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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