 0.534 | 0.011 | 0.548 | |
plot_read_content | 0.439 | 0.003 | 0.443 | |
plot_read_length | 0.293 | 0.002 | 0.298 | |
qual_score_per_read | 0.228 | 0.005 | 0.234 | |
read_base_content | 0.064 | 0.001 | 0.064 | |
read_content | 0.068 | 0.002 | 0.071 | |
read_length | 0.002 | 0.000 | 0.003 | |
run_all | 17.549 | 7.622 | 22.295 | |