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

[Mike Smith]

These errors look like they're actually coming from the OpenBabel library
itself (libopenbabel.a), rather than your package code.  That library is
looking for symbols defined in zlibbioc e.g. bioc_deflateEnd and it's not
finding them now you're linking against the regular zlib.  I think this
means someone needs to recompile the OpenBabel library installed on the
build machine so that it also uses the regular zlib, and then your changes
will be accurate.

Mike

On Wed, 30 Jul 2025 at 14:33, Kevin Horan <khoran using cs.ucr.edu> wrote:

> 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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>
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