| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-27 05:50:40 -0000 (Mon, 27 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6083 |
| 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 | ||||
|
To the developers/maintainers of the qckitfastq package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/qckitfastq.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1572/2195 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| qckitfastq 1.15.0 (landing page) August Guang
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: qckitfastq |
| Version: 1.15.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:qckitfastq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings qckitfastq_1.15.0.tar.gz |
| StartedAt: 2023-03-25 09:44:39 -0000 (Sat, 25 Mar 2023) |
| EndedAt: 2023-03-25 09:46:23 -0000 (Sat, 25 Mar 2023) |
| EllapsedTime: 104.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: qckitfastq.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:qckitfastq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings qckitfastq_1.15.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/qckitfastq.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘qckitfastq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qckitfastq’ version ‘1.15.0’
* 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 ‘qckitfastq’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking C++ specification ... NOTE
Specified C++14: 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 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
run_all 15.71 0.152 15.865
* 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 ...
‘vignette-qckitfastq.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/qckitfastq.Rcheck/00check.log’
for details.
qckitfastq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL qckitfastq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’ * installing *source* package ‘qckitfastq’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ using C++14 g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/RSeqAn/include' -I/usr/local/include -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/RSeqAn/include' -I/usr/local/include -fPIC -g -O2 -c calc_adapter_content.cpp -o calc_adapter_content.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/RSeqAn/include' -I/usr/local/include -fPIC -g -O2 -c gzstream.cpp -o gzstream.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/RSeqAn/include' -I/usr/local/include -fPIC -g -O2 -c read_fastq.cpp -o read_fastq.o g++ -std=gnu++14 -shared -L/usr/local/lib -o qckitfastq.so RcppExports.o calc_adapter_content.o gzstream.o read_fastq.o -lz installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-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) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastq_Klocs] File ( 1/1) '/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastqq] File ( 1/1) '/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastqq] File ( 1/1) '/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastq_Klocs] File ( 1/1) '/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastqq] File ( 1/1) '/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastq_Klocs] File ( 1/1) '/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 37 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 37 ]
>
> proc.time()
user system elapsed
23.835 0.424 24.246
qckitfastq.Rcheck/qckitfastq-Ex.timings
| name | user | system | elapsed | |
| GC_content | 0.151 | 0.000 | 0.151 | |
| adapter_content | 0.000 | 0.004 | 0.005 | |
| calc_adapter_content | 0.003 | 0.000 | 0.003 | |
| calc_format_score | 0 | 0 | 0 | |
| calc_over_rep_seq | 0.056 | 0.000 | 0.056 | |
| dimensions | 0.135 | 0.004 | 0.140 | |
| find_format | 0.001 | 0.000 | 0.001 | |
| gc_per_read | 0.141 | 0.004 | 0.144 | |
| kmer_count | 0.07 | 0.00 | 0.07 | |
| overrep_kmer | 0.384 | 0.008 | 0.393 | |
| overrep_reads | 0.053 | 0.004 | 0.058 | |
| per_base_quality | 0.238 | 0.000 | 0.238 | |
| per_read_quality | 0.233 | 0.000 | 0.232 | |
| plot_GC_content | 0.417 | 0.004 | 0.421 | |
| plot_adapter_content | 0.376 | 0.008 | 0.383 | |
| plot_overrep_kmer | 0.635 | 0.024 | 0.659 | |
| plot_overrep_reads | 0.224 | 0.000 | 0.224 | |
| plot_per_base_quality | 1.430 | 0.008 | 1.439 | |
| plot_per_read_quality | 0.400 | 0.032 | 0.432 | |
| plot_read_content | 0.423 | 0.016 | 0.439 | |
| plot_read_length | 0.267 | 0.000 | 0.267 | |
| qual_score_per_read | 0.229 | 0.004 | 0.233 | |
| read_base_content | 0.082 | 0.000 | 0.082 | |
| read_content | 0.082 | 0.004 | 0.085 | |
| read_length | 0.003 | 0.000 | 0.003 | |
| run_all | 15.710 | 0.152 | 15.865 | |