Gavin Ha
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/TitanCNA |
| Branch: RELEASE_3_10 |
| Last Commit: 7fad13c |
| Last Changed Date: 2019-10-29 13:08:56 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:22:55 -0400 (Wed, 15 Apr 2020).
| Package 1728/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TitanCNA 1.24.0 Gavin Ha
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: TitanCNA |
| Version: 1.24.0 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/TitanCNA_1.24.0.tar.gz && rm -rf TitanCNA.buildbin-libdir && mkdir TitanCNA.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TitanCNA.buildbin-libdir TitanCNA_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL TitanCNA_1.24.0.zip && rm TitanCNA_1.24.0.tar.gz TitanCNA_1.24.0.zip |
| StartedAt: 2020-04-14 19:58:42 -0400 (Tue, 14 Apr 2020) |
| EndedAt: 2020-04-14 19:59:57 -0400 (Tue, 14 Apr 2020) |
| EllapsedTime: 74.6 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/TitanCNA_1.24.0.tar.gz && rm -rf TitanCNA.buildbin-libdir && mkdir TitanCNA.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TitanCNA.buildbin-libdir TitanCNA_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL TitanCNA_1.24.0.zip && rm TitanCNA_1.24.0.tar.gz TitanCNA_1.24.0.zip
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% 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 5034k 100 5034k 0 0 13.6M 0 --:--:-- --:--:-- --:--:-- 13.7M
install for i386
* installing *source* package 'TitanCNA' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c fwd_backC_clonalCN.c -o fwd_backC_clonalCN.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c getPositionOverlapC.c -o getPositionOverlapC.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c register.c -o register.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c viterbiC_clonalCN.c -o viterbiC_clonalCN.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o TitanCNA.dll tmp.def fwd_backC_clonalCN.o getPositionOverlapC.o register.o viterbiC_clonalCN.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/TitanCNA.buildbin-libdir/00LOCK-TitanCNA/00new/TitanCNA/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'TitanCNA'
Warning: replacing previous import 'BiocGenerics::combine' by 'dplyr::combine' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::between' by 'dplyr::between' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::setdiff' by 'dplyr::setdiff' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::collapse' by 'dplyr::collapse' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::desc' by 'dplyr::desc' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::union' by 'dplyr::union' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::first' by 'dplyr::first' when loading 'TitanCNA'
Warning: replacing previous import 'GenomeInfoDb::intersect' by 'dplyr::intersect' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::slice' by 'dplyr::slice' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::last' by 'dplyr::last' when loading 'TitanCNA'
Warning: replacing previous import 'dplyr::select' by 'VariantAnnotation::select' when loading 'TitanCNA'
** help
*** installing help indices
converting help for package 'TitanCNA'
finding HTML links ... done
TitanCNA-dataset html
TitanCNA-output html
TitanCNA-package html
TitanCNA-plotting html
computeSDbwIndex html
correctCN html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpQJcL8B/R.INSTALL206479411769/TitanCNA/man/correctCN.Rd:20: file link 'outputTitanResults' in package 'TitanCNA' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpQJcL8B/R.INSTALL206479411769/TitanCNA/man/correctCN.Rd:23: file link 'outputTitanSegments' in package 'TitanCNA' does not exist and so has been treated as a topic
correctReadDepth html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpQJcL8B/R.INSTALL206479411769/TitanCNA/man/correctReadDepth.Rd:17: file link 'wigToRangedData' in package 'HMMcopy' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpQJcL8B/R.INSTALL206479411769/TitanCNA/man/correctReadDepth.Rd:58: file link 'wigToRangedData' in package 'HMMcopy' does not exist and so has been treated as a topic
filterData html
getPositionOverlap html
haplotype html
loadAlleleCounts html
loadDefaultParameters html
runEMclonalCN html
finding level-2 HTML links ... done
viterbiClonalCN html
wigImport html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'TitanCNA'
Warning: replacing previous import 'BiocGenerics::combine' by 'dplyr::combine' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::between' by 'dplyr::between' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::setdiff' by 'dplyr::setdiff' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::collapse' by 'dplyr::collapse' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::desc' by 'dplyr::desc' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::union' by 'dplyr::union' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::first' by 'dplyr::first' when loading 'TitanCNA'
Warning: replacing previous import 'GenomeInfoDb::intersect' by 'dplyr::intersect' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::slice' by 'dplyr::slice' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::last' by 'dplyr::last' when loading 'TitanCNA'
Warning: replacing previous import 'dplyr::select' by 'VariantAnnotation::select' when loading 'TitanCNA'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'TitanCNA'
Warning: replacing previous import 'BiocGenerics::combine' by 'dplyr::combine' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::between' by 'dplyr::between' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::setdiff' by 'dplyr::setdiff' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::collapse' by 'dplyr::collapse' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::desc' by 'dplyr::desc' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::union' by 'dplyr::union' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::first' by 'dplyr::first' when loading 'TitanCNA'
Warning: replacing previous import 'GenomeInfoDb::intersect' by 'dplyr::intersect' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::slice' by 'dplyr::slice' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::last' by 'dplyr::last' when loading 'TitanCNA'
Warning: replacing previous import 'dplyr::select' by 'VariantAnnotation::select' when loading 'TitanCNA'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'TitanCNA' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c fwd_backC_clonalCN.c -o fwd_backC_clonalCN.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c getPositionOverlapC.c -o getPositionOverlapC.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c register.c -o register.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c viterbiC_clonalCN.c -o viterbiC_clonalCN.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o TitanCNA.dll tmp.def fwd_backC_clonalCN.o getPositionOverlapC.o register.o viterbiC_clonalCN.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/TitanCNA.buildbin-libdir/TitanCNA/libs/x64
** testing if installed package can be loaded
Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::collapse' by 'dplyr::collapse' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::last' by 'dplyr::last' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::union' by 'dplyr::union' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::slice' by 'dplyr::slice' when loading 'TitanCNA'
Warning: replacing previous import 'GenomeInfoDb::intersect' by 'dplyr::intersect' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::setdiff' by 'dplyr::setdiff' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::first' by 'dplyr::first' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::desc' by 'dplyr::desc' when loading 'TitanCNA'
Warning: replacing previous import 'BiocGenerics::combine' by 'dplyr::combine' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::between' by 'dplyr::between' when loading 'TitanCNA'
Warning: replacing previous import 'dplyr::select' by 'VariantAnnotation::select' when loading 'TitanCNA'
* MD5 sums
packaged installation of 'TitanCNA' as TitanCNA_1.24.0.zip
* DONE (TitanCNA)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'TitanCNA' successfully unpacked and MD5 sums checked