August Guang
| Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 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 Mac ARM64 build report for BioC 3.19 |
|
This page was generated on 2024-05-07 11:32:42 -0400 (Tue, 07 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
| 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
| kjohnson3 | macOS 13.6.5 Ventura / 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: 1.20.0 |
| 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: 2024-05-07 00:03:06 -0400 (Tue, 07 May 2024) |
| EndedAt: 2024-05-07 00:04:46 -0400 (Tue, 07 May 2024) |
| EllapsedTime: 100.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: qckitfastq.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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-mac-arm64/meat/qckitfastq.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-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 Ventura 13.6.5
* 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 15.0.0 (clang-1500.1.0.2.5)’
* 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
* 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-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/4.4-arm64/Resources/library’
* installing *source* package ‘qckitfastq’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
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/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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
In file included from calc_adapter_content.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RSeqAn/include/seqan/find.h:44:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RSeqAn/include/seqan/modifier.h:48:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RSeqAn/include/seqan/parallel.h:92:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RSeqAn/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable]
unsigned count = 0;
^
In file included from calc_adapter_content.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RSeqAn/include/seqan/find.h:45:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RSeqAn/include/seqan/score.h:48:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RSeqAn/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable]
for (unsigned row = 0; !atEnd(reader); ++row)
^
In file included from calc_adapter_content.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RSeqAn/include/seqan/find.h:73:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RSeqAn/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable]
TWord len = nl;
^
3 warnings generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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 -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/4.4-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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-arm64/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastq_Klocs] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastqq] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastqq] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
2024-05-07 00:04:39.195 R[13300:41485202] XType: Using static font registry.
[fastq_Klocs] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastqq] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastq_Klocs] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.4-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
5.105 0.358 5.462
qckitfastq.Rcheck/qckitfastq-Ex.timings
| name | user | system | elapsed | |
| GC_content | 0.072 | 0.000 | 0.074 | |
| adapter_content | 0.001 | 0.000 | 0.001 | |
| calc_adapter_content | 0.001 | 0.000 | 0.001 | |
| calc_format_score | 0 | 0 | 0 | |
| calc_over_rep_seq | 0.037 | 0.000 | 0.037 | |
| dimensions | 0.043 | 0.001 | 0.043 | |
| find_format | 0.000 | 0.001 | 0.001 | |
| gc_per_read | 0.071 | 0.000 | 0.071 | |
| kmer_count | 0.023 | 0.000 | 0.023 | |
| overrep_kmer | 0.077 | 0.002 | 0.079 | |
| overrep_reads | 0.037 | 0.001 | 0.037 | |
| per_base_quality | 0.091 | 0.002 | 0.093 | |
| per_read_quality | 0.093 | 0.001 | 0.094 | |
| plot_GC_content | 0.194 | 0.004 | 0.198 | |
| plot_adapter_content | 0.048 | 0.004 | 0.052 | |
| plot_overrep_kmer | 0.121 | 0.002 | 0.124 | |
| plot_overrep_reads | 0.075 | 0.001 | 0.076 | |
| plot_per_base_quality | 0.316 | 0.002 | 0.318 | |
| plot_per_read_quality | 0.129 | 0.002 | 0.131 | |
| plot_read_content | 0.083 | 0.001 | 0.084 | |
| plot_read_length | 0.065 | 0.000 | 0.065 | |
| qual_score_per_read | 0.094 | 0.001 | 0.095 | |
| read_base_content | 0.029 | 0.000 | 0.028 | |
| read_content | 0.029 | 0.001 | 0.030 | |
| read_length | 0.001 | 0.000 | 0.001 | |
| run_all | 3.203 | 0.318 | 3.524 | |