August Guang
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/qckitfastq |
| Branch: master |
| Last Commit: 373bb1f |
| Last Changed Date: 2019-02-22 10:09:04 -0400 (Fri, 22 Feb 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:52:51 -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: /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_0.99.22.tar.gz |
| StartedAt: 2019-04-09 02:54:15 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 02:56:37 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 141.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: qckitfastq.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_0.99.22.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/qckitfastq.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
overrep_kmer 17.274 0.083 3.319
plot_overrep_kmer 16.456 0.076 3.389
run_all 15.402 0.052 12.079
* 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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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: 39 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
434.064 1.819 84.987
qckitfastq.Rcheck/qckitfastq-Ex.timings
| name | user | system | elapsed | |
| GC_content | 0.125 | 0.000 | 0.140 | |
| adapter_content | 0.003 | 0.000 | 0.011 | |
| calc_adapter_content | 0.002 | 0.000 | 0.002 | |
| calc_format_score | 0.001 | 0.000 | 0.000 | |
| calc_over_rep_seq | 0.077 | 0.000 | 0.077 | |
| dimensions | 0.18 | 0.00 | 0.18 | |
| find_format | 0.001 | 0.000 | 0.001 | |
| gc_per_read | 0.181 | 0.004 | 0.185 | |
| kmer_count | 0.097 | 0.000 | 0.097 | |
| overrep_kmer | 17.274 | 0.083 | 3.319 | |
| overrep_reads | 0.071 | 0.008 | 0.079 | |
| per_base_quality | 0.292 | 0.000 | 0.292 | |
| per_read_quality | 0.264 | 0.004 | 0.268 | |
| plot_GC_content | 0.328 | 0.004 | 0.332 | |
| plot_adapter_content | 0.185 | 0.000 | 0.185 | |
| plot_overrep_kmer | 16.456 | 0.076 | 3.389 | |
| plot_overrep_reads | 0.297 | 0.000 | 0.298 | |
| plot_per_base_quality | 0.618 | 0.000 | 0.618 | |
| plot_per_read_quality | 0.507 | 0.000 | 0.506 | |
| plot_read_content | 0.518 | 0.000 | 0.518 | |
| plot_read_length | 0.390 | 0.000 | 0.389 | |
| qual_score_per_read | 0.294 | 0.004 | 0.299 | |
| read_base_content | 0.116 | 0.000 | 0.116 | |
| read_content | 0.121 | 0.000 | 0.120 | |
| read_length | 0.003 | 0.000 | 0.004 | |
| run_all | 15.402 | 0.052 | 12.079 | |