Xiuwen Zheng
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/HIBAG |
| Branch: RELEASE_3_12 |
| Last Commit: 6b35b21 |
| Last Changed Date: 2021-03-21 00:12:59 -0400 (Sun, 21 Mar 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:31:45 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the HIBAG package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 828/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HIBAG 1.26.1 (landing page) Xiuwen Zheng
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: HIBAG |
| Version: 1.26.1 |
| Command: C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/HIBAG_1.26.1.tar.gz && rm -rf HIBAG.buildbin-libdir && mkdir HIBAG.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HIBAG.buildbin-libdir HIBAG_1.26.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL HIBAG_1.26.1.zip && rm HIBAG_1.26.1.tar.gz HIBAG_1.26.1.zip |
| StartedAt: 2021-05-05 16:39:40 -0400 (Wed, 05 May 2021) |
| EndedAt: 2021-05-05 16:43:03 -0400 (Wed, 05 May 2021) |
| EllapsedTime: 203.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/HIBAG_1.26.1.tar.gz && rm -rf HIBAG.buildbin-libdir && mkdir HIBAG.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HIBAG.buildbin-libdir HIBAG_1.26.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL HIBAG_1.26.1.zip && rm HIBAG_1.26.1.tar.gz HIBAG_1.26.1.zip
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install for i386
* installing *source* package 'HIBAG' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c HIBAG.cpp -o HIBAG.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LibHLA.cpp -o LibHLA.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LibHLA_ext_avx.cpp -o LibHLA_ext_avx.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LibHLA_ext_avx2.cpp -o LibHLA_ext_avx2.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign LibHLA_ext_avx512bw.cpp -c -o LibHLA_ext_avx512bw.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign LibHLA_ext_avx512f.cpp -c -o LibHLA_ext_avx512f.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LibHLA_ext_sse2.cpp -o LibHLA_ext_sse2.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LibHLA_ext_sse4_2.cpp -o LibHLA_ext_sse4_2.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o HIBAG.dll tmp.def HIBAG.o LibHLA.o LibHLA_ext_avx.o LibHLA_ext_avx2.o LibHLA_ext_avx512bw.o LibHLA_ext_avx512f.o LibHLA_ext_sse2.o LibHLA_ext_sse4_2.o -LC:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/lib/i386 -ltbb -ltbbmalloc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/HIBAG.buildbin-libdir/00LOCK-HIBAG/00new/HIBAG/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'HIBAG'
finding HTML links ... done
HIBAG-package html
HLA_Type_Table html
HapMap_CEU_Geno html
hlaAASeqClass html
hlaAllele html
hlaAlleleClass html
hlaAlleleDigit html
hlaAlleleSubset html
hlaAssocTest html
hlaAttrBagClass html
hlaAttrBagObj html
hlaAttrBagging html
hlaBED2Geno html
hlaCheckAllele html
hlaCheckSNPs html
hlaClose html
hlaCombineAllele html
hlaCombineModelObj html
hlaCompareAllele html
hlaConvSequence html
hlaDistance html
hlaFlankingSNP html
hlaGDS2Geno html
hlaGeno2PED html
hlaGenoAFreq html
hlaGenoCombine html
hlaGenoLD html
hlaGenoMFreq html
hlaGenoMRate html
hlaGenoMRate_Samp html
hlaGenoSubset html
hlaGenoSwitchStrand html
hlaLDMatrix html
hlaLociInfo html
hlaMakeSNPGeno html
hlaModelFiles html
hlaModelFromObj html
hlaOutOfBag html
hlaParallelAttrBagging html
hlaPredMerge html
hlaPredict html
hlaPublish html
hlaReport html
hlaReportPlot html
hlaSNPGenoClass html
hlaSNPID html
hlaSampleAllele html
hlaSetKernelTarget html
hlaSplitAllele html
hlaSubModelObj html
hlaUniqueAllele html
plot.hlaAttrBagObj html
print.hlaAttrBagClass html
summary.hlaAlleleClass html
summary.hlaSNPGenoClass html
** building package indices
** installing vignettes
'HIBAG.Rmd'
'HLA_Association.Rmd'
'Implementation.Rmd'
** 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 'HIBAG' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c HIBAG.cpp -o HIBAG.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LibHLA.cpp -o LibHLA.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LibHLA_ext_avx.cpp -o LibHLA_ext_avx.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LibHLA_ext_avx2.cpp -o LibHLA_ext_avx2.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -ffixed-xmm16 -ffixed-xmm17 -ffixed-xmm18 -ffixed-xmm19 -ffixed-xmm20 -ffixed-xmm21 -ffixed-xmm22 -ffixed-xmm23 -ffixed-xmm24 -ffixed-xmm25 -ffixed-xmm26 -ffixed-xmm27 -ffixed-xmm28 -ffixed-xmm29 -ffixed-xmm30 -ffixed-xmm31 LibHLA_ext_avx512bw.cpp -c -o LibHLA_ext_avx512bw.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -ffixed-xmm16 -ffixed-xmm17 -ffixed-xmm18 -ffixed-xmm19 -ffixed-xmm20 -ffixed-xmm21 -ffixed-xmm22 -ffixed-xmm23 -ffixed-xmm24 -ffixed-xmm25 -ffixed-xmm26 -ffixed-xmm27 -ffixed-xmm28 -ffixed-xmm29 -ffixed-xmm30 -ffixed-xmm31 LibHLA_ext_avx512f.cpp -c -o LibHLA_ext_avx512f.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LibHLA_ext_sse2.cpp -o LibHLA_ext_sse2.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/include' -I"C:/extsoft/include" -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c LibHLA_ext_sse4_2.cpp -o LibHLA_ext_sse4_2.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o HIBAG.dll tmp.def HIBAG.o LibHLA.o LibHLA_ext_avx.o LibHLA_ext_avx2.o LibHLA_ext_avx512bw.o LibHLA_ext_avx512f.o LibHLA_ext_sse2.o LibHLA_ext_sse4_2.o -LC:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/HIBAG.buildbin-libdir/HIBAG/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HIBAG' as HIBAG_1.26.1.zip
* DONE (HIBAG)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'HIBAG' successfully unpacked and MD5 sums checked