Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:49 -0400 (Fri, 15 Oct 2021).
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1468/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
qckitfastq 1.8.0 (landing page) August Guang
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: qckitfastq |
Version: 1.8.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:qckitfastq.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings qckitfastq_1.8.0.tar.gz |
StartedAt: 2021-10-14 11:10:16 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 11:11:15 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 59.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: qckitfastq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:qckitfastq.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings qckitfastq_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/qckitfastq.Rcheck’ * using R version 4.1.1 (2021-08-10) * 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 ‘1.8.0’ * 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 * 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 8.886 0.116 9.001 * 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-3.13-bioc/meat/qckitfastq.Rcheck/00check.log’ for details.
qckitfastq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL qckitfastq ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘qckitfastq’ ... ** using staged installation ** libs g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RSeqAn/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/RSeqAn/include' -I/usr/local/include -fpic -g -O2 -Wall -c gzstream.cpp -o gzstream.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/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/bbs-3.13-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-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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-3.13-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done. [fastq_Klocs] File ( 1/1) '/home/biocbuild/bbs-3.13-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done. [fastqq] File ( 1/1) '/home/biocbuild/bbs-3.13-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done. [fastqq] File ( 1/1) '/home/biocbuild/bbs-3.13-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done. [fastq_Klocs] File ( 1/1) '/home/biocbuild/bbs-3.13-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done. [fastqq] File ( 1/1) '/home/biocbuild/bbs-3.13-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done. [fastq_Klocs] File ( 1/1) '/home/biocbuild/bbs-3.13-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done. [ FAIL 0 | WARN 2 | SKIP 0 | PASS 37 ] > > proc.time() user system elapsed 14.483 0.436 14.903
qckitfastq.Rcheck/qckitfastq-Ex.timings
name | user | system | elapsed | |
GC_content | 0.117 | 0.000 | 0.118 | |
adapter_content | 0.004 | 0.000 | 0.004 | |
calc_adapter_content | 0.002 | 0.000 | 0.002 | |
calc_format_score | 0 | 0 | 0 | |
calc_over_rep_seq | 0.040 | 0.012 | 0.052 | |
dimensions | 0.119 | 0.000 | 0.120 | |
find_format | 0.000 | 0.002 | 0.002 | |
gc_per_read | 0.108 | 0.002 | 0.110 | |
kmer_count | 0.052 | 0.006 | 0.057 | |
overrep_kmer | 0.317 | 0.009 | 0.327 | |
overrep_reads | 0.058 | 0.000 | 0.058 | |
per_base_quality | 0.183 | 0.011 | 0.194 | |
per_read_quality | 0.185 | 0.008 | 0.193 | |
plot_GC_content | 0.394 | 0.003 | 0.397 | |
plot_adapter_content | 0.184 | 0.000 | 0.184 | |
plot_overrep_kmer | 0.650 | 0.168 | 0.818 | |
plot_overrep_reads | 0.159 | 0.000 | 0.159 | |
plot_per_base_quality | 0.82 | 0.02 | 0.84 | |
plot_per_read_quality | 0.291 | 0.008 | 0.300 | |
plot_read_content | 0.265 | 0.004 | 0.269 | |
plot_read_length | 0.21 | 0.00 | 0.21 | |
qual_score_per_read | 0.169 | 0.008 | 0.178 | |
read_base_content | 0.073 | 0.000 | 0.073 | |
read_content | 0.072 | 0.007 | 0.079 | |
read_length | 0.002 | 0.000 | 0.002 | |
run_all | 8.886 | 0.116 | 9.001 | |