August Guang
| Snapshot Date: 2023-12-06 14:00:17 -0500 (Wed, 06 Dec 2023) |
| git_url: https://git.bioconductor.org/packages/qckitfastq |
| git_branch: devel |
| git_last_commit: 5c15b31 |
| git_last_commit_date: 2023-10-24 11:11:47 -0500 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2023-12-07 11:39:46 -0500 (Thu, 07 Dec 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | R Under development (unstable) (2023-11-11 r85510) -- "Unsuffered Consequences" | 4609 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-11-14 r85524 ucrt) -- "Unsuffered Consequences" | 4369 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2023-11-11 r85510) -- "Unsuffered Consequences" | 4375 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2023-11-01 r85459) -- "Unsuffered Consequences" | 4262 |
| 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 | ||||
| Package 1593/2229 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| qckitfastq 1.19.0 (landing page) August Guang
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | NA | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the qckitfastq package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: qckitfastq |
| Version: 1.19.0 |
| Command: /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD check --install=check:qckitfastq.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library --no-vignettes --timings qckitfastq_1.19.0.tar.gz |
| StartedAt: 2023-12-07 10:27:01 -0000 (Thu, 07 Dec 2023) |
| EndedAt: 2023-12-07 10:28:21 -0000 (Thu, 07 Dec 2023) |
| EllapsedTime: 80.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: qckitfastq.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD check --install=check:qckitfastq.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library --no-vignettes --timings qckitfastq_1.19.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/qckitfastq.Rcheck’
* using R Under development (unstable) (2023-11-01 r85459)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qckitfastq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qckitfastq’ version ‘1.19.0’
* 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++ (GCC) 10.3.1’
* 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 loading without being on the library search path ... 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 15.768 0.148 15.937
* 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-3.19-bioc/meat/qckitfastq.Rcheck/00check.log’
for details.
qckitfastq.Rcheck/00install.out
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###
### Running command:
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### /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD INSTALL qckitfastq
###
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library’
* installing *source* package ‘qckitfastq’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++14
g++ -std=gnu++14 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RSeqAn/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RSeqAn/include' -I/usr/local/include -fPIC -g -O2 -Wall -c calc_adapter_content.cpp -o calc_adapter_content.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RSeqAn/include' -I/usr/local/include -fPIC -g -O2 -Wall -c gzstream.cpp -o gzstream.o
g++ -std=gnu++14 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RSeqAn/include' -I/usr/local/include -fPIC -g -O2 -Wall -c read_fastq.cpp -o read_fastq.o
read_fastq.cpp: In function ‘Rcpp::List qual_score_per_read(std::string)’:
read_fastq.cpp:181:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<int, std::vector<unsigned char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
181 | if (pos_counter <= qual_score_matrix.size()) {
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -shared -L/home/biocbuild/R/R-devel/lib -L/usr/local/lib -o qckitfastq.so RcppExports.o calc_adapter_content.o gzstream.o read_fastq.o -lz -L/home/biocbuild/R/R-devel/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2023.11.02/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) (2023-11-01 r85459) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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/R/R-4.4-devel-2023.11.02/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastq_Klocs] File ( 1/1) '/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastqq] File ( 1/1) '/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastqq] File ( 1/1) '/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastq_Klocs] File ( 1/1) '/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastqq] File ( 1/1) '/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastq_Klocs] File ( 1/1) '/home/biocbuild/R/R-4.4-devel-2023.11.02/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
23.277 0.302 23.598
qckitfastq.Rcheck/qckitfastq-Ex.timings
| name | user | system | elapsed | |
| GC_content | 0.124 | 0.000 | 0.125 | |
| adapter_content | 0.005 | 0.000 | 0.006 | |
| calc_adapter_content | 0.003 | 0.000 | 0.003 | |
| calc_format_score | 0 | 0 | 0 | |
| calc_over_rep_seq | 0.054 | 0.000 | 0.053 | |
| dimensions | 0.134 | 0.000 | 0.135 | |
| find_format | 0.001 | 0.000 | 0.001 | |
| gc_per_read | 0.117 | 0.000 | 0.117 | |
| kmer_count | 0.062 | 0.000 | 0.062 | |
| overrep_kmer | 0.389 | 0.024 | 0.414 | |
| overrep_reads | 0.062 | 0.000 | 0.063 | |
| per_base_quality | 0.227 | 0.000 | 0.228 | |
| per_read_quality | 0.222 | 0.004 | 0.227 | |
| plot_GC_content | 0.596 | 0.004 | 0.601 | |
| plot_adapter_content | 0.236 | 0.012 | 0.248 | |
| plot_overrep_kmer | 0.682 | 0.008 | 0.692 | |
| plot_overrep_reads | 0.250 | 0.000 | 0.252 | |
| plot_per_base_quality | 1.464 | 0.036 | 1.503 | |
| plot_per_read_quality | 0.402 | 0.024 | 0.426 | |
| plot_read_content | 0.451 | 0.004 | 0.456 | |
| plot_read_length | 0.274 | 0.004 | 0.279 | |
| qual_score_per_read | 0.220 | 0.000 | 0.221 | |
| read_base_content | 0.070 | 0.004 | 0.074 | |
| read_content | 0.076 | 0.000 | 0.076 | |
| read_length | 0.003 | 0.000 | 0.003 | |
| run_all | 15.768 | 0.148 | 15.937 | |