[Bioc-devel] chemmineob build failure due to missing zip lib

[Kevin Horan]

I was recently informed to remove the dependence on zlibbioc as it was 
being removed, and replace it with "z". I have done that for my package, 
ChemmineOB. It builds on mac and linux, but it fails on windows:

    g++ -std=gnu++17 -shared -s -static-libgcc -o ChemmineOB.dll tmp.def ChemmineOB.o canonical.o -Lc:/openbabel3/bin/x64/bin -lopenbabel -lz -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text+0x60bc): undefined reference to `bioc_inflateInit2_'
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text+0x644a): undefined reference to `bioc_inflateEnd'
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text+0x7406): undefined reference to `bioc_deflateInit2_'
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text+0x76e9): undefined reference to `bioc_deflateEnd'
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEED1Ev[_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEED1Ev]+0x17): undefined reference to `bioc_inflateEnd'
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcEE8overflowEi[_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcEE8overflowEi]+0x58): undefined reference to `bioc_crc32'
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcEE8overflowEi[_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcEE8overflowEi]+0x79): undefined reference to `bioc_deflate'
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZThn232_N11zlib_stream17basic_zip_istreamIcSt11char_traitsIcEED1Ev[_ZThn232_N11zlib_stream17basic_zip_istreamIcSt11char_traitsIcEED1Ev]+0x3b): undefined reference to `bioc_inflateEnd'
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream17basic_zip_istreamIcSt11char_traitsIcEED0Ev[_ZN11zlib_stream17basic_zip_istreamIcSt11char_traitsIcEED0Ev]+0x3d): undefined reference to `bioc_inflateEnd'
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream17basic_zip_istreamIcSt11char_traitsIcEED1Ev[_ZN11zlib_stream17basic_zip_istreamIcSt11char_traitsIcEED1Ev]+0x3c): undefined reference to `bioc_inflateEnd'
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZThn232_N11zlib_stream17basic_zip_istreamIcSt11char_traitsIcEED0Ev[_ZThn232_N11zlib_stream17basic_zip_istreamIcSt11char_traitsIcEED0Ev]+0x41): undefined reference to `bioc_inflateEnd'
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZTv0_n24_N11zlib_stream17basic_zip_istreamIcSt11char_traitsIcEED1Ev[_ZTv0_n24_N11zlib_stream17basic_zip_istreamIcSt11char_traitsIcEED1Ev]+0x42): undefined reference to `bioc_inflateEnd'
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZTv0_n24_N11zlib_stream17basic_zip_istreamIcSt11char_traitsIcEED0Ev[_ZTv0_n24_N11zlib_stream17basic_zip_istreamIcSt11char_traitsIcEED0Ev]+0x48): more undefined references to `bioc_inflateEnd' follow
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEE7seekposESt4fposI9_MbstatetESt13_Ios_Openmode[_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEE7seekposESt4fposI9_MbstatetESt13_Ios_Openmode]+0x9a): undefined reference to `bioc_inflateInit2_'
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEE7seekoffExSt12_Ios_SeekdirSt13_Ios_Openmode[_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEE7seekoffExSt12_Ios_SeekdirSt13_Ios_Openmode]+0x85): undefined reference to `bioc_inflateEnd'
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEE7seekoffExSt12_Ios_SeekdirSt13_Ios_Openmode[_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEE7seekoffExSt12_Ios_SeekdirSt13_Ios_Openmode]+0xfa): undefined reference to `bioc_inflateInit2_'
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEE9underflowEv[_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEE9underflowEv]+0xa1): undefined reference to `bioc_inflate'
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEE9underflowEv[_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEE9underflowEv]+0x10f): undefined reference to `bioc_crc32'
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEE9underflowEv[_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcEE9underflowEv]+0x1ca): undefined reference to `bioc_inflateReset'
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcEE5flushEv[_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcEE5flushEv]+0x21): undefined reference to `bioc_crc32'
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcEE5flushEv[_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcEE5flushEv]+0x34): undefined reference to `bioc_deflate'
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcEED1Ev[_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcEED1Ev]+0x1c): undefined reference to `bioc_deflateEnd'
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcEED0Ev[_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcEED0Ev]+0x1e): undefined reference to `bioc_deflateEnd'
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(obconversion.cpp.obj):obconversion.c:(.text$_ZN11zlib_stream17basic_zip_ostreamIcSt11char_traitsIcEED1Ev[_ZN11zlib_stream17basic_zip_ostreamIcSt11char_traitsIcEED1Ev]+0x72): undefined reference to `bioc_deflateEnd'
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(pngformat.cpp.obj):pngformat.cpp:(.text+0x73e): undefined reference to `bioc_crc32'
    C:\rtools45\x86_64-w64-mingw32.static.posix\bin/ld.exe: c:/openbabel3/bin/x64/bin/libopenbabel.a(pngformat.cpp.obj):pngformat.cpp:(.text+0x82f): undefined reference to `bioc_crc32'
    collect2.exe: error: ld returned 1 exit status
    no DLL was created
    ERROR: compilation failed for package 'ChemmineOB'

It seems like it's missing the zip library, but '-lz' is given in the 
compile command. Is there a different zip library I need to use for 
windows? Thank you.

https://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineOB/palomino8-install.html

Kevin


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