help with compiling for bioconda

[aryarm]

Hi @rrwick,

Thanks for making Bandage! It's such a useful tool.

I'm trying to figure out how to compile v0.9.0 for bioconda, but I keep running into errors.

Here's my work so far:

• meta.yaml
• build.sh script

And here are the 24 errors I keep getting:

/bin/ld: warning: libXext.so.6, needed by /usr/lib64/libGL.so, not found (try using -rpath or -rpath-link)
/bin/ld: warning: libexpat.so.1, needed by /usr/lib64/libGL.so, not found (try using -rpath or -rpath-link)
/bin/ld: warning: libXau.so.6, needed by /usr/lib64/libxcb-glx.so.0, not found (try using -rpath or -rpath-link)
/bin/ld: /usr/lib64/libGL.so: undefined reference to `XextAddDisplay'
/bin/ld: /usr/lib64/libGL.so: undefined reference to `XextRemoveDisplay'
/bin/ld: /usr/lib64/libGL.so: undefined reference to `XML_SetUserData'
/bin/ld: /usr/lib64/libGL.so: undefined reference to `XML_Parse'
/bin/ld: /lib/libQt5Core.so: undefined reference to `clock_gettime@GLIBC_2.17'
/bin/ld: /usr/lib64/libGL.so: undefined reference to `XMissingExtension'
/bin/ld: /lib64/libxcb.so.1: undefined reference to `XauDisposeAuth'
/bin/ld: /usr/lib64/libGL.so: undefined reference to `XML_ParseBuffer'
/bin/ld: /usr/lib64/libGL.so: undefined reference to `XML_ErrorString'
/bin/ld: /usr/lib64/libGL.so: undefined reference to `XextFindDisplay'
/bin/ld: /usr/lib64/libGL.so: undefined reference to `XML_GetCurrentColumnNumber'
/bin/ld: /usr/lib64/libGL.so: undefined reference to `XML_GetCurrentColumnNumber'
/bin/ld: /usr/lib64/libGL.so: undefined reference to `XML_ParserFree'
/bin/ld: /lib/libQt5Svg.so: undefined reference to `memcpy@GLIBC_2.14'
/bin/ld: /usr/lib64/libGL.so: undefined reference to `XML_ParserCreate'
/bin/ld: /usr/lib64/libGL.so: undefined reference to `XML_GetErrorCode'
/bin/ld: /usr/lib64/libGL.so: undefined reference to `XML_GetCurrentLineNumber'
/bin/ld: /usr/lib64/libGL.so: undefined reference to `XML_SetElementHandler'
/bin/ld: /lib/libQt5Core.so: undefined reference to `getauxval@GLIBC_2.16'
/bin/ld: /usr/lib64/libGL.so: undefined reference to `XML_GetBuffer'
/bin/ld: /usr/lib64/libGL.so: undefined reference to `XextCreateExtension'
/bin/ld: /usr/lib64/libxcb.so.1: undefined reference to `XauGetBestAuthByAddr'

Do you have any suggestions? I suspect I might be linking the libraries incorrectly, but I'm not sure...

[bernt-matthias]

Hey @aryarm check https://github.com/asl/BandageNG and its bioconda recipe .. which unfortunately broke recently bioconda/bioconda-recipes#41091

[aryarm]

thanks for the suggestion, @bernt-matthias . Unfortunately, I fear that the two packages have diverged enough that the BandageNG recipe is not a good reference anymore. For example, the Bandage recipe uses qmake and QT5, but BandageNG uses cmake and requires QT6

---

In the meantime, I've managed to reduce the original set of 24 errors down to just 3! I just had to add a few dependencies. But now I'm pretty stuck.

/bin/ld: /lib/libQt5Core.so: undefined reference to `clock_gettime@GLIBC_2.17'
/bin/ld: /lib/libQt5Svg.so: undefined reference to `memcpy@GLIBC_2.14'
/bin/ld: /lib/libQt5Core.so: undefined reference to `getauxval@GLIBC_2.16'

Does anyone have any suggestions on how to resolve these? Does this imply that Qt5 needs three different versions of the standard library?!

[aryarm]

@willemdek11, as the original creator of the Bandage recipe, do you have any insights or recommendations?