I have a Bioconda (Anaconda) recipe that worked fine for several releases but failed yesterday with an update that did not introduce any new library or requirement, so I guess it can be due either to updates in unpineed dependencies (I couldn't find any to be fair), or more likely in changes in the macOS CI.
The package is SeqFu and the build involves nimble build -y --verbose.
The Azure log (running on macOS 11) says:
2022-09-11T20:48:55.9839190Z 20:48:55 BIOCONDA INFO (ERR) 12: fatal error10:: 'pthread.h' file not found
2022-09-11T20:48:55.9840500Z 20:48:55 BIOCONDA INFO (ERR) #include <sys/types.h>
2022-09-11T20:48:55.9841470Z 20:48:55 BIOCONDA INFO (ERR) ^~~~~~~~~~~~~
2022-09-11T20:48:55.9842440Z 20:48:55 BIOCONDA INFO (ERR) #include <pthread.h>
2022-09-11T20:48:55.9843380Z 20:48:55 BIOCONDA INFO (ERR) ^~~~~~~~~~~
2022-09-11T20:48:55.9844950Z 20:48:55 BIOCONDA INFO (ERR) fatal error: 'pthread.h' file not found
2022-09-11T20:48:55.9847850Z 20:48:55 BIOCONDA INFO (ERR) #include <pthread.h>
2022-09-11T20:48:55.9848880Z 20:48:55 BIOCONDA INFO (ERR) ^~~~~~~~~~~
And I checked in my local macOS12 machine and those headers are readily found in several locations such as:
/Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk/usr/include/pthread/pthread.h
/Library/Developer/CommandLineTools/SDKs/MacOSX11.3.sdk/usr/include/pthread.h
/Library/Developer/CommandLineTools/SDKs/MacOSX12.1.sdk/usr/include/pthread/pthread.h
/Library/Developer/CommandLineTools/SDKs/MacOSX12.1.sdk/usr/include/pthread.h
Being a first time type of error, and being not familiar with C, I'd like to ask:
- If you can spot the source of the problem and advice a change in the building process, or
- If you can advise a debugging strategy
As I have so many questions I can easily follow many rabbit holes... sorry for not being more specific but as I said I need some guidance, thanks!
