August Guang
| Snapshot Date: 2024-04-30 20:18:44 -0400 (Tue, 30 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/qckitfastq |
| git_branch: RELEASE_3_19 |
| git_last_commit: 5fb9174 |
| git_last_commit_date: 2024-04-30 11:13:03 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-01 11:36:36 -0400 (Wed, 01 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4518 |
| 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 1639/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| qckitfastq 1.20.0 (landing page) August Guang
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: qckitfastq |
| Version: 1.20.0 |
| 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_1.20.0.tar.gz |
| StartedAt: 2024-05-01 05:46:18 -0400 (Wed, 01 May 2024) |
| EndedAt: 2024-05-01 05:47:50 -0400 (Wed, 01 May 2024) |
| EllapsedTime: 91.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: qckitfastq.Rcheck |
| Warnings: 0 |
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### 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_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/qckitfastq.Rcheck’
* using R version 4.4.0 beta (2024-04-14 r86421)
* 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 ‘1.20.0’
* 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 12.437 3.474 16.099
* 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-3.19-bioc/meat/qckitfastq.Rcheck/00check.log’
for details.
qckitfastq.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL qckitfastq
###
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* 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)
qckitfastq.Rcheck/tests/testthat.Rout
R version 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup"
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.
2024-05-01 05:47:20.617 R[53253:1692531390] XType: com.apple.fonts is not accessible.
2024-05-01 05:47:20.618 R[53253:1692531390] 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
19.636 3.909 23.807
qckitfastq.Rcheck/qckitfastq-Ex.timings
| name | user | system | elapsed | |
| GC_content | 0.181 | 0.004 | 0.186 | |
| adapter_content | 0.003 | 0.002 | 0.006 | |
| calc_adapter_content | 0.004 | 0.002 | 0.005 | |
| calc_format_score | 0.000 | 0.001 | 0.001 | |
| calc_over_rep_seq | 0.105 | 0.006 | 0.117 | |
| dimensions | 0.115 | 0.005 | 0.121 | |
| find_format | 0.001 | 0.001 | 0.003 | |
| gc_per_read | 0.172 | 0.002 | 0.174 | |
| kmer_count | 0.046 | 0.002 | 0.049 | |
| overrep_kmer | 0.352 | 0.017 | 0.370 | |
| overrep_reads | 0.110 | 0.006 | 0.120 | |
| per_base_quality | 0.211 | 0.013 | 0.225 | |
| per_read_quality | 0.209 | 0.008 | 0.218 | |
| plot_GC_content | 0.624 | 0.017 | 0.642 | |
| plot_adapter_content | 0.215 | 0.018 | 0.234 | |
| plot_overrep_kmer | 0.458 | 0.010 | 0.470 | |
| plot_overrep_reads | 0.223 | 0.005 | 0.228 | |
| plot_per_base_quality | 1.133 | 0.014 | 1.153 | |
| plot_per_read_quality | 0.318 | 0.013 | 0.335 | |
| plot_read_content | 0.281 | 0.008 | 0.291 | |
| plot_read_length | 0.220 | 0.004 | 0.226 | |
| qual_score_per_read | 0.202 | 0.008 | 0.210 | |
| read_base_content | 0.067 | 0.002 | 0.070 | |
| read_content | 0.070 | 0.004 | 0.075 | |
| read_length | 0.004 | 0.001 | 0.005 | |
| run_all | 12.437 | 3.474 | 16.099 | |