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 <kho...@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 > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
