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INSTALL report for InteractionSet on tokay2

This page was generated on 2018-10-17 08:42:12 -0400 (Wed, 17 Oct 2018).

Package 739/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
InteractionSet 1.8.0
Aaron Lun
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/InteractionSet
Branch: RELEASE_3_7
Last Commit: 0f13ecd
Last Changed Date: 2018-04-30 10:35:41 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: InteractionSet
Version: 1.8.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/InteractionSet_1.8.0.tar.gz && rm -rf InteractionSet.buildbin-libdir && mkdir InteractionSet.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=InteractionSet.buildbin-libdir InteractionSet_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL InteractionSet_1.8.0.zip && rm InteractionSet_1.8.0.tar.gz InteractionSet_1.8.0.zip
StartedAt: 2018-10-16 19:37:28 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 19:39:52 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 143.8 seconds
RetCode: 0
Status:  OK  

Command output

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### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/InteractionSet_1.8.0.tar.gz && rm -rf InteractionSet.buildbin-libdir && mkdir InteractionSet.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=InteractionSet.buildbin-libdir InteractionSet_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL InteractionSet_1.8.0.zip && rm InteractionSet_1.8.0.tar.gz InteractionSet_1.8.0.zip
###
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100 84324  100 84324    0     0  1537k      0 --:--:-- --:--:-- --:--:-- 1752k

install for i386

* installing *source* package 'InteractionSet' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c box_bounds.cpp -o box_bounds.o
box_bounds.cpp: In function 'SEXPREC* get_box_bounds(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
box_bounds.cpp:10:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (npts!=Adex.size()) { 
             ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c detect_overlaps.cpp -o detect_overlaps.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c link_overlaps.cpp -o link_overlaps.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c overlap_utils.cpp -o overlap_utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o InteractionSet.dll tmp.def box_bounds.o detect_overlaps.o init.o link_overlaps.o overlap_utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/InteractionSet.buildbin-libdir/InteractionSet/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'InteractionSet'
    finding HTML links ... done
    ContactMatrix-accessors                 html  
    finding level-2 HTML links ... done

    ContactMatrix-class                     html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGe3MjC/R.INSTALL1b1479b5f3e/InteractionSet/man/ContactMatrix-class.Rd:42: file link 'Annotated' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGe3MjC/R.INSTALL1b1479b5f3e/InteractionSet/man/ContactMatrix-class.Rd:51: file link 'Annotated' in package 'S4Vectors' does not exist and so has been treated as a topic
    ContactMatrix-distances                 html  
    ContactMatrix-overlaps                  html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGe3MjC/R.INSTALL1b1479b5f3e/InteractionSet/man/ContactMatrix-overlaps.Rd:33: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGe3MjC/R.INSTALL1b1479b5f3e/InteractionSet/man/ContactMatrix-overlaps.Rd:37: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGe3MjC/R.INSTALL1b1479b5f3e/InteractionSet/man/ContactMatrix-overlaps.Rd:100: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
    ContactMatrix-sorting                   html  
    ContactMatrix-subset                    html  
    GInteractions-class                     html  
    InteractionSet-class                    html  
    boundingBox                             html  
    conversion                              html  
    distances                               html  
    granges-methods                         html  
    interaction-accessors                   html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGe3MjC/R.INSTALL1b1479b5f3e/InteractionSet/man/interaction-accessors.Rd:170: file link 'mcols' in package 'S4Vectors' does not exist and so has been treated as a topic
    interaction-bind                        html  
    interaction-compare                     html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGe3MjC/R.INSTALL1b1479b5f3e/InteractionSet/man/interaction-compare.Rd:216: file link 'pcompare' in package 'S4Vectors' does not exist and so has been treated as a topic
    interaction-subset                      html  
    linearize                               html  
    linkOverlaps                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGe3MjC/R.INSTALL1b1479b5f3e/InteractionSet/man/linkOverlaps.Rd:32: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGe3MjC/R.INSTALL1b1479b5f3e/InteractionSet/man/linkOverlaps.Rd:63: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
    overlaps                                html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGe3MjC/R.INSTALL1b1479b5f3e/InteractionSet/man/overlaps.Rd:92: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGe3MjC/R.INSTALL1b1479b5f3e/InteractionSet/man/overlaps.Rd:97: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGe3MjC/R.INSTALL1b1479b5f3e/InteractionSet/man/overlaps.Rd:100: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGe3MjC/R.INSTALL1b1479b5f3e/InteractionSet/man/overlaps.Rd:131: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpGe3MjC/R.INSTALL1b1479b5f3e/InteractionSet/man/overlaps.Rd:244: file link 'findOverlaps' in package 'GenomicRanges' does not exist and so has been treated as a topic
    pairs                                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'InteractionSet' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c box_bounds.cpp -o box_bounds.o
box_bounds.cpp: In function 'SEXPREC* get_box_bounds(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
box_bounds.cpp:10:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (npts!=Adex.size()) { 
             ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c detect_overlaps.cpp -o detect_overlaps.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c link_overlaps.cpp -o link_overlaps.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c overlap_utils.cpp -o overlap_utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o InteractionSet.dll tmp.def box_bounds.o detect_overlaps.o init.o link_overlaps.o overlap_utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/InteractionSet.buildbin-libdir/InteractionSet/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'InteractionSet' as InteractionSet_1.8.0.zip
* DONE (InteractionSet)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'InteractionSet' successfully unpacked and MD5 sums checked
In R CMD INSTALL