Aaron Lun
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/InteractionSet |
| Branch: master |
| Last Commit: bcbcf98 |
| Last Changed Date: 2019-03-16 21:16:43 -0400 (Sat, 16 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 12:26:32 -0400 (Tue, 09 Apr 2019).
| Package 805/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| InteractionSet 1.11.2 Aaron Lun
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | [ OK ] | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | OK |
| Package: InteractionSet |
| Version: 1.11.2 |
| Command: rm -rf InteractionSet.buildbin-libdir && mkdir InteractionSet.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=InteractionSet.buildbin-libdir InteractionSet_1.11.2.tar.gz |
| StartedAt: 2019-04-09 08:17:25 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 08:18:59 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 93.7 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: InteractionSet_1.11.2.zip |
| PackageFileSize: 1.821 MiB |
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### Running command:
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### rm -rf InteractionSet.buildbin-libdir && mkdir InteractionSet.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=InteractionSet.buildbin-libdir InteractionSet_1.11.2.tar.gz
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install for i386
* installing *source* package 'InteractionSet' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/tmpdir/Rtmpu4qani/R.INSTALL1ef46ff2433e/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-3.9-bioc/tmpdir/Rtmpu4qani/R.INSTALL1ef46ff2433e/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-3.9-bioc/tmpdir/Rtmpu4qani/R.INSTALL1ef46ff2433e/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-3.9-bioc/tmpdir/Rtmpu4qani/R.INSTALL1ef46ff2433e/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-3.9-bioc/tmpdir/Rtmpu4qani/R.INSTALL1ef46ff2433e/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-3.9-bioc/tmpdir/Rtmpu4qani/R.INSTALL1ef46ff2433e/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-3.9-bioc/tmpdir/Rtmpu4qani/R.INSTALL1ef46ff2433e/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-3.9-bioc/tmpdir/Rtmpu4qani/R.INSTALL1ef46ff2433e/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-3.9-bioc/tmpdir/Rtmpu4qani/R.INSTALL1ef46ff2433e/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-3.9-bioc/tmpdir/Rtmpu4qani/R.INSTALL1ef46ff2433e/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-3.9-bioc/tmpdir/Rtmpu4qani/R.INSTALL1ef46ff2433e/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-3.9-bioc/tmpdir/Rtmpu4qani/R.INSTALL1ef46ff2433e/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-3.9-bioc/tmpdir/Rtmpu4qani/R.INSTALL1ef46ff2433e/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-3.9-bioc/tmpdir/Rtmpu4qani/R.INSTALL1ef46ff2433e/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:/Rtools/mingw_64/bin/g++ -std=gnu++11 -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:/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˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/InteractionSet.buildbin-libdir/InteractionSet/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'InteractionSet' as InteractionSet_1.11.2.zip
* DONE (InteractionSet)