August Guang
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/qckitfastq |
| Branch: RELEASE_3_12 |
| Last Commit: 38d9c8e |
| Last Changed Date: 2020-10-27 11:43:39 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:36:14 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the qckitfastq package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1421/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| qckitfastq 1.6.0 (landing page) August Guang
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: qckitfastq |
| Version: 1.6.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:qckitfastq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings qckitfastq_1.6.0.tar.gz |
| StartedAt: 2021-05-06 05:02:47 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 05:04:12 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 84.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: qckitfastq.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:qckitfastq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings qckitfastq_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/qckitfastq.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qckitfastq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qckitfastq’ version ‘1.6.0’
* 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
* 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 11.077 2.101 13.203
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.12-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/Versions/Current/Resources/bin/R CMD INSTALL qckitfastq
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘qckitfastq’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RSeqAn/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RSeqAn/include' -I/usr/local/include -fPIC -Wall -g -O2 -c calc_adapter_content.cpp -o calc_adapter_content.o
In file included from calc_adapter_content.cpp:12:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RSeqAn/include' -I/usr/local/include -fPIC -Wall -g -O2 -c gzstream.cpp -o gzstream.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RSeqAn/include' -I/usr/local/include -fPIC -Wall -g -O2 -c read_fastq.cpp -o read_fastq.o
In file included from read_fastq.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
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;
^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -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/usr/local/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/4.0/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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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/4.0/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastq_Klocs] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastqq] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastqq] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastq_Klocs] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastqq] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[fastq_Klocs] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' done.
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 37 ]
>
> proc.time()
user system elapsed
19.668 2.452 22.139
qckitfastq.Rcheck/qckitfastq-Ex.timings
| name | user | system | elapsed | |
| GC_content | 0.217 | 0.006 | 0.227 | |
| adapter_content | 0.003 | 0.002 | 0.005 | |
| calc_adapter_content | 0.003 | 0.000 | 0.003 | |
| calc_format_score | 0.001 | 0.000 | 0.001 | |
| calc_over_rep_seq | 0.107 | 0.003 | 0.111 | |
| dimensions | 0.129 | 0.004 | 0.134 | |
| find_format | 0.001 | 0.000 | 0.001 | |
| gc_per_read | 0.198 | 0.002 | 0.199 | |
| kmer_count | 0.054 | 0.002 | 0.057 | |
| overrep_kmer | 0.385 | 0.014 | 0.399 | |
| overrep_reads | 0.106 | 0.002 | 0.108 | |
| per_base_quality | 0.241 | 0.010 | 0.252 | |
| per_read_quality | 0.244 | 0.006 | 0.250 | |
| plot_GC_content | 0.544 | 0.014 | 0.561 | |
| plot_adapter_content | 0.192 | 0.002 | 0.235 | |
| plot_overrep_kmer | 0.772 | 0.025 | 0.799 | |
| plot_overrep_reads | 0.238 | 0.004 | 0.243 | |
| plot_per_base_quality | 1.270 | 0.010 | 1.283 | |
| plot_per_read_quality | 0.389 | 0.011 | 0.400 | |
| plot_read_content | 0.302 | 0.004 | 0.309 | |
| plot_read_length | 0.248 | 0.001 | 0.250 | |
| qual_score_per_read | 0.227 | 0.003 | 0.231 | |
| read_base_content | 0.061 | 0.002 | 0.063 | |
| read_content | 0.065 | 0.004 | 0.069 | |
| read_length | 0.002 | 0.000 | 0.003 | |
| run_all | 11.077 | 2.101 | 13.203 | |