Back to Multiple platform build/check report for BioC 3.11
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

INSTALL report for FastqCleaner on tokay2

This page was generated on 2020-10-17 11:56:33 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE FastqCleaner PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 584/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FastqCleaner 1.6.0
Leandro Roser
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/FastqCleaner
Branch: RELEASE_3_11
Last Commit: 691d0d4
Last Changed Date: 2020-04-27 15:17:10 -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  WARNINGS  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: FastqCleaner
Version: 1.6.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/FastqCleaner_1.6.0.tar.gz && rm -rf FastqCleaner.buildbin-libdir && mkdir FastqCleaner.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FastqCleaner.buildbin-libdir FastqCleaner_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL FastqCleaner_1.6.0.zip && rm FastqCleaner_1.6.0.tar.gz FastqCleaner_1.6.0.zip
StartedAt: 2020-10-16 18:31:09 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 18:33:49 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 160.6 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/FastqCleaner_1.6.0.tar.gz && rm -rf FastqCleaner.buildbin-libdir && mkdir FastqCleaner.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FastqCleaner.buildbin-libdir FastqCleaner_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL FastqCleaner_1.6.0.zip && rm FastqCleaner_1.6.0.tar.gz FastqCleaner_1.6.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 5173k  100 5173k    0     0  47.4M      0 --:--:-- --:--:-- --:--:-- 50.5M

install for i386

* installing *source* package 'FastqCleaner' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/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/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c cpp_GC_content.cpp -o cpp_GC_content.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c cpp_base_content.cpp -o cpp_base_content.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c cpp_check_quality_threshold.cpp -o cpp_check_quality_threshold.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c cpp_create_stringvec.cpp -o cpp_create_stringvec.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c cpp_which_true.cpp -o cpp_which_true.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o FastqCleaner.dll tmp.def RcppExports.o cpp_GC_content.o cpp_base_content.o cpp_check_quality_threshold.o cpp_create_stringvec.o cpp_which_true.o -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/FastqCleaner.buildbin-libdir/00LOCK-FastqCleaner/00new/FastqCleaner/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'FastqCleaner'
    finding HTML links ... done
    adapter_filter                          html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpiyapcl/R.INSTALL1f60495c607f/FastqCleaner/man/adapter_filter.Rd:16: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
    asc2int                                 html  
    check_encoding                          html  
    check_onclick_                          html  
    complex_filter                          html  
    create_cleanfunction_                   html  
    create_uniform_width                    html  
    fixed_filter                            html  
    inject_letter_random                    html  
    int2asc                                 html  
    isNaturalNumber                         html  
    launch_fqc                              html  
    length_filter                           html  
    matching                                html  
    messageFun_                             html  
    myPlot                                  html  
    n_filter                                html  
    outputClean_                            html  
    plotA                                   html  
    plotB                                   html  
    plotC                                   html  
    plotD                                   html  
    plotE                                   html  
    plotF                                   html  
    plotG                                   html  
    plotH                                   html  
    plotI                                   html  
    plotJ                                   html  
    plotObjects                             html  
    processingFunction_                     html  
    qmean_filter                            html  
    random_length                           html  
    random_qual                             html  
    random_seq                              html  
    seq_filter                              html  
    seq_names                               html  
    trim3q_filter                           html  
    unique_filter                           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 'FastqCleaner' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/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/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c cpp_GC_content.cpp -o cpp_GC_content.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c cpp_base_content.cpp -o cpp_base_content.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c cpp_check_quality_threshold.cpp -o cpp_check_quality_threshold.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c cpp_create_stringvec.cpp -o cpp_create_stringvec.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I../inst/include/ -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c cpp_which_true.cpp -o cpp_which_true.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o FastqCleaner.dll tmp.def RcppExports.o cpp_GC_content.o cpp_base_content.o cpp_check_quality_threshold.o cpp_create_stringvec.o cpp_which_true.o -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/FastqCleaner.buildbin-libdir/FastqCleaner/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FastqCleaner' as FastqCleaner_1.6.0.zip
* DONE (FastqCleaner)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'FastqCleaner' successfully unpacked and MD5 sums checked