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INSTALL report for qckitfastq on tokay2

This page was generated on 2020-10-17 11:57:31 -0400 (Sat, 17 Oct 2020).

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 1386/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
qckitfastq 1.4.0
August Guang
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/qckitfastq
Branch: RELEASE_3_11
Last Commit: a63d3a4
Last Changed Date: 2020-04-27 15:24:27 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: qckitfastq
Version: 1.4.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/qckitfastq_1.4.0.tar.gz && rm -rf qckitfastq.buildbin-libdir && mkdir qckitfastq.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qckitfastq.buildbin-libdir qckitfastq_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL qckitfastq_1.4.0.zip && rm qckitfastq_1.4.0.tar.gz qckitfastq_1.4.0.zip
StartedAt: 2020-10-16 17:36:57 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 17:38:52 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 115.3 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/qckitfastq_1.4.0.tar.gz && rm -rf qckitfastq.buildbin-libdir && mkdir qckitfastq.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=qckitfastq.buildbin-libdir qckitfastq_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL qckitfastq_1.4.0.zip && rm qckitfastq_1.4.0.tar.gz qckitfastq_1.4.0.zip
###
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100  747k  100  747k    0     0  11.0M      0 --:--:-- --:--:-- --:--:-- 12.1M

install for i386

* installing *source* package 'qckitfastq' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RSeqAn/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RSeqAn/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c calc_adapter_content.cpp -o calc_adapter_content.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RSeqAn/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c gzstream.cpp -o gzstream.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RSeqAn/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c read_fastq.cpp -o read_fastq.o
read_fastq.cpp: In function 'Rcpp::List qual_score_per_read(std::__cxx11::string)':
read_fastq.cpp:181:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::map<int, std::vector<unsigned char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
                 if (pos_counter <= qual_score_matrix.size()) {
                     ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw32/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-3.11-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-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:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RSeqAn/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RSeqAn/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c calc_adapter_content.cpp -o calc_adapter_content.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RSeqAn/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c gzstream.cpp -o gzstream.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.11-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RSeqAn/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c read_fastq.cpp -o read_fastq.o
read_fastq.cpp: In function 'Rcpp::List qual_score_per_read(std::__cxx11::string)':
read_fastq.cpp:181:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::map<int, std::vector<unsigned char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
                 if (pos_counter <= qual_score_matrix.size()) {
                     ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw64/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-3.11-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/qckitfastq.buildbin-libdir/qckitfastq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'qckitfastq' as qckitfastq_1.4.0.zip
* DONE (qckitfastq)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'qckitfastq' successfully unpacked and MD5 sums checked