Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:56:53 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE InteractionSet PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 882/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
InteractionSet 1.16.0 Aaron Lun
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK |
Package: InteractionSet |
Version: 1.16.0 |
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/InteractionSet_1.16.0.tar.gz && rm -rf InteractionSet.buildbin-libdir && mkdir InteractionSet.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=InteractionSet.buildbin-libdir InteractionSet_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL InteractionSet_1.16.0.zip && rm InteractionSet_1.16.0.tar.gz InteractionSet_1.16.0.zip |
StartedAt: 2020-10-16 17:58:48 -0400 (Fri, 16 Oct 2020) |
EndedAt: 2020-10-16 18:00:40 -0400 (Fri, 16 Oct 2020) |
EllapsedTime: 112.6 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/InteractionSet_1.16.0.tar.gz && rm -rf InteractionSet.buildbin-libdir && mkdir InteractionSet.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=InteractionSet.buildbin-libdir InteractionSet_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL InteractionSet_1.16.0.zip && rm InteractionSet_1.16.0.tar.gz InteractionSet_1.16.0.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 84353 100 84353 0 0 836k 0 --:--:-- --:--:-- --:--:-- 905k install for i386 * installing *source* package 'InteractionSet' ... ** 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'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 of integer expressions of different signedness: 'const size_t' {aka 'const unsigned int'} and 'R_xlen_t' {aka 'int'} [-Wsign-compare] if (npts!=Adex.size()) { ~~~~^~~~~~~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c detect_overlaps.cpp -o detect_overlaps.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.cpp -o init.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c link_overlaps.cpp -o link_overlaps.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c overlap_utils.cpp -o overlap_utils.o C:/rtools40/mingw32/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-3~1.11-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/InteractionSet.buildbin-libdir/00LOCK-InteractionSet/00new/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-3.11-bioc/tmpdir/RtmpkFMIeC/R.INSTALLc54cc411f1/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-3.11-bioc/tmpdir/RtmpkFMIeC/R.INSTALLc54cc411f1/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-3.11-bioc/tmpdir/RtmpkFMIeC/R.INSTALLc54cc411f1/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-3.11-bioc/tmpdir/RtmpkFMIeC/R.INSTALLc54cc411f1/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-3.11-bioc/tmpdir/RtmpkFMIeC/R.INSTALLc54cc411f1/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-3.11-bioc/tmpdir/RtmpkFMIeC/R.INSTALLc54cc411f1/InteractionSet/man/interaction-accessors.Rd:174: 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-3.11-bioc/tmpdir/RtmpkFMIeC/R.INSTALLc54cc411f1/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-3.11-bioc/tmpdir/RtmpkFMIeC/R.INSTALLc54cc411f1/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-3.11-bioc/tmpdir/RtmpkFMIeC/R.INSTALLc54cc411f1/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-3.11-bioc/tmpdir/RtmpkFMIeC/R.INSTALLc54cc411f1/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-3.11-bioc/tmpdir/RtmpkFMIeC/R.INSTALLc54cc411f1/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-3.11-bioc/tmpdir/RtmpkFMIeC/R.INSTALLc54cc411f1/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-3.11-bioc/tmpdir/RtmpkFMIeC/R.INSTALLc54cc411f1/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-3.11-bioc/tmpdir/RtmpkFMIeC/R.INSTALLc54cc411f1/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 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 'InteractionSet' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] if (npts!=Adex.size()) { ~~~~^~~~~~~~~~~~~ "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c detect_overlaps.cpp -o detect_overlaps.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.cpp -o init.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c link_overlaps.cpp -o link_overlaps.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -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:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c overlap_utils.cpp -o overlap_utils.o C:/rtools40/mingw64/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-3~1.11-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/InteractionSet.buildbin-libdir/InteractionSet/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'InteractionSet' as InteractionSet_1.16.0.zip * DONE (InteractionSet) * installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library' package 'InteractionSet' successfully unpacked and MD5 sums checked