Package: qckitfastq

Version: 1.0.1

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qckitfastq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings qckitfastq_1.0.1.tar.gz

StartedAt: 2019-10-16 06:14:33 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:17:13 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 160.0 seconds

RetCode: 0

Status:  OK

CheckDir: qckitfastq.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:qckitfastq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings qckitfastq_1.0.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/qckitfastq.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'qckitfastq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'qckitfastq' version '1.0.1'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/qckitfastq/libs/i386/qckitfastq.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/qckitfastq/libs/x64/qckitfastq.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
run_all 9.53   3.91   13.39
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
run_all 9.97   3.57   13.55
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/qckitfastq.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/qckitfastq_1.0.1.tar.gz && rm -rf qckitfastq.buildbin-libdir && mkdir qckitfastq.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qckitfastq.buildbin-libdir qckitfastq_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL qckitfastq_1.0.1.zip && rm qckitfastq_1.0.1.tar.gz qckitfastq_1.0.1.zip
###
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  748k  100  748k    0     0  10.5M      0 --:--:-- --:--:-- --:--:-- 11.7M

install for i386

* installing *source* package 'qckitfastq' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RSeqAn/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RSeqAn/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c calc_adapter_content.cpp -o calc_adapter_content.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RSeqAn/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c gzstream.cpp -o gzstream.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RSeqAn/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c read_fastq.cpp -o read_fastq.o
read_fastq.cpp: In function 'Rcpp::List qual_score_per_read(std::string)':
read_fastq.cpp:181:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if (pos_counter <= qual_score_matrix.size()) {
                                 ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o qckitfastq.dll tmp.def RcppExports.o calc_adapter_content.o gzstream.o read_fastq.o -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/qckitfastq.buildbin-libdir/00LOCK-qckitfastq/00new/qckitfastq/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'qckitfastq'
    finding HTML links ... done
    GC_content                              html  
    adapter_content                         html  
    calc_adapter_content                    html  
    calc_format_score                       html  
    calc_over_rep_seq                       html  
    dimensions                              html  
    find_format                             html  
    gc_per_read                             html  
    kmer_count                              html  
    overrep_kmer                            html  
    overrep_reads                           html  
    per_base_quality                        html  
    per_read_quality                        html  
    plot_GC_content                         html  
    plot_adapter_content                    html  
    plot_outliers                           html  
    plot_overrep_kmer                       html  
    plot_overrep_reads                      html  
    plot_per_base_quality                   html  
    plot_per_read_quality                   html  
    plot_read_content                       html  
    plot_read_length                        html  
    qual_score_per_read                     html  
    read_base_content                       html  
    read_content                            html  
    read_length                             html  
    run_all                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'qckitfastq' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RSeqAn/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RSeqAn/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c calc_adapter_content.cpp -o calc_adapter_content.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RSeqAn/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c gzstream.cpp -o gzstream.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RSeqAn/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c read_fastq.cpp -o read_fastq.o
read_fastq.cpp: In function 'Rcpp::List qual_score_per_read(std::string)':
read_fastq.cpp:181:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 if (pos_counter <= qual_score_matrix.size()) {
                                 ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o qckitfastq.dll tmp.def RcppExports.o calc_adapter_content.o gzstream.o read_fastq.o -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/qckitfastq.buildbin-libdir/qckitfastq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'qckitfastq' as qckitfastq_1.0.1.zip
* DONE (qckitfastq)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'qckitfastq' successfully unpacked and MD5 sums checked

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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) 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastq_Klocs] File ( 1/1) 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' 	done.
[fastqq] File ( 1/1) 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastqq] File ( 1/1) 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastq_Klocs] File ( 1/1) 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' 	done.
[fastqq] File ( 1/1) 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastq_Klocs] File ( 1/1) 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' 	done.
[1] "adapter_content not available for Windows; skipping"
== testthat results  ===========================================================
[ OK: 27 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  20.12    5.25   23.28 

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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) 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastq_Klocs] File ( 1/1) 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' 	done.
[fastqq] File ( 1/1) 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastqq] File ( 1/1) 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastq_Klocs] File ( 1/1) 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' 	done.
[fastqq] File ( 1/1) 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastq_Klocs] File ( 1/1) 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/qckitfastq/extdata/10^5_reads_test.fq.gz' 	done.
[1] "adapter_content not available for Windows; skipping"
== testthat results  ===========================================================
[ OK: 27 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  22.68    5.04   26.23