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This page was generated on 2024-06-21 13:21 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4690
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4404
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4353
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 1591/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qckitfastq 1.21.0  (landing page)
August Guang
Snapshot Date: 2024-06-20 14:00 -0400 (Thu, 20 Jun 2024)
git_url: https://git.bioconductor.org/packages/qckitfastq
git_branch: devel
git_last_commit: 1e671c4
git_last_commit_date: 2024-04-30 11:13:03 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for qckitfastq on nebbiolo2

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.

raw results


Summary

Package: qckitfastq
Version: 1.21.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:qckitfastq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings qckitfastq_1.21.0.tar.gz
StartedAt: 2024-06-21 02:30:36 -0400 (Fri, 21 Jun 2024)
EndedAt: 2024-06-21 02:31:49 -0400 (Fri, 21 Jun 2024)
EllapsedTime: 73.1 seconds
RetCode: 0
Status:   OK  
CheckDir: qckitfastq.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:qckitfastq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings qckitfastq_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/qckitfastq.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘qckitfastq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qckitfastq’ version ‘1.21.0’
* 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 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 code 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 8.874  0.176   9.014
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/qckitfastq.Rcheck/00check.log’
for details.


Installation output

qckitfastq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL qckitfastq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘qckitfastq’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++14
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/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/bbs-3.20-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-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/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)

Tests output

qckitfastq.Rcheck/tests/testthat.Rout


R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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/bbs-3.20-bioc/R/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastq_Klocs] File ( 1/1) '/home/biocbuild/bbs-3.20-bioc/R/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz' 	done.
[fastqq] File ( 1/1) '/home/biocbuild/bbs-3.20-bioc/R/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastqq] File ( 1/1) '/home/biocbuild/bbs-3.20-bioc/R/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastq_Klocs] File ( 1/1) '/home/biocbuild/bbs-3.20-bioc/R/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz' 	done.
[fastqq] File ( 1/1) '/home/biocbuild/bbs-3.20-bioc/R/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastq_Klocs] File ( 1/1) '/home/biocbuild/bbs-3.20-bioc/R/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 
 13.842   0.357  14.161 

Example timings

qckitfastq.Rcheck/qckitfastq-Ex.timings

nameusersystemelapsed
GC_content0.1200.0040.125
adapter_content0.0040.0000.004
calc_adapter_content0.0020.0000.003
calc_format_score000
calc_over_rep_seq0.0540.0000.053
dimensions0.1220.0040.125
find_format0.0020.0000.001
gc_per_read0.1460.0000.147
kmer_count0.0620.0000.062
overrep_kmer0.2660.0070.274
overrep_reads0.0510.0000.051
per_base_quality0.1970.0080.205
per_read_quality0.1950.0030.199
plot_GC_content0.4840.0490.531
plot_adapter_content0.1530.0150.169
plot_overrep_kmer0.4410.0010.440
plot_overrep_reads0.1590.0000.160
plot_per_base_quality0.9560.0080.965
plot_per_read_quality0.3150.0030.319
plot_read_content0.2560.0040.260
plot_read_length0.1880.0030.192
qual_score_per_read0.1920.0040.195
read_base_content0.0770.0000.076
read_content0.0790.0000.079
read_length0.0020.0010.002
run_all8.8740.1769.014