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This page was generated on 2024-07-22 12:45 -0400 (Mon, 22 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4688
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4455
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4404
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 1597/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qckitfastq 1.21.0  (landing page)
August Guang
Snapshot Date: 2024-07-21 14:00 -0400 (Sun, 21 Jul 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 lconway

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:qckitfastq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings qckitfastq_1.21.0.tar.gz
StartedAt: 2024-07-21 23:33:20 -0400 (Sun, 21 Jul 2024)
EndedAt: 2024-07-21 23:34:54 -0400 (Sun, 21 Jul 2024)
EllapsedTime: 94.1 seconds
RetCode: 0
Status:   OK  
CheckDir: qckitfastq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:qckitfastq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings qckitfastq_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/qckitfastq.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qckitfastq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qckitfastq’ version ‘1.21.0’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
run_all 12.977   3.15  16.318
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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


Installation output

qckitfastq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL qckitfastq
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘qckitfastq’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++14
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RSeqAn/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RSeqAn/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c calc_adapter_content.cpp -o calc_adapter_content.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RSeqAn/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c gzstream.cpp -o gzstream.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RSeqAn/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c read_fastq.cpp -o read_fastq.o
read_fastq.cpp:30:32: warning: unused variable 'it' [-Wunused-variable]
    std::vector<int>::iterator it;
                               ^
read_fastq.cpp:158:36: warning: unused variable 'qual_by_col_it' [-Wunused-variable]
    std::vector<uint8_t>::iterator qual_by_col_it;
                                   ^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o qckitfastq.so RcppExports.o calc_adapter_content.o gzstream.o read_fastq.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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) '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastq_Klocs] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' 	done.
[fastqq] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastqq] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
2024-07-21 23:34:23.779 R[24732:431954262] XType: com.apple.fonts is not accessible.
2024-07-21 23:34:23.780 R[24732:431954262] XType: XTFontStaticRegistry is enabled.
[fastq_Klocs] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' 	done.
[fastqq] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastq_Klocs] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 
 20.388   3.747  24.425 

Example timings

qckitfastq.Rcheck/qckitfastq-Ex.timings

nameusersystemelapsed
GC_content0.1770.0050.185
adapter_content0.0040.0020.007
calc_adapter_content0.0030.0020.004
calc_format_score000
calc_over_rep_seq0.1090.0040.114
dimensions0.1050.0050.110
find_format0.0010.0000.001
gc_per_read0.1620.0020.165
kmer_count0.0510.0020.052
overrep_kmer0.3170.0150.333
overrep_reads0.0910.0020.093
per_base_quality0.1930.0090.203
per_read_quality0.1970.0080.206
plot_GC_content0.6190.0160.638
plot_adapter_content0.1950.0190.215
plot_overrep_kmer0.5760.0090.586
plot_overrep_reads0.2520.0040.257
plot_per_base_quality1.2840.0171.309
plot_per_read_quality0.3720.0120.386
plot_read_content0.3210.0040.326
plot_read_length0.2330.0040.239
qual_score_per_read0.2000.0070.207
read_base_content0.0640.0020.066
read_content0.0640.0050.070
read_length0.0020.0000.004
run_all12.977 3.15016.318