############################################################################## ############################################################################## ### ### Running command: ### ### chmod a+r GrafGen -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data GrafGen ### ############################################################################## ############################################################################## * checking for file 'GrafGen/DESCRIPTION' ... OK * preparing 'GrafGen': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes ----------------------------------- * installing *source* package 'GrafGen' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.3.0' using C++ compiler: 'G__~1.EXE (GCC) 13.3.0' g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c AncestrySnps.cpp -o AncestrySnps.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BedFileSnpGeno.cpp -o BedFileSnpGeno.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BimFileAncestrySnps.cpp -o BimFileAncestrySnps.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FamFileSamples.cpp -o FamFileSamples.o gcc -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GrafGenHp_init.c -o GrafGenHp_init.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GrafPop.cpp -o GrafPop.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SampleGenoAncestry.cpp -o SampleGenoAncestry.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SampleGenoDist.cpp -o SampleGenoDist.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Util.cpp -o Util.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c VcfSampleAncestrySnpGeno.cpp -o VcfSampleAncestrySnpGeno.o g++ -std=gnu++17 -shared -s -static-libgcc -o GrafGen.dll tmp.def AncestrySnps.o BedFileSnpGeno.o BimFileAncestrySnps.o FamFileSamples.o GrafGenHp_init.o GrafPop.o SampleGenoAncestry.o SampleGenoDist.o Util.o VcfSampleAncestrySnpGeno.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: VcfSampleAncestrySnpGeno.o:VcfSampleAncestrySnpGeno.cpp:(.text+0xa6a): undefined reference to `gzopen' C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: VcfSampleAncestrySnpGeno.o:VcfSampleAncestrySnpGeno.cpp:(.text+0xc47): undefined reference to `gzread' C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: VcfSampleAncestrySnpGeno.o:VcfSampleAncestrySnpGeno.cpp:(.text+0xcf9): undefined reference to `gzclose' C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: VcfSampleAncestrySnpGeno.o:VcfSampleAncestrySnpGeno.cpp:(.text+0x1b11): undefined reference to `gzeof' C:\rtools44\x86_64-w64-mingw32.static.posix\bin/ld.exe: VcfSampleAncestrySnpGeno.o:VcfSampleAncestrySnpGeno.cpp:(.text+0x1f9f): undefined reference to `gzerror' collect2.exe: error: ld returned 1 exit status no DLL was created ERROR: compilation failed for package 'GrafGen' * removing 'E:/biocbuild/bbs-3.21-bioc/tmpdir/RtmpM7u4os/Rinst1cbe015802c38/GrafGen' ----------------------------------- ERROR: package installation failed