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CHECK report for qckitfastq on merida2

This page was generated on 2019-04-09 13:39:24 -0400 (Tue, 09 Apr 2019).

Package 1256/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qckitfastq 0.99.22
August Guang
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/qckitfastq
Branch: master
Last Commit: 373bb1f
Last Changed Date: 2019-02-22 10:09:04 -0400 (Fri, 22 Feb 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: qckitfastq
Version: 0.99.22
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_0.99.22.tar.gz
StartedAt: 2019-04-09 03:04:54 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:06:40 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 106.8 seconds
RetCode: 0
Status:  OK 
CheckDir: qckitfastq.Rcheck
Warnings: 0

Command output

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### Running 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_0.99.22.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/qckitfastq.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘0.99.22’
* 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 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 or elapsed time > 5s
          user system elapsed
run_all 17.549  7.622  22.295
* 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-3.9-bioc/meat/qckitfastq.Rcheck/00check.log’
for details.



Installation output

qckitfastq.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘qckitfastq’ ...
** libs
clang++ -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RSeqAn/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RSeqAn/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c calc_adapter_content.cpp -o calc_adapter_content.o
clang++ -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RSeqAn/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c gzstream.cpp -o gzstream.o
clang++ -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RSeqAn/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c read_fastq.cpp -o read_fastq.o
clang++ -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/3.6/Resources/library/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
* DONE (qckitfastq)

Tests output

qckitfastq.Rcheck/tests/testthat.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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/3.6/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastq_Klocs] File ( 1/1) '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' 	done.
[fastqq] File ( 1/1) '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastqq] File ( 1/1) '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastq_Klocs] File ( 1/1) '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' 	done.
[fastqq] File ( 1/1) '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastq_Klocs] File ( 1/1) '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' 	done.
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 39 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 38.439  15.201  32.858 

Example timings

qckitfastq.Rcheck/qckitfastq-Ex.timings

nameusersystemelapsed
GC_content0.2230.0020.228
adapter_content0.0030.0010.004
calc_adapter_content0.0030.0010.004
calc_format_score0.0010.0000.000
calc_over_rep_seq0.1370.0030.142
dimensions0.1330.0070.140
find_format0.0010.0000.001
gc_per_read0.2600.0020.262
kmer_count0.0790.0030.080
overrep_kmer1.8150.9681.007
overrep_reads0.1540.0030.164
per_base_quality0.3680.0110.389
per_read_quality0.2920.0040.299
plot_GC_content0.5570.0130.571
plot_adapter_content0.1880.0010.189
plot_overrep_kmer2.0071.1401.080
plot_overrep_reads0.3550.0050.370
plot_per_base_quality0.5330.0090.545
plot_per_read_quality0.5340.0110.548
plot_read_content0.4390.0030.443
plot_read_length0.2930.0020.298
qual_score_per_read0.2280.0050.234
read_base_content0.0640.0010.064
read_content0.0680.0020.071
read_length0.0020.0000.003
run_all17.549 7.62222.295