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

[Andres Wokaty]

I will recompile OpenBabel on palomino8.

Andres Wokaty (they/them)

Waldron Lab at CUNY SPH
Bioconductor Core Team
________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Kevin Horan <khoran using cs.ucr.edu>
Sent: Thursday, July 31, 2025 9:27 AM
To: Mike Smith <grimbough using gmail.com>; Kevin Horan <khoran using cs.ucr.edu>; bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] chemmineob build failure due to missing zip lib

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Thanks Mike, that sounds like the likely cause.

Could someone from bioc please re-compile OpenBabel on palomino8 using
the "z" library instead of "zlibbioc". Thank you.

Kevin

On 7/30/25 10:14 AM, Mike Smith wrote:
> 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://urldefense.com/v3/__https://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineOB/palomino8-install.html__;!!LRXxDv2l!RXiyZeke5PJp1-6B6FxJDjS6xOGskS09BaPpfB8QhxBHHoe9J3rWVe2QqdpM31tRGgIYU7zV8IlGUlpTSH9DUbEW_tiq$
>
>     Kevin
>
>
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>
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>
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