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 <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
