August Guang
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/qckitfastq |
| git_branch: RELEASE_3_17 |
| git_last_commit: 985d8f5 |
| git_last_commit_date: 2023-04-25 11:08:31 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:09 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1593/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| qckitfastq 1.16.0 (landing page) August Guang
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the qckitfastq package: - 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: 1.16.0 |
| 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_1.16.0.tar.gz |
| StartedAt: 2023-10-18 16:35:40 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 16:37:55 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 135.3 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_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/qckitfastq.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qckitfastq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qckitfastq’ version ‘1.16.0’
* 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 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 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 12.474 1.164 21.085
* 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
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/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/4.3-arm64/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 arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RSeqAn/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RSeqAn/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c calc_adapter_content.cpp -o calc_adapter_content.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RSeqAn/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gzstream.cpp -o gzstream.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RSeqAn/include' -I/opt/R/arm64/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 arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/4.3-arm64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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) '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastq_Klocs] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastqq] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastqq] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
2023-10-18 16:37:11.403 R[57324:44342092] XType: com.apple.fonts is not accessible.
2023-10-18 16:37:11.409 R[57324:44342092] XType: XTFontStaticRegistry is enabled.
[fastq_Klocs] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastqq] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastq_Klocs] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.3-arm64/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
19.828 1.462 32.552
qckitfastq.Rcheck/qckitfastq-Ex.timings
| name | user | system | elapsed | |
| GC_content | 0.193 | 0.007 | 0.308 | |
| adapter_content | 0.004 | 0.002 | 0.007 | |
| calc_adapter_content | 0.003 | 0.001 | 0.009 | |
| calc_format_score | 0 | 0 | 0 | |
| calc_over_rep_seq | 0.119 | 0.004 | 0.192 | |
| dimensions | 0.125 | 0.005 | 0.201 | |
| find_format | 0.002 | 0.001 | 0.004 | |
| gc_per_read | 0.187 | 0.003 | 0.294 | |
| kmer_count | 0.060 | 0.003 | 0.097 | |
| overrep_kmer | 0.330 | 0.013 | 0.532 | |
| overrep_reads | 0.121 | 0.003 | 0.188 | |
| per_base_quality | 0.236 | 0.010 | 0.370 | |
| per_read_quality | 0.234 | 0.006 | 0.364 | |
| plot_GC_content | 0.592 | 0.013 | 0.930 | |
| plot_adapter_content | 0.206 | 0.015 | 0.343 | |
| plot_overrep_kmer | 0.559 | 0.015 | 0.888 | |
| plot_overrep_reads | 0.280 | 0.006 | 0.434 | |
| plot_per_base_quality | 1.298 | 0.018 | 2.038 | |
| plot_per_read_quality | 0.384 | 0.009 | 0.605 | |
| plot_read_content | 0.383 | 0.007 | 0.589 | |
| plot_read_length | 0.244 | 0.004 | 0.373 | |
| qual_score_per_read | 0.233 | 0.006 | 0.370 | |
| read_base_content | 0.072 | 0.002 | 0.110 | |
| read_content | 0.075 | 0.005 | 0.123 | |
| read_length | 0.002 | 0.000 | 0.003 | |
| run_all | 12.474 | 1.164 | 21.085 | |