August Guang
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/qckitfastq |
| Branch: RELEASE_3_9 |
| Last Commit: 077b5a5 |
| Last Changed Date: 2019-09-17 16:06:14 -0400 (Tue, 17 Sep 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:17:37 -0400 (Wed, 16 Oct 2019).
| Package 1282/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| qckitfastq 1.0.1 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 | |
| Package: qckitfastq |
| Version: 1.0.1 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:qckitfastq.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings qckitfastq_1.0.1.tar.gz |
| StartedAt: 2019-10-16 04:11:16 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:12:35 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 78.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: qckitfastq.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:qckitfastq.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings qckitfastq_1.0.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/qckitfastq.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 ‘qckitfastq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qckitfastq’ version ‘1.0.1’
* 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 ‘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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
run_all 29.245 0.145 12.390
plot_overrep_kmer 13.334 0.042 2.443
overrep_kmer 7.671 0.026 1.579
* 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
‘/home/biocbuild/bbs-3.9-bioc/meat/qckitfastq.Rcheck/00check.log’
for details.
qckitfastq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL qckitfastq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘qckitfastq’ ... ** using staged installation ** libs g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RSeqAn/include" -I/usr/local/include -fpic -O3 -march=native -mtune=native -fPIC -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RSeqAn/include" -I/usr/local/include -fpic -O3 -march=native -mtune=native -fPIC -c calc_adapter_content.cpp -o calc_adapter_content.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RSeqAn/include" -I/usr/local/include -fpic -O3 -march=native -mtune=native -fPIC -c gzstream.cpp -o gzstream.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/RSeqAn/include" -I/usr/local/include -fpic -O3 -march=native -mtune=native -fPIC -c read_fastq.cpp -o read_fastq.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o qckitfastq.so RcppExports.o calc_adapter_content.o gzstream.o read_fastq.o -lz -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-qckitfastq/00new/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 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 (qckitfastq)
qckitfastq.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(qckitfastq)
>
> test_check("qckitfastq")
[fastqq] File ( 1/1) '/home/biocbuild/bbs-3.9-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastq_Klocs] File ( 1/1) '/home/biocbuild/bbs-3.9-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastqq] File ( 1/1) '/home/biocbuild/bbs-3.9-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastqq] File ( 1/1) '/home/biocbuild/bbs-3.9-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastq_Klocs] File ( 1/1) '/home/biocbuild/bbs-3.9-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastqq] File ( 1/1) '/home/biocbuild/bbs-3.9-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastq_Klocs] File ( 1/1) '/home/biocbuild/bbs-3.9-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 37 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
>
> proc.time()
user system elapsed
91.231 0.433 26.206
qckitfastq.Rcheck/qckitfastq-Ex.timings
| name | user | system | elapsed | |
| GC_content | 0.122 | 0.001 | 0.137 | |
| adapter_content | 0.003 | 0.000 | 0.010 | |
| calc_adapter_content | 0.002 | 0.000 | 0.002 | |
| calc_format_score | 0.000 | 0.000 | 0.001 | |
| calc_over_rep_seq | 0.059 | 0.000 | 0.059 | |
| dimensions | 0.107 | 0.011 | 0.120 | |
| find_format | 0.001 | 0.000 | 0.001 | |
| gc_per_read | 0.108 | 0.000 | 0.108 | |
| kmer_count | 0.062 | 0.000 | 0.061 | |
| overrep_kmer | 7.671 | 0.026 | 1.579 | |
| overrep_reads | 0.083 | 0.000 | 0.083 | |
| per_base_quality | 0.273 | 0.000 | 0.273 | |
| per_read_quality | 0.248 | 0.004 | 0.252 | |
| plot_GC_content | 0.578 | 0.004 | 0.581 | |
| plot_adapter_content | 0.255 | 0.000 | 0.255 | |
| plot_overrep_kmer | 13.334 | 0.042 | 2.443 | |
| plot_overrep_reads | 0.184 | 0.000 | 0.184 | |
| plot_per_base_quality | 0.991 | 0.000 | 0.991 | |
| plot_per_read_quality | 0.348 | 0.008 | 0.356 | |
| plot_read_content | 0.339 | 0.000 | 0.340 | |
| plot_read_length | 0.262 | 0.000 | 0.262 | |
| qual_score_per_read | 0.178 | 0.000 | 0.179 | |
| read_base_content | 0.081 | 0.000 | 0.080 | |
| read_content | 0.085 | 0.000 | 0.084 | |
| read_length | 0.002 | 0.000 | 0.003 | |
| run_all | 29.245 | 0.145 | 12.390 | |